Attachment L Assurance

Attachment L Assurance.pdf

Adult and Pediatric HIV/AIDS Confidential Case Reports for National HIV/AIDS Surveillance

Attachment L Assurance

OMB: 0920-0573

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Attachment G. Supplemental Surveillance Activity 2: Variant, atypical and Resistant
HIV Surveillance (VARHS) Data Elements
Status: new
Description: These data elements will be an electronic extension of the case report forms
(Attachment C); as such, there is no new form for this activity.

Standard Variant, Atypical, and Resistant HIV Surveillance (VARHS) Data Elements OMB No. 0920-0573 Exp. XX/XX/XX

Name
PrimaryIDType
PrimaryID
AlternateIDType

Type
Text
Text
Text

AlternateID
INELIG

Text
Text

ANONYM
SITENUM

Text
Text

SITEEXT

Text

YEAR
SEQNUM
SPECIMENID

Text
Text
Text

Lengt Valid Value
50
Text
14
Text
50
PEMS_ClientID
PEMS_FormID
PCN
HARS_CityNo
Code-base Stateno
Other Local ID
50
Text
1
0 = Eligible (default)
1 = Confirmatory tests non-reactive
or negative
2 = Diagnosed before specified time
period
3 = ARV drugs
4 = Other
1
1=yes; 0=no
50
Text; list of valid site numbers will
be provided by each project area
50
Text; for areas that have
extensions, otherwise blank
50
YY
50
Text
50
Text

ACCESNUM
DRAWDTTM
TUBETYPE

Text
Text
Text

15
50
1

BLDCOMP

Text

Updated: 26/Oct/2006

Label
Primary ID Type
Primary ID
AlternateID Type

AlternateID
Eligibility of Case

Anonymous Tester?
Site Number
Site Extention
Year of Blood Draw
Sequence Number
SpecimenTracking ID
14 character field, left zero filled
positions 1-4 = area number
positions 5-8 = site number
positions 9-10 = last 2 digits of year of draw date
positions 11-14 = consecutive numbers for each
participant enrolled, zero filled on left
The last four digits need to be in ascending order
for a given year, but not necessarily consecutive.
Laboratory Accession Number
Date and Time of Draw Date
Type of Tube Used for Blood Collection

Text
YYYYMMDDHHMM
1 = Clot tube (Red top tube - for
serum)
2 = SST tube (Red and gray tiger
top tube - for serum)
3 = EDTA tube (Purple top tube for plasma)
4 = ACD tube (Yellow top tube - for
plasma)
5 = PPT tube (White top tube - for
plasma)
6 = CPT tube (Blue and black tiger
top tube - for cells or plasma)
7 = Finger stick - no tube
9 = Other
0 = No information provided
Type of Specimen Sent from Collection Site
1= Serum
2= Plasma
3= Whole anticoagulated blood
4= Dried Blood Spot
5= Cells
6= Dried Serum Spot
Data Elements

Page 1

Standard Variant, Atypical, and Resistant HIV Surveillance (VARHS) Data Elements OMB No. 0920-0573 Exp. XX/XX/XX

Name

Type

BLDLAB

Text

COURDTTM
DRECDTTM
CENTDTTM
SEPDTTM
VOLUME
COND

Text
Text
Text
Text
Text
Text

SpecimenFrozen
FREZ1DTM

Text
Text

Lengt Valid Value
7= Dried Plasma Spot
8= Clotted blood
1
0= No information provided
1= Serum
2= Plasma
3= Whole anticoagulated blood
4= Dried Blood Spot
5= Cells
6= Dried Serum Spot
7= Dried Plasma Spot
8= Clotted blood
50
YYYYMMDDHHMM
50
YYYYMMDDHHMM
50
YYYYMMDDHHMM
50
YYYYMMDDHHMM
3
Text
1
Enter highest relevent number
0= no hemolysis
1= low hemolysis
2= moderate hemolysis
3= high hemolysis
4= lipemic
5= contaminated
50
1=yes; 0=no
50
YYYYMMDDHHMM

THAW1DTM

Text

YYYYMMDDHHMM

FREZ2DTM

Text

YYYYMMDDHHMM

THAW2YN

Text

1=yes; 0=no

EIADTTM
ALIQDTTM
VOLGENO
GFRZ1DTM

Text
Text
Text
Text

50
50
3
50

YYYYMMDDHHMM
YYYYMMDDHHMM
Text
YYYYMMDDHHMM

Was the Specimen Frozen Before Aliquoting?
Date and Time of First Freeze of Specimen before
Aliquoting
Date and Time of First Thaw of Specimen before
Aliquoting
Date and Time of Second Freeze of Specimen
before Aliquoting
Were There Two or More Thaws of Specimen
before Aliquoting?
Date and Time of First Reactive EIA
Date and Time of Aliquoting
Volume Aliquoted for Genotyping
Date and Time of First Freeze of Genotyping Aliquot

GTHW1DTM

Text

YYYYMMDDHHMM

Date and Time of First Thaw of Genotyping Aliquot

GFRZ2DTM

Text

YYYYMMDDHHMM

GTHAW2YN

Text

1=yes; 0=no

VOLBACK
BFRZ1DTM
BTHW1DTM
BFRZ2DTM
BTHAW2YN
CNPOSDAT

Text
Text
Text
Text
Text
Text

3
50
50
50
1
50

Text
YYYYMMDDHHMM
YYYYMMDDHHMM
YYYYMMDDHHMM
1=yes; 0=no
YYYYMMDDHHMM

GSHPDATE
GRESDATE
NOTSENT

Text
Text
Text

50
50
1

YYYYMMDD
YYYYMMDDHHMM
0= Specimen was sent (default)
1= QNS
2= Viral Load Not detectable

Date and Time of Second Freeze of Genotyping
Aliquot
Were there 2 or More Thaws of Specimen Before
Aliquoting? (Specimen for Genotyping)
Volume Aliquoted for Back-up Specimen
Date and Time of First Freeze of Back-up Specimen
Date and Time of First Thaw of Back-up Specimen
Date and Time of Second Freeze of Back-up
Were there 2 or More Thaws Before Aliquoting?
Date of Western Blot or Other Confirmatory Positive
Test
Date of Shipment to Geno Lab
Date and Time Genotyping Results Received at
If Specimen was not sent for genotyping, what was
the reason for this?

Updated: 26/Oct/2006

Data Elements

Label

Type of Specimen Sent for Resistance Testing

Date and Time of Courier Pick-up From Collection
Date and Time of Receipt in Diagnostic Lab
Date and Time of Centrifugation
Date and Time of Separation
Volume of Serum/Plasma After Separation
Condition of the Serum/Plasma

Page 2

Standard Variant, Atypical, and Resistant HIV Surveillance (VARHS) Data Elements OMB No. 0920-0573 Exp. XX/XX/XX

Lengt Valid Value
3= Low Viral Load
4= Lost
5= Other
50
0= Yes (default)
1= No
8= Not attempted or unavailable for
attempt
9 = Unknown
50
YYYYMMDDHHMM
4
Text
50
1 = Standard Laboratory
2 = Mobile Laboratory
3 = Field
4 = Clinic
5 = Other
50
Text
4
1 = HIV Diagnostic Lab
0 = Site other than HIV Diagnostic
Lab
50
1 = Yes
2 = No
9 = Unknown
4
1 = DFS Collection Site
2 = Public Health Laboratory
3 = Other Laboratory
4 =Storage Facility
5 = Hospital
6 = Other
9 = Unknown
4
1 = Room Temperature
2 = 4ºC
3 = -20ºC
4 = -70ºC
50
YYYYMMDDHHMM

Name

Type

AMPLIFY

Text

SPOTDTTM
DRYTIME
DRYLOC

Text
Text
Text

SPECIFYLOC
DIAGDFS

Text
Text

RNALATER

Text

LocationType

Long

StoreTemp

Long

StoreDTM

Text

StoreDes

Long
4
Integer
Long
4
Integer

TransMeth

1 = US Mail
2 = FedEx/UPS/DHL
3 = Local Courier
4 = Lab/Health Department Staff
5 = Other
YYYYMMDDHHMM

TransDTM

Text

TransCool

Long
4
1=yes; 0=no
Integer
Text
3000 Text

Nucleic Acid
Sequence

1=yes; 0=no

Label

Did the Specimen Amplify?

Date and Time of Spotting
Length of Drying Time (Hours)
Drying Location:

Specify the drying location if DRYLOC = Other
Where was dried fluid spot made?

Was Specimen Collection Card Pretreated with
RNALater?
Type of Site Where Specimen Was Handled

Storage Temperature at Site

Date and Time of Refrigeration or Freeze and
Desiccant Addition at Site
Was Desiccant Changed Before or After Transport
from This Site to Next Site?
Method of Transport from This Site to Next Site

Date and Time of Removal from Refrigeration or
Freeze at Site
Was cooler or dry ice used for transport?
Nucleic Acid Sequence

Public reporting burden of this collection of information is estimated to average 5 minutes per response, including the time for reviewing instructions, searching existing
data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. An agency may not conduct or sponsor, and a
person is not required to respond to a collection of information unless it displays a currently valid OMB control number. Send comments regarding this burden estimate
or any other aspect of this collection of information, including suggestions for reducing this burden to CDC, Project Clearance Officer, 1600 Clifton Road, MS D-74,
Atlanta, GA 30333, ATTN: PRA (0920-0573). Do not send completed form to this address.

Updated: 26/Oct/2006

Data Elements

Page 3

Guidance for Variant, Atypical, and Resistant
HIV Surveillance

October 31, 2006

HIV Incidence and Case Surveillance Branch
Division of HIV/AIDS Prevention
National Center for HIV/AIDS, Viral Hepatitis, STD, and
TB Prevention
Centers for Disease Control and Prevention

Updated: 31/Oct/2006

Table of Contents

1.0 Variant, Atypical, and Resistant HIV Surveillance Overview

1.1 Objectives

1.2 Methods

1.3 Participating Surveillance Areas

2.0 Introduction

2.1 Background

2.2 Justification and Surveillance Usefulness

2.3 Objectives

2.4 Implementing Variant, Atypical, and Resistant HIV Surveillance Guidance

3.0 Variant, Atypical, and Resistant HIV Surveillance Methods: Population and Design

3.1 Inclusion Criteria

3.2 Exclusion Criteria

3.3 Surveillance Design

3.4 Obtaining and Eligible HIV-Positive Specimens

3.5 Obtaining and Handling VARHS Specimen Aliquots

3.5.1. Tube type for HIV diagnostic specimens

3.5.2. Specimen handling

3.5.3. Serum and plasma processing

3.5.4. Diagnostic and clinical testing and freezing of serum or plasma aliquots

3.5.5. Determining eligibility/ handling of specimens

3.5.6. Cryovials and Aliquots

3.5.7. Specimen information to be recorded in VARHS specimen log or database

3.5.8. Shipment to the VARHS genotyping laboratory

3.6 Returning VARHS Results

3.7 Required Data Elements

3.7.1. Demographic and clinical data

3.7.2. HIV incidence data and related data items for calculation of the incidence of transmitted HIV drug
resistance
19
3.7.3. Data used for VARHS eligibility determination

