Component Description
Human papillomavirus (HPV) infection is one of the most common sexually transmitted infections in the United States. Cervical infection with certain types of HPV is a major risk factor for cervical cancer in women. The “high-risk” types of HPV (e.g., HPV 16, 18) are associated with cervical cancer as well as other anogenital cancers, and “low-risk” types of HPV (e.g., HPV 6, 11) can cause genital warts. No national surveillance system exists to measure the full burden of HPV infection, and no reliable national population estimate of HPV prevalence exists, other than through NHANES. NHANES offers a unique opportunity to assess the prevalence of HPV infection in the general population.
Reducing the prevalence of HPV infection is a
Developmental Healthy People 2020 objective: “Reducing the number of new HPV
cases can help minimize the overall number of cases of high risk subtypes
associated with cervical cancer in females...” Detection and typing of HPV DNA
in vaginal swabs will allow evaluation of trends in prevalence of type-specific
HPV infection by age, sexual behavior, and race/ethnicity. Three HPV vaccines
(Gardasil, Gardasil 9, and Cervarix) are licensed and recommended for use in females.
Two vaccines are licensed and recommended for use in males (Gardasil and
Gardasil 9). In mid-2006, the Advisory Committee on Immunizations (ACIP) recommended
routine vaccination of females aged 11 or 12 years and for those 13-26 years
not previously vaccinated. In December 2011, ACIP recommended routine
vaccination of males aged 11 or 12 years and for those aged 13 through 21 years
not previously vaccinated. As a vaccine becomes more widely used, the national
prevalence of HPV infection will be critical for evaluating vaccination
strategies in the United States.
Eligible Sample
Examined female participants aged 14-59 years were
eligible. This limited access data file includes data for examined participants
aged 18 to 59 years. Information on participants aged
14-17 years are available in a separate dataset: HPVS_J_R. Both datasets may be accessed through the NCHS Research Data Center.
Description of Laboratory Methodology
This assay used the Roche Linear Array HPV Genotyping
test that is based on HPV L1 consensus polymerase chain reaction (PCR) with biotinylated
PGMY09/11 primer sets. It also includes biotinylated β-globin primers as an
internal control for sample amplification. The primer mix amplified essentially
all HPV types found in the genital tract along with the human β-globin gene.
After amplification, the samples were typed by hybridization to the typing
strips followed by colorimetric detection. The strip is a linear array of
probes specific for 37 HPV types (6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42,
45, 51, 52, 53, 54, 55, 56, 58, 59, 61, 62, 64, 66, 67, 68, 69, 70, 71, 72, 73,
81, 82, 83, 84, 89, and IS39) and for the positive β-globin control as well.
Types were read by comparing the reaction pattern to the typing template.
Samples that were negative for HPV and the β-globin control indicated lack of a
suitable sample and were considered inadequate for interpretation (Linear Array HPV Genotyping Test Application manual, 2008).
Refer to the Laboratory Method Files section for a
detailed description of the laboratory methods used.
There were no changes to the lab method, lab equipment,
or lab site for this component in the NHANES 2017-2018 cycle.
Laboratory Method Files
HPV Vaginal Swab Linear Array Laboratory Procedure Manual.pdf
(December 2020)
Laboratory Quality Assurance and Monitoring
Vaginal swab samples were processed, stored, and shipped to
the Chronic Viral Diseases Branch, Division of High-Consequence Pathogens and
Pathology, National Center for Emerging and Zoonotic Infectious Diseases,
Centers for Disease Control and Prevention, Atlanta, GA for analysis.
Detailed instructions on specimen collection and
processing are discussed in the NHANES
Laboratory Procedures Manual (LPM). Swabs were stored
at room temperature until they were shipped to the National Center for Emerging
and Zoonotic Infectious Diseases for testing.
Detailed QA/QC instructions are discussed in the NHANES LPM.
Mobile Examination Centers (MECs)
Laboratory team performance is monitored using several
techniques. NCHS and contract consultants use a structured competency
assessment evaluation during visits to evaluate both the quality of the
laboratory work and the QC procedures. Each laboratory staff member is observed
for equipment operation, specimen collection and preparation; testing
procedures and constructive feedback are given to each staff member. Formal
retraining sessions are conducted annually to ensure that required skill levels
were maintained.
Analytical Laboratories
NHANES
uses several methods to monitor the quality of the analyses performed by the
contract laboratories. In the MEC, these methods include performing blind split
samples collected during “dry run” sessions. In addition, contract laboratories
randomly perform repeat testing on 2% of all specimens.
Progress
reports containing any problems encountered during shipping or receipt of
specimens, summary statistics for each control pool, QC graphs, instrument
calibration, reagents, and any special considerations are submitted to NCHS
quarterly. The reports are reviewed for trends or shifts in the data. The
laboratories are required to explain any identified areas of concern.
Data Processing and Editing
The data were reviewed. Incomplete data or improbable values were
sent to the performing laboratory for confirmation.
Analytic Notes
Refer to the 2017-2018 Laboratory Data Overview for general information on NHANES laboratory data.
There are over 800
laboratory tests performed on NHANES participants. However, not all
participants provided biospecimens or enough volume for all the tests to be
performed. The specimen availability can also vary by age or other population
characteristics. Analysts should evaluate the extent of missing data in the
dataset related to the outcome of interest as well as any predictor variables
used in the analyses to determine whether additional re-weighting for item
non-response is necessary.
Please refer to the NHANES Analytic
Guidelines and the on-line NHANES Tutorial for details on the use of sample weights and other analytic issues.
Sample Weights
MEC exam sample weights should be used for analyses.
Demographic and Other Related Variables
The analysis of NHANES laboratory data must be conducted
using the appropriate survey design and demographic variables. The NHANES 2017-2018 Demographics File contains demographic
data, health indicators, and other related information collected during
household interviews as well as the sample design variables. The recommended
procedure for variance estimation requires use of stratum and PSU variables
(SDMVSTRA and SDMVPSU, respectively) in the demographic data file.
This laboratory data file can be linked to the other
NHANES data files using the unique survey participant identifier (i.e., SEQN).
The Questionnaire data files contain socio-economic data, health indicators, and other related information collected during household interviews on participants 18 years of age and older.
HPV vaginal swab data for youth aged 14-17 and adults aged
18-59 years are available through the NCHS Research Data Center (RDC).
HPV Summary Variable
The HPV PCR Summary variable (LBDRPCR) indicates if at
least one type is positive (LBDRPCR=1); the sample is negative (LBDRPCR=2); the
sample is inadequate (LBDRPCR=3); or the sample is missing (LBDRPCR=.).
If beta-globin is not present, both LBDRHP and LBDRLP are
negative in the sample and no HPV type is detected, the sample is coded as “Inadequate”.
If any of the types on the strips (LBDR06-LBDRPI) are
positive, the sample is coded as positive. If all of the types on the strip are
coded as negative, and beta-globin is detected (either LBDRHP or LBDRLP is
positive), the sample is coded as negative.
Variables LBDRHP through LBDRPI are from the RUO Roche
Linear Array HPV typing assay, however LBDR52 also includes information from a
type-specific assay for HPV 52. The Linear Array typing strip includes an XR
probe that hybridizes with HPV 52 as well as HPV types 33, 35 and 58. Samples
positive for the XR probe and 33, 35, or 58 require specific testing to confirm
the presence of HPV 52 (Onyekwuluje et al., 2012).