3.7.4 Laboratory data

Updated: 31/Oct/2006

4.0 Security and Confidentiality of Variant, Atypical, and Resistant HIV Surveillance Data

5.0 Data Handling and Analysis

5.1 Data Management

5.2 Data entry and merging of data

5.3 Data handling, encryption, and transfer

5.4 Data Analysis

5.5 Data Dissemination

6.0 Variant, Atypical and Resistant HIV Surveillance Responsibilities

6.1 Variant, Atypical, and Resistant HIV Surveillance Coordination

6.2 Epidemiological Oversight

6.3 Laboratory liaison from the health department

6.4 Laboratory liaison based at a participating HIV diagnostic laboratory

6.5 Data Management

7.0 Public Health Benefit

References

Appendix A. National Center for HIV, STD, and TB Prevention’s Non-research Determination for HIV
Variant, Atypical, and Resistant HIV Surveillance

Appendix B. Epidemiologic Flow Chart for Variant, Atypical, and Resistant HIV Surveillance

Appendix C. Operational Laboratory Flow Chart for Variant, Atypical, and Resistant HIV Surveillance 35
Appendix D Guidelines for the Processing, Storage, and Shipment of Variant, Atypical and Resistant HIV
Surveillance (VARHS) Specimens to Genotyping Labs for Antiretroviral Drug Resistance Testing
36
Appendix E. Purpose of Required Data Elements

Updated: 31/Oct/2006

1.0 Variant, Atypical, and Resistant HIV Surveillance Overview
1.1 Objectives
1. Incorporate surveillance of transmitted strains of variant, atypical, and resistant HIV into
routine HIV surveillance activities by:
a. amplifying and sequencing relevant regions of the HIV pol gene from remnant
HIV diagnostic specimens to evaluate mutations associated with HIV drug
resistance and HIV-1 subtypes among all persons newly diagnosed with HIV
b. evaluating mutations associated with resistance and HIV-1 subtype in the subset
of diagnostic specimens with evidence of recent infection determined by
laboratory testing using the serologic testing algorithm for recent HIV
seroconversion (STARHS) or another CDC-approved method
2. Provide HIV drug resistance data and HIV-1 subtype data to assist local HIV prevention
and treatment program planning and evaluation.
1.2 Methods
Variant, atypical, and resistant HIV surveillance (VARHS) evaluates the prevalence of HIV drug
resistance and HIV-1 subtypes among individuals newly diagnosed with HIV in public health
settings and other clinical and diagnostic settings collaborating with the state, county, or large
city Departments of Health. Ideally, specimens from all individuals newly diagnosed with HIV
in the state, county, or large city should be included. If sufficient volume is available, aliquots of
remnant sera will be set aside for HIV drug resistance testing from each blood specimen drawn
for HIV diagnosis from eligible persons in participating sites. For individuals meeting VARHS
criteria, HIV genetic sequencing (genotyping) will be performed on the reverse transcriptase and
protease regions of the HIV pol gene to detect the presence of mutations associated with HIV
drug resistance. HIV-1 subtype will also be identified based on the pol gene sequence.

The CDC Office of the Director awarded a non-research determination to variant, atypical, and
resistant HIV surveillance (VARHS) on June 25, 2004 (see Appendix A); VARHS was
incorporated nationally into routine HIV surveillance as of July 1, 2004. The document that
serves as the basis for the Federal Regulations for protecting human research participants is Title
45 of the Code of Federal Regulations part 46 (45 CFR 46, available at
http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.htm). Subpart A, subsection 46.101c
states, “the (Federal) Department or Agency heads retain final judgment as to whether a
particular activity is covered by this policy”. “This policy” refers to the requirements for human

Updated: 31/Oct/2006

subjects protection review for research protocols under the 45 CFR 46 regulations. Disease
surveillance is one of the four major public health practice activities that usually involve data
collection, but are not research and do not need review by an Institutional Review Board (IRB)
according to 45 CFR 46. VARHS was determined to be a disease surveillance activity by CDC,
the appropriate federal agency, and thus does not require IRB review. This finding does not
supersede state or local laws or regulations that may require IRB review, or notification to an
IRB, for public health surveillance activities.

HIV drug resistance testing for VARHS is performed utilizing standard tests that are widely used
clinically. These tests are not experimental and do not require specific informed consent. The
use of a remnant diagnostic specimen for drug resistance testing is routinely performed without
informed consent for tuberculosis, urinary tract infections, and sexually transmitted diseases, and
drug resistance results are collected as part of public health surveillance for these and other
conditions.[3,5,7] Like drug resistance testing in other infectious disease surveillance systems,
testing diagnostic specimens for HIV drug resistance and HIV-1 subtype surveillance is not
experimental and does not require informed consent. Project areas must notify individuals that a
HIV DR test may be performed on the diagnostic specimen.

Genotyping results and information from the HIV surveillance case report will be used to make
population-based estimates of the prevalence of HIV drug resistance and HIV-1 subtypes among
individuals newly diagnosed with HIV. Prevalence estimates will also be made for relevant
demographic groups and HIV exposure categories. In areas performing variant, atypical and
resistant HIV surveillance and HIV incidence surveillance, evaluation of recent HIV infection
using a testing history and STARHS (Serologic Testing Algorithm for Recent HIV
Seroconversion) will be collected as part of HIV surveillance for most newly diagnosed
individuals. HIV incidence results in combination with the sequencing result, testing history
data, and clinical information about disease progression at diagnosis will be used for populationbased HIV estimates of the incidence of transmitted HIV drug resistance and HIV-1 subtypes.
HIV sequence information may also be used to track the spread and clustering of atypical HIV
strains of interest nationally.

Updated: 31/Oct/2006

For newly diagnosed individuals whose specimens are amplified and genotyped successfully, an
individual hard copy report of results will be made available by the health department to a
provider designated by the individual.

1.3 Participating Surveillance Areas
Listed below are the areas funded as of April 2004 to participate in variant, atypical, and resistant
HIV surveillance (including sites that participated in the antiretroviral drug resistance testing
(ARVDRT) evaluation project).
1.
2.
3.
4.
5.
6.
7.
8.

9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.

Chicago Department of Public Health
Colorado Department of Public Health and Environment
District of Columbia Department of Health
Florida Department of Health
Illinois Department of Public Health
Indiana State Department of Health
Louisiana Office of Public Health
Maryland Department of Health and Mental Hygiene
Massachusetts Department of Public Health
Michigan Department of Public Health
Mississippi State Department of Health
New Jersey Department of Health and Senior Services
New York City Department of Health and Mental Hygiene
New York State Department of Health
North Carolina Department of Health
Pennsylvania Department of Health
Puerto Rico Department of Health
Seattle and King County Public Health
South Carolina Department of Health
Texas Department of State Health Services
Virginia Department of Health
Washington State Department of Health

Updated: 31/Oct/2006

2.0 Introduction
2.1 Background
The Centers for Disease Control and Prevention (CDC) is responsible for maintaining a national
surveillance system that provides data on the HIV/AIDS epidemic that can be used for national,
state, and local public health HIV/AIDS prevention program planning and evaluation. Clinical
and laboratory testing information data items have been incorporated into HIV/AIDS
surveillance based on their utility on a population basis in characterizing the HIV epidemic or
triggering particular public health action. HIV genetic sequence data based on the pol gene has
now been incorporated into HIV/AIDS surveillance to evaluate the distribution of HIV-1
subtypes and mutations associated with HIV drug resistance among individuals newly diagnosed
with HIV and the subset of recently infected persons.

In the late 1990s, several new nucleoside reverse transcriptase inhibitors (NRTI), non-nucleoside
reverse transcriptase inhibitors (NNRTI), and protease inhibitors (PI) were approved for treating
HIV infection in the United States. These newer drugs, combined with the NRTIs already
available, provide clinicians with a variety of choices for initiating and changing antiretroviral
treatment for patients infected with HIV-1. A panel representing international expertise in
antiretroviral research and HIV patient care convened by the International AIDS Society – USA
[13] and a Public Health Service interagency work group with expert consultation [9] have
continually updated recommendations for prophylaxis or therapy that, for specific purposes,
include all of the antiretroviral drugs currently approved by the FDA and in use in the US, and
for HIV drug resistance testing.

The therapeutic purposes of antiretroviral drugs include prophylaxis after known occupational
exposure (post-exposure prophylaxis), vertical transmission prophylaxis, treatment of primary
infection (four to seven weeks after infection), initial treatment from early (little or no
immunological damage) to late infection (substantial immunological damage), and changes in
treatment regimens depending on virological and immunological response.[10,11,4,9,6,13]
Clinical trials are being performed to evaluate pre-exposure prophylaxis with antiretroviral

Updated: 31/Oct/2006

drugs. Studies have demonstrated that HIV drug resistance results (both genotype and
phenotype) can be used to predict clinical outcome and to guide drug treatment choices.[6]

CDC is currently working with state and local health departments to integrate VARHS into
routine HIV core surveillance similar to the way tuberculosis molecular surveillance was
incorporated into tuberculosis surveillance. Like other public health surveillance activities,
CDC’s human subject protection process determined that the implementation of variant, atypical,
and resistant HIV surveillance is not research (Appendix A).
2.2 Justification and Surveillance Usefulness
Studies have shown that pol gene sequencing results indicating the presence of mutations known
to be associated with HIV drug resistance predict phenotypic sensitivity to antiretroviral drugs
and clinical response.[6,9,13] VARHS supports the evaluation of HIV drug resistance (HIVDR)
and factors associated with resistance in persons newly diagnosed with HIV in participating
areas. Previous surveys have been based on convenience samples; VARHS is the first large
surveillance system in the US designed to evaluate all persons diagnosed in participating sites in
successive years. Representative sampling and ongoing collection of data through routine
surveillance will provide information on trends in transmission of HIVDR. VARHS will
determine the distribution of viral genotypes among persons newly diagnosed with HIV.
Analyses will support evaluation of first-line HIV antiretroviral drug treatment and prophylaxis
strategies in participating geographic areas by providing information to clinicians,
pharmaceutical researchers, and public health authorities making treatment recommendations
and developing new treatments. Information on the distribution of HIV-1 subtypes in the U.S.
and in specific geographic areas will also be provided by VARHS, and will support selection of
diagnostic and clinical tests appropriate for use with various HIV-1 subtypes, and the
development of vaccines. Finally, phylogenetic analysis of the sequences generated by VARHS
will allow investigation of the spread or clustering of atypical strains of interest, and contribute
to analyses of evolution of HIV in the U.S. and worldwide.

Updated: 31/Oct/2006

2.3 Objectives
1. Incorporate surveillance of transmitted strains of variant, atypical, and resistant HIV into
routine HIV surveillance activities by:
a. amplifying and sequencing relevant regions of the HIV pol gene from remnant
HIV diagnostic specimens to evaluate mutations associated with HIV drug
resistance and HIV-1 subtypes among all persons newly diagnosed with HIV
b. evaluating mutations associated with resistance and HIV-1 subtype in the subset
of diagnostic specimens with evidence of recent infection by laboratory testing
using the serologic testing algorithm for recent HIV seroconversion (STARHS) or
another CDC-approved method
2. Provide HIV drug resistance data and HIV-1 subtype data to assist local HIV prevention
and treatment program planning and evaluation.

2.4 Implementing Variant, Atypical, and Resistant HIV Surveillance Guidance
This guidance is designed to provide assistance to HIV/AIDS core surveillance areas on
implementing variant, atypical, and resistant HIV surveillance (VARHS). Guidance is provided
on the design of the surveillance system, the identification of cases for testing, specimen
collection and transport for HIV genetic sequencing and other HIV drug resistance tests, data
management, confidentiality and security procedures, and personnel procedures. The appendices
and references include supporting documentation such as a non-research determination by CDC,
VARHS flow charts, specimen handling and shipping procedures, and guidance on the data
elements to be used in evaluating HIV drug resistance and HIV-1 subtype prevalence nationally
and in sub-populations.

VARHS will generally be implemented in areas already performing HIV incidence surveillance.
It is recommended that HIV incidence surveillance procedures be in place before VARHS
implementation is planned in detail. In some circumstances, simultaneous implementation of
both types of surveillance may be suitable, but the default is for VARHS implementation to
follow the implementation of HIV incidence surveillance. Areas should consult their CDC HIV
incidence surveillance epidemiologist and the VARHS project officer about the appropriate time
to plan and implement VARHS. In addition, prior to VARHS implementation, a site visit must

Updated: 31/Oct/2006

be conducted by CDC. Sites should not begin collecting samples for VARHS until they have
been approved to begin implementation by the CDC VARHS Project Officer.

At the end of selected sections of this document, a task box, like the one shown below, titled
“VARHS Implementation Task” will provide guidance on the specific task that the surveillance
area will need to address in order to implement variant, atypical, and resistant HIV surveillance.
A description of the procedures to be used in an area to address the task should be included as
part of the area-specific version of this guidance which may be submitted to CDC by the
VARHS coordinator. Completion of the tasks is a key consideration in the successful
implementation of VARHS.

SAMPLE VARHS Implementation Task
Variant, atypical, and resistant HIV surveillance areas
should complete each implementation task appearing at
the end of selected sections in this document.

3.0 Variant, Atypical, and Resistant HIV Surveillance Methods: Population and Design
3.1 Inclusion Criteria
•

Specimens from all newly diagnosed HIV cases tested confidentially and eligible to be
reported to the HIV case surveillance system are included in VARHS.

3.2 Exclusion Criteria
•
•
•

Any case that has had a documented positive HIV test >3 months (before the specimen
collected for VARHS) is excluded from VARHS.
Any case with a previous specimen successfully sequenced for VARHS is excluded from
HIV sequencing of an additional specimen in VARHS
Any case known to have had previous exposure to antiretroviral drugs (before collection
of the specimen for VARHS).

3.3 Surveillance Design
Variant, atypical, and resistant HIV surveillance is an extension of the existing national
population-based HIV/AIDS case surveillance system. With over 20 years experience with case

Updated: 31/Oct/2006

surveillance, state and local health department partners and CDC will use the case surveillance
infrastructure to collect the information necessary to estimate the prevalence of transmitted HIV
drug resistance and HIV-1 subtypes. In addition to data collected in the current case surveillance
system, variant, atypical, and resistant HIV surveillance requires an aliquot of the remnant blood
specimen made from an HIV diagnostic test or a follow-up test such as a confirmatory test made
within three months of the original HIV diagnosis (Appendices 2 and 3).

3.4 Obtaining Eligible HIV-Positive Specimens
To minimize the possibility that a newly diagnosed individual might begin taking antiretroviral
drugs before a specimen is obtained, HIV genetic sequencing for VARHS must be performed on
an HIV-positive specimen collected at HIV diagnosis or from a follow-up HIV diagnostic blood
draw no more than three months after HIV diagnosis. If volume and logistics permit, a remnant
specimen for VARHS will be obtained from all eligible confirmed HIV-positive diagnostic
specimens. A follow-up specimen drawn no more than three months from HIV diagnosis may
also be used. Specimen types suitable for VARHS include serum, plasma, and blood. The use
of dried fluid spots (DFS) for VARHS is currently being evaluated as an alternative specimen
collection type and is a separately funded activity; areas that are not funded for this evaluation
should not collect DFS specimens. In each surveillance area, laboratories that could potentially
participate in VARHS will be identified from a review of local HIV surveillance data and
laboratory licensing records.

In practice, VARHS will usually begin in public health laboratories working closely with the
health department. Clinical facilities with their own HIV diagnostic laboratories may also be
recruited for participation in VARHS. National commercial reference laboratories and other
private laboratories where HIV diagnostic or clinical testing is performed can also participate in
VARHS if resources are available to allow remnant specimens to be processed within the time
frames described in the sections below.

The default practice for VARHS is that eligible specimens tested at or shipped to the central
public health laboratory or laboratories in the area are shipped by the central laboratory for HIV

Updated: 31/Oct/2006

VARHS testing. However, selected laboratories may ship eligible specimens for VARHS
directly if the health department determines that the procedure will save resources and labor.

No funds are currently available from CDC to reimburse commercial reference laboratories for
VARHS specimen handling costs on a national basis. The need for, and use of, reimbursement
to local commercial and other private laboratories will be determined by each surveillance area
and made available by the area as resources allow. The mechanism and type of reimbursement,
if any, will be established locally, based on local policies. Shipping costs associated with
sending specimens from state public health laboratories to the genotyping laboratory should be
budgeted in the cooperative agreements CDC has with each participating area.

VARHS Implementation Task 3.4.A
Variant, atypical, and resistant HIV surveillance areas should identify laboratories
required to report HIV positive tests to their HIV/AIDS surveillance system, the total
number of new HIV positive diagnoses made annually in each laboratory, and the
number of HIV positive specimens suitable for VARHS (plasma, serum, or blood) from
which new HIV diagnoses are made annually in each laboratory.

3.5 Determining Eligibility and Obtaining and Handling VARHS Specimen Aliquots
Specimen handling and transport procedures should be decided by the public health laboratory
and blood-drawing sites. If necessary, procedures can be modified when new aspects of a
surveillance system are instituted. Sections under 3.5 describe tube types, transport times, and
processing times that are optimal for VARHS. Decision-makers should take these factors into
account when considering local procedures. Decisions on specimen handling and transport
should be made primarily to optimize HIV diagnostic testing and the best use of local resources
for major public health priorities; obtaining optimal specimens for VARHS has a lower priority.

One or more central public health laboratories will generally process and ship VARHS
specimens to the genotyping laboratory. The project area VARHS coordinator may also agree
that some VARHS specimens may be processed and shipped directly from selected non-public-

Updated: 31/Oct/2006

health laboratories if fewer resources and less labor are required for direct shipment and provided
standard procedures are followed. These agreements should be discussed with the CDC project
officer. Detailed shipping procedures for serum and plasma specimens can be found in
Appendix D.

Since the use of dried fluid spots (DFS) for HIV genetic sequencing is still uncommon and is
being evaluated by a limited number of public health departments as of July 2006, DFS handling
procedures are not included in the main body of this guidance or in the VARHS shipping
procedures appendix (Appendix D).

3.5.1. Tube type for HIV diagnostic specimens
Decision on tube type used for HIV diagnostic blood draws and follow-up specimens
should be made on the basis of local diagnostic and surveillance needs and available
resources. If changes are being considered to current practice, it should be noted that to
ensure sufficient volume for additional HIV surveillance uses including VARHS, the
HIV diagnostic blood draw would be at least eight-ml (optimal volume is ten-ml), drawn
into a red-top Vacutainer clot tube or Serum Separator tube (SST). Eight- or ten-ml tubes
with anticoagulant, or Plasma Separator tubes (PST), are suitable for diagnostic or
follow-up specimens from which remnant plasma will be aliquoted for VARHS.

3.5.2. Specimen handling
After the blood draw and prior to serum or plasma separation, it is optimal to store the
tube of blood at room temperature. The blood draw and specimen transport should be
timed so that specimens arrive at the HIV testing laboratory and are processed (separated,
aliquoted, and frozen) within 96 hours from the draw. Specimens processed up to 96
hours after the blood draw are still likely to be amplifiable for genetic sequencing.
Specimens processed after that period may have a reduced likelihood of amplification,
but should still be sent for VARHS.

Updated: 31/Oct/2006

3.5.3. Serum and plasma processing
During separation, it is recommended both for the purposes of HIV testing and for
VARHS that the specimens be centrifuged to remove red blood cells and prevent
hemolysis. (Successful HIV amplification for sequencing is less likely with hemolysed
specimens.) After separation of the serum, samples will optimally be maintained
constantly at refrigeration temperature (4 degrees C) or on ice until samples are EIA
tested and eligible aliquots are frozen for potential use in VARHS.

3.5.4. Diagnostic and clinical testing and freezing of serum or plasma aliquots
To maximize chances for successful amplification for genetic sequencing, HIV
diagnostic testing or other relevant clinical testing will optimally begin immediately after
centrifugation. Sera or plasma should be kept on the bench at room temperature for as
short a time as possible before being returned to the refrigerator or placed on ice. If
volume appears sufficient for the purposes of all basic laboratory tests and other local
priorities such as archiving, for HIV incidence surveillance, and for VARHS, a one-ml
aliquot from all EIA reactive samples will be frozen at –70 degrees C as soon as possible
following the first reactive EIA. At this point, the aliquot is still considered a HIV
diagnostic specimen; it will not be defined as a VARHS specimen until the specimen is
confirmed as HIV positive, and until it is clear that the needs for serum for all higher
priority laboratory tests, including diagnostic HIV testing and HIV incidence testing,
have been fulfilled. Aliquots frozen as potential VARHS specimens should be thawed at
any time if needed for higher priority tests. The freeze-thaw cycle will not affect the HIV
diagnostic test results.

Optimally, the –70 degrees C freeze will occur within 96 hours of the blood draw.
Preliminary data from four public health departments in CDC’s ARVDRT pilot
evaluation suggests that sera frozen within 96 hours of the blood draw have a great than
90% chance of having HIV amplified for HIV genetic sequencing. However, specimens
frozen beyond 96 hours may still be sent for HIV genetic sequencing.

Updated: 31/Oct/2006

Once frozen, specimens for genotyping should not be thawed until they reach the
genotyping laboratory. A freeze-thaw cycle will reduce the chance of successful
amplification for genotyping.

3.5.5. Determining eligibility/ handling of specimens
When specimens have been confirmed as HIV-positive by Western blot or any other
method acceptable to the Department of Health, all HIV-negative specimens should be
handled according to standard laboratory procedures. The VARHS coordinator will
identify which of the remaining confirmed positive frozen aliquots are eligible for
VARHS by matching information with the laboratory, HARS, or other HIV surveillance
databases. Aliquots associated with individuals found to be diagnosed with HIV greater
than three months previously, or who have specimens already tested as part of VARHS
from another site, are not eligible for VARHS and should be handled according to
standard laboratory procedures. Frozen aliquots from specimens yielding indeterminate
or negative Western blot results will be handled according to standard laboratory
procedures.

3.5.6. Cryovials and Aliquots
Cryovials for the sera or plasma aliquoted for VARHS should be two ml in size,
polypropylene, with screw caps and external threads. If labels will not be not used, the
tube should have a writing area. After the VARHS ID is generated locally, the cryovials
should be labeled with the appropriate permanent markers or pre-typed labels. Labels
that will stick on frozen tubes can be supplied at no cost from CDC, or the VARHS ID
may be written directly onto the appropriate writing area with permanent marker.

Ideally, one ml per specimen is to be aliquoted for HIV genetic sequencing to be sent to
the CDC-contracted Stanford University laboratory or the laboratory contracted by the
local health department. When the volume is limited, priority is given first to the
laboratory’s standard operating procedures for HIV diagnostic and clinical testing and
serum archiving, second to HIV incidence surveillance activities, and third to VARHS. If
serum volume is insufficient to meet all these requirements, basic diagnostic and clinical

Updated: 31/Oct/2006

and archiving needs should be met first, HIV incidence surveillance needs second, HIV
genetic sequencing for VARHS third, and any site-specific VARHS back-up specimen
needs last. If less than one ml is available for genetic sequencing when all other needs
have been met, the specimen should still be sent for sequencing.

3.5.7. Specimen information to be recorded in VARHS specimen log or database
The diagnostic testing laboratory should maintain a VARHS specimen tracking log or
database to provide information for evaluation if problems in amplification for genetic
sequencing, specimen mix-up, or specimen contamination occur. Recommended
elements of information are listed in Appendix E. A MS-Access database is supplied by
CDC for data entry of this information.

Information may be recorded first on individual lab slips, specimen labels, or on batch
slips. Batch slips may be used for initial recording of information applicable to batches
of specimens, such as blood draw site, lists of patient identification numbers for
specimens transported in a batch, time/date of receipt in the diagnostic laboratory, lab
accession number range for a batch, time/date of centrifugation, time/date of separation,
time/date of first positive EIA, time/date of aliquoting, time/date aliquots were frozen.
All or some of this information may also be captured from in-house laboratory databases.
Information will be transferred to the log or database for each individual specimen that is
confirmed as HIV positive and not identified as ineligible. Laboratory or Health
Department personnel may work with CDC to develop methods of information transfer to
minimize duplicate recording of information.

3.5.8. Shipment to the VARHS genotyping laboratory
For persons not previously reported to HARS/eHARS with a diagnostic date > 3 months
earlier than the blood draw, not otherwise found to have a previous positive specimen > 3
months earlier than the blood draw, and not found to have a previous specimen
successfully sequenced in VARHS, surveillance staff will compile a list of specimens to
be packaged and shipped by the state or local public health laboratory to the genotyping

Updated: 31/Oct/2006

laboratory. Specimen ID numbers should be recorded on the specimen manifest; a copy
of the manifest should be kept by the VARHS coordinator.

Shipments to the genotyping laboratory should take place at least monthly. Specimens
will be handled, packaged, and shipped according to the CDC VARHS laboratory
shipping protocol (Appendix D). Specimens shipped as diagnostic specimens and using
dry ice for packing must follow the procedures for packing and shipping specimens using
dry ice (Appendix D).
VARHS Implementation Task 3.5.A
Variant, atypical, and resistant HIV surveillance areas should include a detailed laboratory
procedures component in the local version of this guidance. Procedures described should
include information on obtaining and processing specimens, determining eligibility,
recording specimen tracking variables for local use, storing specimens, and shipping
specimens. All procedures should be developed by the VARHS coordinator in
consultation with participating laboratories.

VARHS Implementation Task 3.5.B
Variant, atypical, and resistant HIV surveillance areas should identify the laboratories that
will transport specimens to a central public health laboratory in the area for VARHS
shipping, and the laboratories, if any, that will ship specimens directly to the genotyping
laboratory. The local version of this guidance should include descriptions of the
procedures for the VARHS coordinator to receive specimen tracking information
monthly, to receive shipping manifests whenever shipments are made, and to
communicate at least quarterly with laboratories making the shipments.

3.6 Returning VARHS Results to Individuals
HIV genetic sequencing is often performed for clinical purposes for patients receiving treatment
for HIV, and clinicians who treat patients for HIV are familiar with the formats in which results
are reported for individual patients. Individual VARHS results will be made available in such a
format. Because interpretation of results requires familiarity and training, VARHS results are
not returned directly to individuals, but to their providers.

Updated: 31/Oct/2006

When newly diagnosed HIV-positive clients return for post-test counseling or follow-up, they
should receive a brief explanation of VARHS. Counselors should instruct clients on how to
designate a provider to receive VARHS results if they wish to do so, either at that time or later.
Clients will also be informed that the information gathered through VARHS will be used to help
understand transmission of HIV and the transmission of drug resistant strains in the local
geographic area. A hard-copy report similar to clinical HIV drug resistance testing reports with
which physicians are familiar will be available to the Health Department from the genotyping
laboratory no more than one month after the specimen is received in the genotyping laboratory.
The counselor should inform the client of the time period before results will be sent to the
provider from the Health Department.

If the blood draw that produced a VARHS remnant specimen was performed at a clinical site to
which a participant is returning for medical consultation or care, the health department may
arrange for the VARHS individual report to be returned directly to the participant’s provider at
that clinical site.

VARHS Implementation Task 3.6.A
Arrangements should be described in detail in local variant, atypical, and resistant HIV
surveillance guidance for clients to identify a provider to whom the client’s VARHS report
should be sent. The arrangements should include a method for the client to designate a
provider at the time of the encounter or at a later time (up to five years is suggested).
Methods for designating a provider used in pilot areas include a telephone number that can be
called or a card that can be sent to the Health Department.

3.7 Required Data Elements
Appendix E outlines the minimum set of data elements and the purpose of each element required
for evaluating HIV drug resistance and HIV-1 subtype prevalence in the population and in
subgroups within the population. Appendix E also describes the recommended specimen
tracking elements that allow evaluation of potential or actual problems with HIV amplification
for genetic sequencing, contamination, or specimen duplication.

Updated: 31/Oct/2006

3.7.1. Demographic and clinical data
No demographic or clinical data are collected specifically for VARHS. Relevant
demographic and clinical data are merged in from the main HIV/AIDS reporting system
(HARS) database or equivalent. The demographic data used in the HIV drug resistance
prevalence estimates include age, sex, race/ethnicity, region of origin, and exposure
categories associated with HIV infection. The elements will allow for prevalence
estimates of HIV drug resistance and HIV-1 subtypes among persons newly diagnosed
with HIV to be made in major subgroups nationally, and also locally if numbers are
sufficient. These elements will also allow weighting of estimates to take into account the
characteristics of newly diagnosed persons in the area not included in VARHS.
3.7.2. HIV incidence data and related data items for calculation of the incidence of
transmitted HIV drug resistance
Measures of transmitted HIV drug resistance and HIV-1 subtypes in a specific year will
focus on the population recently infected with HIV and diagnosed in that year. HIV
incidence surveillance data (results from a test using the STARHS algorithm and assay
type) and date of the last negative HIV test, if available in the HIV surveillance system,
are the key elements for this estimate. CD4 and viral load counts, and dates of
occurrence of opportunistic infections and other AIDS-defining conditions, may also be
used for modeling to estimate incidence of transmitted variant and resistant strains of
HIV in past years. Demographic and clinical data from HARS will be used to weight
these estimates.

3.7.3. Data used for VARHS eligibility determination
HARS and other surveillance databases will serve as the primary means of screening for
eligibility by date of first positive HIV test and for previous use of ARV drugs. Matching
of specimen information with HIV surveillance databases will be attempted to evaluate
whether the participant was reported to the HIV surveillance systems with a positive HIV
test more than three months before the relevant blood draw. Matching with routine
laboratory surveillance databases containing HIV test information may also be possible to
evaluate whether a participant has had a previous positive result greater than three

Updated: 31/Oct/2006

months before the current specimen was drawn. However, shipment of specimens for
VARHS should not be delayed for more than one month for the purposes of such
evaluation, given the commitment to make reports available to providers in “real time” (if
possible, within six weeks of the HIV diagnostic test or other blood draw).

Information on dates of HIV diagnostic test results and dates of prescription of
antiretroviral drugs may not be available in HIV/AIDS surveillance reports until after
VARHS specimens are shipped. Once these data become available, the results may
define an individual case as VARHS-ineligible after HIV genetic sequencing is
performed for VARHS. Persons diagnosed with HIV more than three months before the
blood draw for VARHS, or receiving antiretroviral drugs before the blood draw for
VARHS, will be excluded from the VARHS analysis.

It should be noted that, in contrast to HIV incidence estimates, persons diagnosed with
AIDS and HIV simultaneously are not excluded from the estimate of HIV drug resistance
prevalence or HIV-1 subtype prevalence among persons newly diagnosed with HIV.

3.7.4 Laboratory data

The VARHS database includes laboratory tracking information described in Appendix D.

The VAHRS database contains information on whether HIV could be amplified from
each specimen. Stanford University lab or the local genotyping laboratory will transmit
information on amplification to the Health Department and to CDC. For specimens from
which HIV was successfully amplified and genotyped, the genotyping laboratory will
transmit the complete sequence of the protease region, and at least the first 240 codons of
the reverse transcriptase (RT) region, both as nucleotides and amino acids. The
laboratory will also transmit a separate list of all mutations (associated with HIVDR and
not associated with HIVDR) in any strain that differs from the reference strain used at the
laboratory. The conversion of the sequence information into HIV drug resistance and

Updated: 31/Oct/2006

subtype variables in the VARHS database by a CDC program is described in subsequent
sections.

Hard copy laboratory reports that will be accessible to the health care provider of the
client’s choosing will be generated by the genotyping laboratory and sent to the Health
Department. The Health Department will act as a repository for these hard copy
resistance testing reports for a locally specified period of time from the diagnostic HIV
test date.

VARHS Implementation Task 3.7.A
Variant, Atypical, and Resistant HIV Surveillance areas should review Appendix 5 and
review the percentage of HIV reports that record HIV/AIDS surveillance elements used for
analysis in VARHS. Because all the demographic and clinical data elements used are key
elements for general HIV surveillance, areas may wish to explore methods to increase
reporting of these elements. For instance, some pilot areas have added specific elements
such as country of birth to their counseling and testing system laboratory request forms.

4.0 Confidentiality and Security of Variant, Atypical, and Resistant HIV Surveillance Data
Only data that are part of, or are being incorporated into, the routine HIV/AIDS surveillance
system will be used. The only identifying information held in local public health departments
will be information routinely held in the HIV/AIDS surveillance system or their equivalent. This
information is governed by the U.S. Department of Health and Human Service’s (DHHS)
manual on security and confidentiality.[2] Policies and procedures, based on these guidelines
and local laws, are already in place at state and local health departments and are used to secure
hard copy and electronic information to protect the confidentiality of persons reported as having
HIV infection. Additionally, laboratory staff that is responsible for the transmission and/or
receipt of specimen shipping manifests and/or result reports must be trained on the DHHS
Security and Confidentiality guidelines for HIV/AIDS surveillance data. These measures will be
extended to protect the VARHS information held locally. Access by surveillance staff to
information in HARS and VARHS data will be governed by the same security and
confidentiality requirements. Under these guidelines, information that could identify an

Updated: 31/Oct/2006

individual (e.g., name, address, ZIP code) will not be included in the data set that is transmitted
from local surveillance areas to CDC.
HIV testing is a medical procedure. Therefore, policies and procedures are in place to protect the
confidentiality of tested individuals and their medical records. VARHS will be performed only
on specimens that have tested positive for HIV or specimens used for follow-up of a confirmed
HIV positive result. All information related to variant, atypical, and resistant HIV surveillance
will be subject to the same confidentiality and medical record protections as those for HIVpositive status.
VARHS Implementation Task 4.0.A
Variant, atypical, and resistant HIV surveillance areas should review their confidentiality
requirements and draft specific procedures for handling variant, atypical, and resistant
HIV data if needed or add VARHS components to the existing protocol.

5.0 Data Handling and Analysis
5.1 Data Management
All data will be considered part of routine HIV surveillance data. Data will be held to the
standards of security and confidentiality for HIV/AIDS surveillance outlined in the U.S.
Department of Health and Human Services manual and will take place at local health
departments and CDC.[2] Data entry and management will take place at state or local health
departments by using HARS and software developed by CDC or software that is compatible with
CDC software. Surveillance data and laboratory tracking data will be merged locally into the
local VARHS database provided by CDC. A program is available from CDC to merge
information from HARS into the VARHS database, which will be updated when HARS is
replaced by the eHARS document-based data entry system for HIV/AIDS surveillance. It is
planned that the data management system that will in turn replace eHARS in the future will
include the HIV pol gene sequence used for VARHS, and regularly updated programs to
interpret the sequence and place the information into the main database. Once this system is
deployed it will be able to accommodate all data fields required for variant, atypical, and

Updated: 31/Oct/2006

resistant HIV surveillance. During the period when HARS and eHARS are in use, the VARHS
database will remain a stand-alone adjunct system to HARS and eHARS, capable of merging
core HIV/AIDS surveillance variables with HIV drug resistance and HIV-1 subtype surveillance
information for analysis purposes.

From the VARHS database, a subset of HARS data for VARHS, and selected specimen tracking
variables, will be transmitted to CDC over the Secure Data Network (SDN) on a monthly basis.
Data transmitted to CDC will not include personal identifiers and will be encrypted and
password protected.

VARHS Implementation Task 5.1.A
Variant, atypical, and resistant HIV surveillance areas should review their protocol for
handling and storing data in secure locations and outline how VARHS data will be stored
and secured. Personnel with access to the data should receive training on security and
confidentiality procedures and should sign a confidentiality statement outlining the
procedures and consequences for violating the guidelines.

VARHS Implementation Task 5.1.B
Variant, atypical, and resistant HIV surveillance coordinators should include in their local
guidance the procedures for merging HARS, specimen tracking, and genotyping data into
the VARHS database, and for transmitting data to CDC. The frequency with which data
will be transmitted to CDC should be included. Persons transmitting VARHS data must
apply for and be approved for a Secure Data Network certificate from CDC for
transmission of VARHS data, or have the transmission of VARHS data added as an
approved activity to an existing SDN certificate.

5.2 Data entry and merging of data

The VARHS database is a Microsoft Access database supplied by CDC with tables for
laboratory tracking, demographic and clinical data, HIV incidence data, and HIV drug resistance
and subtyping data. An additional table is available for local data entry, for which fields can be
created locally. All data except identification numbers, laboratory tracking data, and data

Updated: 31/Oct/2006

entered into the local table are merged into the VARHS database electronically and do not
require manual data entry.

A VARHS identification number will be assigned to each specimen sent for genotyping and used
for merging HIV genetic sequencing information into the VARHS database. The variant,
atypical, and resistant HIV surveillance resistance identification number (VARHS ID) is a 14
digit number. It should be assigned as follows:
• Digits 1-4: The four digits representing the FIPS code of the project area
• Digits 5-8: The four digits representing the site (site number) where the blood draw was
performed
• Digits 9-10: The last two digits of the year
• Digits 11-14: The four digit sequence number as assigned by the local health department
The VARHS database includes functions to allow areas to enter their FIPS (Federal Information
Processing Standard, http://www.census.gov/geo/www/fips/fips.html) code only once, and to
create a menu of blood drawing sites and their codes. The VARHS ID will be created
automatically in the VARHS database when a minimal amount of information is entered for each
specimen. The VARHS ID number should be recorded on the cryovial used for aliquoting
serum or plasma before transport (after the specimen is confirmed as HIV seropositive).
Electronic genetic sequence information will be sent back encrypted from the genotyping
laboratory identified only by the VARHS ID number and merged into the database. Specimen
tracking information will also be recorded using this number. The specimen accession number
may also be entered into the database for local use.

The HARS state case number (STATENO), when assigned, is entered into the VARHS database
for the purpose of merging in relevant variables from HARS.

Additional information for the use of local HIV surveillance staff, for the purposes of returning
results or for eligibility determination, may be recorded in a local table in the Access database.

Updated: 31/Oct/2006

5.3 Data handling, encryption, and transfer
Electronic VARHS data will be sent encrypted and password protected to the Health Department
from the genotyping laboratory in the form of a text file representing the HIV pol gene sequence
attached to the relevant VARHS identification number. In the future, CDC may provide a
regularly-updated program to interpret this sequence and incorporate information on individual
mutations of interest, level of resistance to each antiretroviral drug in common use, and HIV-1
subtype, into the “resistance person-view” table of the VARHS Access database. Additional
programs are provided by CDC to export a SAS file to be used for local analysis, and to export a
subset of non-identifying variables to be transferred to CDC.

Encryption software will be used for receipt of files from the genotyping laboratory and CDC.
Areas receiving genotyping data from the Stanford University laboratory must purchase “Pretty
Good Privacy” (PGP) software with at least 128-bit encryption in order to receive and send
encrypted HIV genetic sequencing data. PGP Personal Desktop edition is suitable; a perpetual
license is recommended. Data transferred electronically from a local genotyping laboratory must
be encrypted using PGP or equivalent encryption software. PGP encryption keys must be
exchanged between the genotyping laboratory and data transfer personnel at the health
department. Data will be encrypted and transmitted from the health department to CDC through
the SDN already in use for HIV/AIDS reporting. Either the SEAL encryption software used
traditionally for HARS data transfer or PGP encryption software may be used for transfer of data
to CDC through the SDN. Data sent from CDC to VARHS areas for the purposes of data quality
assurance will be encrypted using PGP software and transferred through the SDN. PGP
encryption keys must be exchanged between CDC and the health department.

VARHS Implementation Task 5.3.A
At least one month before specimen collection starts, variant, atypical and resistant
HIV surveillance areas should purchase and install PGP encryption software with at
least 128-bit encryption capacity. Encryption keys should be exchanged with the
genotyping laboratory and with the VARHS data managers and the laboratory liaison
at CDC before the first specimen shipment.

Updated: 31/Oct/2006

5.4 Data Analysis
Nationally and locally, the overall prevalence of resistance to at least one antiretroviral drug
among individuals newly diagnosed with HIV, and among the subset of individuals recently
infected with HIV, should be reported annually. The prevalence of resistance to individual ARV
drugs and categories of commonly used ARV drugs (currently nucleoside reverse transcriptase
inhibitors, non-nucleoside reverse transcriptase inhibitors, and protease inhibitors) among these
two groups will also be reported, as well as the prevalence of HIV-1 subtypes.

The data will be stratified by factors such as demographic or exposure category factors for
subpopulation analyses at the national and local levels. If the sampling procedure has sufficient
statistical power, this stratification will allow comparisons among different geographic areas and
different exposure categories. Results will be extrapolated to those who did not have specimens
tested in VARHS.

Additional modeling of HIV drug resistance transmission may be performed using clinical and
HIV incidence information to approximate times of infection on a population basis.
Furthermore, in areas where anonymously tested specimens confirmed as HIV positive were
collected for VARHS, a separate analysis will be performed for these specimens.

5.5 Data Dissemination
It is expected that analyses, interpretation, and dissemination of VARHS data will be the primary
responsibility of CDC with the appropriate contributions from surveillance areas. Results from
the aggregate CDC database will be analyzed regularly and feedback provided to areas.
Aggregate results will also be published by CDC once a sufficient number of areas are
participating. Area-specific analyses will be conducted at the discretion of participating areas.
As appropriate, results will be presented at conferences and published in peer reviewed journals.
The number of representative authors from areas and CDC will be determined for each
presentation or paper.

Updated: 31/Oct/2006

VARHS Implementation Task 5.5.A
Variant, atypical and resistant HIV surveillance areas should include in the local
version of these guidelines a description of the proposed plan for reporting and
dissemination, data elements to be disseminated, and the process for data
dissemination.

6.0 Variant, Atypical and Resistant HIV Surveillance Responsibilities
Implementation of variant, atypical, and resistant HIV surveillance requires personnel with
specific skills and dedicated time to integrate VARHS into the existing core HIV/AIDS
surveillance system effectively. Generally, personnel who work primarily on HIV incidence
surveillance or core HIV/AIDS surveillance will develop work plans to integrate VARHS into
core HIV/AIDS surveillance in selected sites in coordination with their other responsibilities.
CDC has identified functions considered essential to the implementation and maintenance of
surveillance of variant, atypical, and resistance HIV. Individuals with VARHS responsibilities
should have an understanding of HIV surveillance, HIV incidence surveillance, and HIV drug
resistance surveillance, good communication skills, a basic understanding of the functioning of
HIV diagnostic laboratories and their relationship to the public health system, good
communication skills, and enthusiasm. Staff members with VARHS responsibilities should
work closely with CDC, other states, local HIV diagnostic and clinical sites, private providers,
and laboratories.

CDC recommends that persons be identified to perform the following functions: (1) coordination
of variant, atypical, and resistant HIV surveillance, (2) VARHS epidemiological oversight and
data analysis, (3) liaison between the health department and HIV diagnostic laboratories and the
genotyping laboratory, (4) liaison between participating HIV diagnostic laboratories and the
health department and genotyping laboratory, and (5) data management. These responsibilities of
these staff members are described below.

6.1 Variant, Atypical and Resistant HIV Surveillance Coordination
•
•

Provide overall management of VARHS
Serve as the primary point of contact for CDC on VARHS

Updated: 31/Oct/2006

•
•
•
•
•
•

•
•

Work with surveillance epidemiologists, the HIV incidence coordinator, and laboratory
liaison to the development of the area-specific procedures for and implementation of
variant, atypical, and resistant HIV surveillance
Directly manage or oversee the system for determining eligibility of specimens for
VARHS
Collaborate with the HIV diagnostic laboratory liaison(s) on developing specimen
tracking and specimen transfer procedures
Liaise with the genotyping laboratory to develop procedures for shipment of specimens
and receipt of data
Oversee data collection processes
o Describe the process and identify personnel involved in data collection and
merging of data into the VARHS database
Work with individuals providing epidemiological oversight to develop procedures for
o Data entry and quality assessment
o Data editing and file correction
o Data transfer procedures
o Preparation of monthly reports
o Security and confidentiality procedures
Develop and manage the system for returning VARHS results to providers identified by
newly diagnosed individuals
Participate in CDC site visits, trainings, and workshops

6.2 Epidemiological Oversight
•
•
•
•
•

•

Plan and implement integration of VARHS activities with HIV core surveillance and HIV
incidence surveillance activities
Develop a VARHS analysis plan
Develop systems to ensure data quality, analyze local VARHS data and produce reports
Develop presentations for local clinical and diagnostic sites and laboratories to explain
variant, atypical, and resistant HIV surveillance
Participate in data dissemination activities
o Collaborate with stakeholders to determine data needs and frequency of reporting
o Identify results and surveillance issues for review and dissemination
o Develop a data dissemination plan in collaboration with person coordinating
VARHS and CDC
Participate in CDC site visits, trainings, and workshops

6.3 Laboratory liaison from the health department
This function will often be performed by the person with VARHS coordination responsibility
•
•

Act as the liaison between the public health department and laboratories from which
specimens are being shipped
Oversee transfer of specimen tracking data from laboratories to the VARHS database at
the health department

Updated: 31/Oct/2006

•
•
•
•

In collaboration with liaisons based at participating laboratories, develop local procedures
for processing and shipping of specimens to the genotyping laboratory
In collaboration with liaisons based at participating laboratories, develop quality control
procedures outlined for preparing specimens
Develop and oversee procedures to maintain security and confidentiality of specimens
Participate in CDC site visits, trainings, and workshops

6.4 Laboratory liaison based at a participating HIV diagnostic laboratory
•
•
•
•

Liaise with the person coordinating VARHS and the health department laboratory liaison
to develop the laboratory-specific plan for processing, storing, determining eligibility,
tracking, and shipping specimens to the genotyping laboratory
Oversee preparation and shipping of VARHS specimens to the genotyping laboratory
Monitor quality control procedures outlined for preparing VARHS specimens
Record specimen tracking data in the log or database

6.5 Data Management
•
•

•

•
•

Assist the person coordinating VARHS activities with daily management of VARHS data
Serve as subject matter expert on VARHS data elements and data management programs
o Apply to receive certification to send HIV drug resistance data through the CDC
Secure Data Network (SDN) or to add the resistance component to an existing
certificate
o Identify at least one back-up person to receive CDC SDN certificate, and take
responsibility for maintaining and updating a list of persons with certification and
ensuring CDC is informed of changes
o Conduct data quality assessments
Conduct data management
o With CDC data managers, modify CDC’s generic data management programs for
use at the local area level
o Run programs to merge data into the VARHS database regularly
o Develop and implement edit checks and conduct data cleaning.
o Perform data export and transfer to CDC
o Receive genotyping data from the genotyping laboratory and run programs to
merge these data into the local database
o Run programs to export the local SAS analysis database
o Collaborate with persons working on VARHS and other area surveillance and
prevention staff, as needed, on data cleaning, data entry, and data set preparation
o Prepare data sets for local analysis
Maintain security and confidentiality of data.
Participate in CDC site visits, trainings, and workshops

Updated: 31/Oct/2006

VARHS Implementation Task 6.0.A
Variant, atypical, and resistant HIV surveillance areas should describe the
responsibilities for planning and implementation of VARHS locally, and the duties
and time to be spent on VARHS for each staff member who will be assigned these
responsibilities.

7.0 Public Health Benefit
VARHS will determine the distribution of viral genotypes among persons newly diagnosed with
HIV, supporting efforts to characterize and track the HIV epidemic nationally in the U.S.
Analyses will support evaluation of first-line HIV antiretroviral drug treatment strategies
nationally in participating geographic areas, and provide information useful to research scientists
developing new antiretroviral drugs. Strategies for use of specific drugs in HIV pre- and postexposure HIV prophylaxis will be enhanced by HIV drug resistance surveillance information.

VARHS will support evaluation of the utility of baseline clinical HIV drug resistance testing in
particular geographic areas. Current Department of Health and Human Services guidelines for
treatment of HIV infection suggest that testing performed before treatment begins may be
clinically useful up to three years after seroconversion. Given that many mutations appear to
remain detectable for at least this period of time, the guidelines go on to state, “….Using
resistance testing…in patients with chronic HIV infection is less straightforward…It may be
reasonable to consider such testing…when there is a significant probability that the patient was
infected with a drug-resistant virus…A recent study suggested that baseline testing may be costeffective when the prevalence of drug resistance in the relevant drug-naïve population is > 5%,
but such data are infrequently available.”[12] This International AIDS Society-U.S.A.
recommends HIV drug resistance testing for all recently infected persons, and adds “It is often
difficult to ascertain how long an individual has been infected, and consideration should be given
to HIV drug resistance testing when the duration is uncertain and the expected regional
prevalence of resistance is >5%.”[13] Both sets of guidelines refer to an analyses that suggests
the HIV drug resistance testing is cost-effective in drug-naïve persons if the regional prevalence
of resistance is >5%.[12] VARHS will supply an estimate of the prevalence of resistance both
in chronically and recently infected persons newly diagnosed with HIV, providing support for

Updated: 31/Oct/2006

clinical decision-making whether baseline clinical testing is likely to be cost-effective before
treatment is started.

Studies have demonstrated that the HIV pol gene sequence can be used to evaluate HIV-1
subtypes (and also HIV-2 subtypes, although the rarity of HIV-2 in the U.S. makes it unlikely
that such an evaluation will be required). A high prevalence of HIV-1 subtypes other than
subtype B in a geographic area has implications for appropriate selection of HIV diagnostic and
clinical tests both for populations and individuals.[1] VARHS will provide public health and
clinical personnel with prevalence estimates for non-B HIV-1 strains circulating in particular
geographic areas. In addition, if prevalence of HIV-1 non-B subtypes is shown to be increasing,
this finding could have implications for vaccine studies. Also, should specific mutations
associated with drug resistance be shown to be associated with some non-B subtypes, this could
have implications for treatment guidelines.

In surveillance of other organisms, such as M. tuberculosis, molecular surveillance has allowed
identification of atypical strains of special interest.[7,8] Although no such strains have currently
been identified for HIV, routine surveillance based on routine sequencing of the HIV pol gene
will also allow phylogenetic analyses to follow the spread of atypical HIV strains of interest
through geographic areas and within particular subgroups, supporting evaluation and targeting of
prevention strategies. HIV genetic sequencing surveillance data collected over period of years
will also contribute to analyses of the evolution of HIV within the U.S. and worldwide.

Updated: 31/Oct/2006

References
1. Bennett DE, HIV Genetic Diversity Surveillance, JID, in press.
2. Centers for Disease Control and Prevention. Appendix C: security and confidentiality. In:
Guidelines for HIV/AIDS Surveillance. 1998. Atlanta, GA, U.S. Department of Health and
Human Services.
3. Centers for Disease Control and Prevention. Implementation of A Public Health Action
Plan to Combat Antimicrobial Resistance. 2, 1-43. 2003. Atlanta, GA.
4. Centers for Disease Control and Prevention. Management of Possible Sexual, InjectingDrug-Use, or Other Nonoccupational Exposure to HIV, Including Considerations Related
to Antiretroviral Therapy - MMWR - Morbidity & Mortality Weekly Report 54(RR-2):118, 2005.
5. Centers for Disease Control and Prevention. Reported Tuberculosis in the United States,
2003. 2004. Atlanta, GA, US Department of Health and Human Services.
6. Hirsch MS, Brun-Vezinet F, Clotet B et al. Antiretroviral Drug Resistance Testing in
Adults Infected with Human Immunodeficiency Virus Type 1: 2003 Recommendations of
an International AIDS Society--USA Panel. Clinical Infectious Diseases 2003; 37:113-28.
7. Lewis B; Granich R; Courval J; Kammerer JS; Rosenblum L; et al Epidemiology of
Multi-drug resistance Mycobacterium tuberculosis in the United States, 1996-2000.
Abstract 105. American Public Health Association Annual Conference, 2003.
8. Munsiff SS; Nivin B; Sacajiu G; Mathema B; Bifani P; Kreiswirth BN. Persistence of a
highly resistant strain of tuberculosis in New York City during 1990-1999. JID 2003; 188;
356-363.
9. Panel of Clinical Practices for the Treatment of HIV Infection. Guidelines for the Use of
Antiretroviral Agents in HIV-1-Infected Adults and Adolescents. 2005: 1-108. DHHS,
http://aidsinfo.nih.gov/guidelines/adult/AA_040705.pdf
10. US Public Health Service Task Force. Recommendations for Use of Antiretroviral Drugs
in Pregnant HIV-1-Infected Women for Maternal Health and Interventions to Reduce
Perinatal HIV-1 Transmission in the United States. MMWR - Morbidity & Mortality
Weekly Report 51(RR-7):1-55, 2005.
11.US Public Health Service Task Force. Updated U.S. Public Health Service Guidelines for
the Management of Occupational Exposures to HBV, HCV, and HIV and
Recommendations for Postexposure Prophylaxis - MMWR - Morbidity & Mortality
Weekly Report 50(RR-1):1-43, 2001.
12.Weinstein MC, Goldie SJ, Losina E et al. Use of genotypic resistance testing to guide HIV
therapy: clinical impact and cost-effectiveness. Ann Intern Med 2001; 134:440-50.
13.Yeni PG, Hammer SM, Carpernter CCJ et al. Antiretroviral Treatment for Adult HIV
Infection: Updated Recommendations of the International AIDS Society-USA Panel.
JAMA 2002; 288:222-35.

Updated: 31/Oct/2006

Appendix A. National Center for HIV, STD, and TB Prevention’s Non-research
Determination for HIV Variant, Atypical, and Resistant HIV Surveillance

Updated: 31/Oct/2006

Appendix B. Epidemiologic Flow Chart for Variant, Atypical, and Resistant HIV Surveillance
Individual attends HIV diagnostic site for HIV testing
Blood drawn for HIV diagnostic test
First EIA reactive

Aliquot one ml of
serum and freeze
at -70 degrees
Centigrade

Specimen is further
tested and confirmed
HIV positive.
Yes

Yes

Aliquot for HIV
incidence testing
with STAHRS
algorithm if
eligible

Check against HARS/CTS-CTREIA/Laboratory/other surveillance databases
for diagnosis > 3 months previously. Check
VARHS database for previous inclusion.
Is individual eligible and not already in
VARHS?

Handle aliquots as per lab protocol.
No

Yes

If HARS eligible, HARS number
assigned as per protocol; HARS
data entered into HARS database.

Label aliquot(s) with VARHS ID, ship to
genotyping laboratory
Genotyping results including hard copy report and
electronic sequence files sent to DOH within 2-4
weeks of receipt in geno lab.

Individual hard
copy report to
provider

Run local HIV drug resistance
information and HARS
download program

VARHS Access Database

Local SAS analysis database
Data queried, cleaned,
harmonized

Local analysis, report,
dissemination
Updated: 31/Oct/2006

HIV incidence data
merged

Monthly download to CDC
national database

National analysis, report,
dissemination

Appendix C: VARHS Operational Laboratory Flow Chart
Specimen handled and testing for HIV initiated per standard laboratory protocol

EIA reactive

EIA non-reactive

Specimen handled per standard
laboratory protocol

Remove one aliquot (1ml);
freeze at -70ºC*

Proceed with HIV testing

Confirmatory HIV test (+)

Aliquot(s) for HIV
Incidence testing
made if eligible*

Confirmatory HIV test (-)

Coordinator checks
whether specimen
eligible for VARHS

NO
YES
Place VARHS ID on aliquot
for genotyping

At least monthly, fill in specimen
manifest and prepare for shipping as in
guidelines

Batch and send as dangerous goods to
HIV drug resistance laboratory for
genotyping

Genotyping performed; Result sent to
health department 2-4 weeks
from receipt date
* Priorities if specimen volume is limited:
1. HIV diagnostic testing- all aliquots remain available for diagnostic testing until confirmation is completed
2. HIV incidence testing using STARHS
3. HIV drug resistance genotyping
4. HIV drug resistance testing back-up (if applicable)
Updated: 31/Oct/2006

Appendix D
Guidelines for the Processing, Storage and Shipment of Variant,
Atypical and Resistant HIV Surveillance (VARHS) Specimens to
Genotyping Labs for Antiretroviral Drug Resistance Testing

HIV Incidence and Case Surveillance Branch
Division of HIV/AIDS Prevention
National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention
Centers for Disease Control and Prevention

Updated: 31/Oct/2006

Table of Contents

1.0 Purpose

2.0 Introduction

3.0 The Setting and Personnel Required for Specimen Processing

4.0 Materials

5.0 Specimen Collection and Processing

6.0 Shipping

6.1
6.2
6.3
6.4
6.5
6.6
6.7
6.8

Planning for shipment to Stanford Lab
Packing procedures for shipment to Stanford Lab
Procedures for shipment to Stanford Lab
Planning for shipment to a locally-contracted genotyping lab
Packing procedures for shipment to a locally-contracted genotyping lab
Procedures for shipment to a locally-contracted genotyping lab
Procedures for local transport to a locally-contracted genotyping lab

41
42
45
46
46
46
46

Local Transfer from the processing area to the genotyping area within 47
one laboratory

Appendix D-1: Training and Certification for Shipping Infectious Substances

Appendix D-2: CDC VARHS Genotyping Manifest

Appendix D-3: Stanford Shipping Box Return

Updated: 31/Oct/2006

1.0

Purpose
This standard operating procedure describes the methods for the handling, storage, and
shipment of Variant, Atypical, and Resistant HIV surveillance (VARHS) serum and/or
plasma specimens that will be tested for HIV antiretroviral drug resistance and HIV-1
subtyping.

2.0

Introduction
Serum or plasma from HIV diagnostic specimens is to be collected and frozen at minus
70 degrees Centigrade. For the purposes of resistance testing, the serum is to ideally be
separated within 48 hours of the blood draw and frozen within 96 hours of the blood
draw. Frozen serum or plasma will be shipped to a CDC designated testing laboratory for
genotype analysis.
NOTE: Back-up specimens will no longer be sent to the CDC Serum Bank. Project
areas may elect to store a “back-up” aliquot for use in the event that something happens
to the original aliquot sent to the lab or if a specimen needs to be re-tested for any reason.

3.0

The Setting and Personnel Required for Specimen Processing
3.1

Centrifugation, aliquoting, and shipping should be performed at or under the
auspices of a laboratory that is CLIA certified for handling HIV+ specimens.

3.2

All personnel handling specimens should receive blood borne pathogens training.
3.2.1

4.0

See OSHA’s Occupational Exposure to Bloodborne Pathogens Standard:
http://www.osha.gov/pls/oshaweb/owadisp.show_document?p_table=STA
NDARDS&p_id=10051.

3.3

Personnel handling or processing specimens should have the appropriate
laboratory training in the relevant laboratory techniques for handling HIV+
specimens and for performing the specific tasks required.

3.4

The setting in which centrifugation, aliquoting, and shipping occurs should meet
Biosafety level 2 specifications required by the U.S. Department of Health and
Human Services for handling of specimens containing HIV
(http://www.cdc.gov/od/ohs/biosfty/bmbl4/bmbl4s2.htm).

Materials
4.1

The following materials are required for the collection and shipment of VARHS
specimens:

Updated: 31/Oct/2006

4.1.1

Cryogenic vials: 1.5 to 2 ml with screw cap, external threads, O-ring, and
made of polypropylene

4.1.2

Freezer labels that will remain on the tubes upon freezing. Many
cryogenic vials have a label area printed on them that is suitable for
writing with a permanent marker. This is acceptable in place of labels.

4.1.3

Cardboard storage boxes for cryogenic vials: 81 spaces/box

4.1.4

Low temperature freezer: - 70° Centigrade
4.1.4.1 If not already in practice, it is recommended that a daily
temperature log be kept to ensure that the freezer is operating
properly.
4.1.4.2 The freezer should be housed in a location with proper ventilation
to avoid overheating and freezer failure.
4.1.4.3 Staff must be certain there is adequate space in the - 70° C freezer
to house VARHS specimens.

5.0

4.1.5

A supply of dry ice in pellet form

4.1.6

Saf-T-Pak (http://www.saftpak.com) STP 320 insulated shipping
containers certified to ship frozen diagnostic specimens (i.e., HIV+ sera
and dry ice)

4.1.7

Shipping courier air bills

4.1.8

Materials for shipper packing (Refer to Section 6.2.4.1)

Specimen Collection and Processing
5.1

All processing of specimens should be done by personnel qualified to handle
HIV+ specimens under the auspices of a laboratory equipped for the handling of
HIV+ specimens (http://www.cdc.gov/od/ohs/biosfty/bmbl4/bmbl4s2.htm).

5.2

As soon as possible after separation, the serum should be aliquoted from the
collection tube to the corresponding vial (1 ml per cryogenic vial is optimal).

5.3

If sufficient serum appears to be available for all diagnostic needs and HIV
incidence testing, one 1-ml (optimal volume) aliquot should be made for HIV
drug resistance testing. This aliquot should be shipped to Stanford University or
to the locally-contracted genotyping laboratory. Project areas may elect to store a

Updated: 31/Oct/2006

“back-up” aliquot for use in the event that something happens to the original
aliquot sent to the lab or if a specimen needs to be re-tested for any reason.
5.4

Place the aliquots in cardboard boxes for cryogenic vials in a - 70° C freezer.
Optimally, the - 70° C freeze will occur within 96 hours of the blood draw.

5.5

Sera aliquoted and frozen as potential specimens for HIV drug resistance testing
remain HIV diagnostic specimens until all HIV diagnostic tests and any other
basic laboratory tests have been completed. If additional serum is needed for
diagnostic testing or HIV incidence testing, sera aliquoted for potential HIV drug
resistance testing should be thawed and used for those purposes. If a back-up
specimen was made, this specimen should be used first. If more volume is
required, the specimen for the genotyping laboratory may also be used.

5.6

After a positive HIV confirmatory test, or at the time determined by the standard
laboratory procedures, each cryogenic vial is labeled with the appropriate
VARHS Specimen ID. The VARHS ID is a 14-digit number that is assigned to
each specimen sent for genotyping.
5.6.1

The 14-digit VARHS Specimen ID consists of the following:
5.6.1.1 The four-digit Project Area (digits 1-4), which corresponds to the
FIPS code of the project area (state or city).
5.6.1.2 The four-digit Site Number (digits 5-8) where the blood draw or
finger-stick was performed.
5.6.1.3 The last two digits of the blood draw year (digits 9-10).
5.6.1.4 The four-digit Sequence Number (digits 11-14) assigned by the
health department as planned locally.

5.7

6.0

Every specimen that is eligible for VARHS should be entered into a specimen
handling and processing log or a database. Each project area is expected to
develop its own log or database, or use the specimen tracking database provided
by CDC. In addition, each project area is responsible for ensuring that all
information is logged for each specimen before the specimen is shipped.

Shipping
6.1

Preliminary planning for shipping to Stanford University genotyping
laboratory
6.1.1

Updated: 31/Oct/2006

Specimens for genotypic resistance testing should be sent to the Stanford
University laboratory. All specimens should be shipped as diagnostic
specimens using International Air Transport Association (IATA) Packing
Instructions 650. Dry ice will be included with each shipment using IATA
Packing Instructions 904.

6.1.2

Because shipping specimens involves using dry ice, shipping personnel
must be trained and certified to ship dangerous goods. See Appendix D-1
for a list of companies that provide training.

6.1.3

Establish contact with the point person at the Stanford University
laboratory.
6.1.3.1 Stanford Virology Main Lab: (650) 725-7165
6.1.3.2 Mary Arroyo: (650) 725-4146

6.1.4

A “test” shipment must be sent prior to the first shipment of VARHS
specimens to assure that all procedures are in place. The test shipment
should exactly duplicate a real shipment (i.e., ship frozen liquid in
cryogenic vials on dry ice) and only needs to be sent once. See the
procedures outlined in sections 6.1.5 – 6.1.8 below.
6.1.4.1 The purpose of the test shipment is to familiarize the sender with
the shipment notification process and the diagnostic specimen and
dry ice shipping process. Shipping frozen water on dry ice without
the infectious substance labels will accomplish the purpose of the
shipment.

6.1.5

Arrange for the preparation of the “test” and the initial shipment to be
overseen by laboratory staff experienced in the shipment of comparable
specimens.

6.1.6

Notify Stanford lab that the “test” shipment is on the way by calling the
main lab at (650) 725-7165 or by email without emailing or faxing the
specimen manifest.
6.1.6.1 In the call/email, please include the number of samples being
shipped and the Fed Ex tracking #, if applicable. Remember, per
CDC’s Security and Confidentiality Guidelines for HIV
Surveillance, do not email or fax the specimen manifest, but
continue to include the manifest with the shipment.

6.2

6.1.7

Ensure that adequate STP 320 shipping containers or equivalent are
available. The Stanford laboratory will return these to the shipping lab, as
these are expensive shippers and need to be re-used.

6.1.8

Ensure that an adequate supply of shipping courier air bills is available.

Packing procedures for shipment to Stanford University laboratory
6.2.1

Updated: 31/Oct/2006

Specimens must be shipped on the same day that they are packed. Plan to
begin the packing process early enough to make the last shipping courier

pick-up of the day. Packing and shipping should only be done Monday
through Wednesday. Never pack and ship the week of Thanksgiving,
Christmas, New Year’s, or July 4th.
6.2.2

The shipping laboratory should read and walk through all of these steps
prior to starting the preparation of the actual shipment in order to be
familiar with what is required.

6.2.3

Put on gloves and a laboratory coat.

6.2.4

Bring the STP 320 shipper that is to be used for the shipment and other
materials needed for packing the specimens into the area where the
shipment is being prepared.
6.2.4.1 If the shipper is new and being used for the first time, check to be
sure that it includes the following items:
6.2.4.1.1
6.2.4.1.2
6.2.4.1.3
6.2.4.1.4
6.2.4.1.5
6.2.4.1.6

2 sheets of bubble wrap
2 STP 710 or equivalent certified secondary containers
2 250-ml absorbent strips
Class 9 label and dry ice quantity label
Other hazard and handling labels
1 instruction sheet

6.2.5

For a diagram of the above contents, refer to the Saf-T-Pak catalog
(http://www.saftpak.com). Use only what is needed of the above contents
for each individual shipment. Save left over supplies for future shipments.

6.2.6

If the STP 320 shipper is being re-used, the labels will already be in place
on the outer cardboard container.

6.2.7

Ensure that adequate supplies of the other materials listed in 6.2.4.1 are on
hand.

6.2.8

Prepare three copies of the shipping manifest (Appendix D-2). On the
manifest, list the specimen project number on each vial to be shipped, the
specimen draw date, and the specimen freeze date. Note: The freeze date
entered here should be the last freeze date for the aliquot being shipped.
Indicate (circle) whether the specimens are serum or plasma. Bring the
copy of the manifest that is going to be shipped into the area in which the
shipment is being prepared.
6.2.8.1 Copy 1 of the shipping manifest should be included in the
shipment to the Stanford laboratory
6.2.8.2 Copy 2 of the shipping manifest should be sent to CDC (Refer to
Section 6.3.2)

Updated: 31/Oct/2006

6.2.8.3 Copy 3 of the shipping manifest should be kept by the project
area’s VARHS Coordinator or the laboratory sending the samples
to the Stanford laboratory
6.2.9

Prepare the shipping courier air bill (Appendix D-3) that Stanford will use
to send the shipper back for re-use. Fill in the air bill with the shipping
laboratory’s complete return address, Stanford’s address, and the billing
number. The air bill should be stapled to the shipping box return form.
Bring the copy of the air bill that is going to be shipped into the area in
which the shipment is being prepared.

6.2.10 If dry ice is in another location which requires leaving the area in which
the shipment is being prepared, use a separate container to bring the dry
ice that is needed for shipping back into the shipping area at this time.
6.2.11 Go to the freezer and remove the entire 2-inch freezer box containing the
specimens to be sent.
6.2.12 Bring the specimens to the area in which the shipment is being prepared.
Please remember that these specimens are to remain frozen at all times
and therefore should not be removed from a -70° C environment for
more than a few minutes.
6.2.13 Re-check the screw-cap lids on the specimen vials and tighten if
necessary.
6.2.14 Place the freezer box containing the specimens to be sent into the
secondary leak-proof container and make sure the samples are surrounded
by bubble wrap and absorbent strips. The vials should not move around or
rattle inside the vessel.
6.2.15 Place the secondary vessel into the inner box and place the inner box into
the polystyrene cooler.
6.2.16 Pack pelleted dry ice in the shipper and around the inner box. The
STP320 shipper will hold ~8 kg of dry ice (~10lbs) and if packed
completely, will keep the contents frozen for greater than 80 hours.
6.2.17 Do not put dry ice inside the inner box.
6.2.18 Place the lid on the polystyrene cooler.
6.2.19 Place one copy of the VARHS shipping manifest on top of the shipping
box return form with the air bill that Stanford lab will use to recycle the
shipper the shipping lab, fold in half and place on top of the polystyrene
lid.

Updated: 31/Oct/2006

6.2.20 Fold over the top flaps and seal the shipping container with clear shipping
tape.
6.2.21 The outer box must have a mark in the form of a square set at an angle of
45° (diamond shaped). The mark must be at least 2 inches by 2 inches and
include the UN 3373 designation. The proper shipping name “Diagnostic
Specimens” must be marked on the outer package adjacent to the diamond
shaped mark. Labels can be purchased to place on the outer box that
fulfills this requirement.
6.2.22 Apply the Class 9 Hazard Label over the lower diamond shaped outline on
the box.
6.2.23 Apply the net quantity dry ice label to the outlined area adjacent to the
Class 9 Hazard Label. Write the approximate amount (in kg) of dry ice
used to pack the container.
6.2.24 Prepare the shipping courier paper work as directed by the shipping
training and certification course, and select the overnight shipping option.
6.2.25 If the aforementioned steps are not completed prior to the last shipping
courier pick-up, unpack the specimens and place them back in the - 70° C
freezer and begin the process again on the next appropriate day.

6.3

Procedures for Shipment to Stanford University laboratory
6.3.1

Ship only Monday through Wednesday. Never ship the week of
Thanksgiving, Christmas, New Year’s, July 4th, or major local holidays.

6.3.2

Send the second copy of the specimen manifest to Richard Kline at CDC
via the SDN (preferred) or by US mail. On the manifest, indicate the date
that the specimens were shipping to Stanford. Do not email or fax the
specimen manifest to the CDC or to Stanford lab.
6.3.2.1 Mailing Address:
Attn: Richard Kline
Centers for Disease Control and Prevention
1600 Clifton Rd. NE. MS-E-47
Atlanta, GA. 30333
Phone: 404-639-4958

6.3.3

Updated: 31/Oct/2006

Keep the third copy of the specimen manifest.

6.3.4

Notify Stanford lab that a shipment is on the way by calling the main lab
at (650) 725-7165 or by email without emailing or faxing the specimen
manifest.
6.3.4.1 In the call/email, please include the number of samples being
shipped and the Fed Ex tracking #, if applicable. Remember, do
not email or fax the specimen manifest, but continue to include
the manifest with the shipment.

6.3.5

Track the shipment using the 10-12 digit FedEx tracking number listed on
the air bill. This can be done via the website www.fedex.com or by calling
1-800-GO-FEDEX.
6.3.5.1 If a problem is identified, please notify:
Stanford Main Lab: (650) 725-7165 and
Richard Kline: (404) 639-4958

6.3.6

6.4

Preliminary planning for shipping to a locally-contracted genotyping
laboratory
6.4.1

6.5

Follow the procedures listed in section 6.2 above substituting local
procedures wherever applicable and the locally-contracted laboratory for
the Stanford laboratory.

Procedures for Shipment from the processing laboratory to a locallycontracted genotyping laboratory
6.6.1

6.7

Follow the procedures listed in section 6.1 above, substituting the locallycontracted laboratory’s contact information with Stanford’s contacts in
sections 6.1.3 and 6.1.6.

Packing procedures for shipment to a locally-contracted genotyping
laboratory
6.5.1

6.6

The shipping laboratory will receive acknowledgement for successful
receipt of shipment from the Stanford laboratory within 48 hours via the
agreed upon system. If the shipping lab does not receive this notification,
the Stanford Lab should be contacted.

Follow the procedures listed in section 6.3 above substituting local
procedures wherever applicable and the locally-contracted laboratory for
the Stanford laboratory.

Procedures for local transport from the processing laboratory to a locallycontracted genotyping laboratory

Updated: 31/Oct/2006

6.7.1

Follow the procedures listed in 6.2.1 – 6.2.20 above or substitute local
procedures as discussed with Richard Kline at CDC to ensure that
specimens remain frozen during transport and until ready for genotyping
at the genotyping laboratory.
6.7.1.1 Always include a copy of the shipping manifest in the shipment.

6.7.2

Whenever specimens are transported, send a copy of the specimen
manifest to Richard Kline at CDC via the SDN (preferred) or by US mail.
On the manifest, indicate the date that the specimens were shipping to the
genotyping lab. Do not email or fax the specimen manifest to the CDC or
the genotyping laboratory.
6.7.2.1 Mailing Address:
Attn: Richard Kline
Centers for Disease Control and Prevention
1600 Clifton Rd. NE. MS-E-47
Atlanta, GA. 30333
Phone: 404-639-4958

6.7.3

Transport specimens only Monday through Thursday, unless local
guidelines specify otherwise. If local HIV surveillance or laboratory staff
are not personally handling the transport, do not transport specimens
during the weeks of Thanksgiving, Christmas, New Year’s, July 4th, or
major local holidays.

6.7.4

Track the shipment through the FedEx or other courier’s tracking system.
6.7.4.1 If there are problems with the transfer, please notify:
Richard Kline: (404) 639-4958 and
The appropriate personnel at the genotyping laboratory
6.7.4.2 Develop an acknowledgement system so that the genotyping
laboratory informs the shipping laboratory when the shipment has
arrived.

6.8

Local Transfer from the processing area to the genotyping area within one
laboratory (where the HIV diagnostic testing and genotyping for HIV drug
resistance surveillance are performed within the same laboratory).
6.8.1

Updated: 31/Oct/2006

If HIV testing and genotyping are performed in the same laboratory, and
diagnostic testing is complete and aliquots are identified as VARHS
specimens, please complete the following:

6.8.1.1 Send a copy of the specimen manifest (Appendix D-2) to Richard
Kline at CDC via the SDN (preferred) or by US mail. On the
manifest, indicate the date that the specimens were shipping to the
genotyping lab. Do not email or fax the specimen manifest to the
CDC or the genotyping laboratory.
6.8.1.1.1

Mailing Address:
Attn: Richard Kline
Centers for Disease Control and Prevention
1600 Clifton Rd. NE. MS-E-47
Atlanta, GA. 30333
Phone: 404-639-4958

6.8.2

Ideally, the initial freezing of specimens should be done in a freezer
convenient to the genotyping laboratory, so that transfer of frozen
specimens will not be necessary.

6.8.3

If frozen specimens are to be transferred from a freezer in one area to a
freezer in another area, a biohazard bag, cooler, and dry ice or cool-packs
should be ready before the specimens are removed from the freezer.
Specimens should be kept in their storage box and placed in the biohazard
bag. The bag should be placed in the cooler with dry ice or freezer bags
and transported as quickly as possible to the other freezer.

6.8.4

If there are problems with the transfer, please notify:
Richard Kline: (404) 639-4958 and
The appropriate personnel at the genotyping laboratory

Updated: 31/Oct/2006

APPENDIX D-1
TRAINING AND CERTIFICATION FOR SHIPPING
INFECTIOUS SUBSTANCES

These are some companies that provide training for dangerous goods shipping. The
Centers for Disease Control and Prevention does not endorse any particular company.

1. FedEx:
• 1-800-GO-FEDEX
• 3 day IATA based training
• Covers all hazardous materials
• Cost is ~$550

2. Saf-T-Pak
• 1-800-814-7484
• Specifically for infectious and diagnostic substances, and dry ice
• 3 options: One day seminar, on-site programs, or interactive CD (can be
completed in 3-5 hours)
• Certificate is valid for 2 years or until regulations change
• Cost is ~$250

3. Viking Packaging (Oklahoma)
• 1-800-788-8525, Contact: David Weilert
• Seminars monthly in Tulsa@ ~ $300 per person
• Covers all nine classes of hazardous materials
• Covers shipping under IATA
• Certificate good for 2 years
• Will do group classes in local area @ ~$3,000 plus travel costs

Updated: 31/Oct/2006

APPENDIX D-2
CDC VARHS GENOTYPING MANIFEST

Updated: 31/Oct/2006

CDC VARHS Genotyping Manifest

Stanford Hospital and Clinics
300 Pasteur Drive
Stanford, CA 94035

Clinical Microbiology/Virology H1526
(650) 723-6671
Directors: Steven Foung, MD / EJ Baron, PhD

Date specimens sent to Stanford: ____________
Link project number
(VARHS ID number)

Draw Date

Freeze Date

Serum or Plasma
(CIRCLE)

Volume
(if < 1ml)

Stanford Lab number
(STANFORD USE)

Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Serum or Plasma
Shipping Instructions:

1) Call Stanford Virology Lab (650) 725-7165 when package is sent (keep a record of tracking number)
2) Complete this manifest form and include a copy with the specimens
3) Package and ship on Monday, Tuesday or Wednesday only
4) Shipping Address: Virology Laboratory Specimen Processing
Stanford Hospital and Clinics
820 Quarry Road RM H1537A
Palo Alto, CA 94304

Mail hard copy of the report to:

Attn: _____________________________
Location __________________________
Street Address ______________________
City _______________________________
State ________________
Zip code __________________

Contact person name and phone number:
_______________________________ (
) __ __ __ - __ __ __ __
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Stanford Virology Test Code: AVRT
(for office use only)
Billing done:______
Original: Box # __________
Extract: Box # __________
Product: Box #___________

APPENDIX D-3
STANFORD SHIPPING BOX RETURN

Sender: Attach return FedEx air bill. All sections must be filled out, except for the date which will be completed
at Stanford. See example below.
Stanford Virology Receiving Desk: Give the empty shipping box, packing materials, and return FedEx air bill to
Hina in Virology for return to sender.

Appendix E. Uses for VARHS Data Elements
Table 1
The following data elements are used for estimations of the national prevalence and incidence of
transmitted HIV drug resistance and distribution of HIV-1 subtypes and for making estimates for major
subpopulations.
Data Element

HIV drug
resistance
Prevalence

HIV drug
resistance
incidence

HIV-1 subtype
distributions

X
X
X
X
X
X
X

X
X
X

X
X
X
X
X

X
X
X

Demographic Data
Age
Sex
Race/ethnicity
Exposure category for HIV infection
Country of origin
Current residence
State of residence at the first HIV positive
test
Laboratory Data
STARHS result
STARHS assay type
HIV pol gene genetic sequence
HIV drug resistance phenotyping results
Mutation-specific assays
Previous HIV Testing Data
Date of first HIV test specimen
Date of first positive HIV test specimen
Reason for first positive HIV test
First positive HIV test performed
Date of last documented negative HIV test
Clinical Data
AIDS diagnosis date
Available CD4 counts
Dates of CD4 counts
Available viral loads
Dates of viral loads
Recent/current use of antiretroviral agents
Antiretroviral agents used
Timing of antiretroviral use
Date(s) of opportunistic infection diagnosis

X
X
X

X
X
X
X
X
X
X
X
X
X
X
X
X
X

Table 2. Evaluation of Laboratory Tracking Data
The following laboratory data elements are used for local tracking of specimens, evaluating problems with
amplification of HIV for genotyping, supporting plans to optimize specimen handling processes for
surveillance purposes, and evaluating problems with contamination

VARHS ID
Accession number
Site of blood draw
Tube type
Date and time of blood draw
Date and time of separation
Date and time of freeze
Volume aliquoted, if < 1 ml

Tracking
X
X
X
X
X
X
X
X

Amplification
X
X
X
X
X
X
X

Handling processes
X
X
X
X
X
X

Contamination
X
X
X
X

File Type	application/pdf
File Title	Microsoft Word - Attachment G cover.doc
Author	pas3
File Modified	2006-11-02
File Created	2006-11-01