Human papillomavirus (HPV) infection is one of the most common sexually
transmitted infections in the United States. There is no national surveillance
system that currently exists to measure the full burden of HPV infection.
Although HPV can infect men and women, less is known about HPV prevalence in
men. In 2011, routine HPV vaccination was recommended by the Advisory Committee
on Immunization Practices (ACIP) for males aged 11-12 years. Vaccination was
also recommended for men through aged 21 years if not previously vaccinated.
Information on the national prevalence of HPV infection is important for
planning vaccination strategies and monitoring the impact of vaccination in the
Examined male participants aged 14-59 years were eligible. This public data
file only includes examined participants aged 18 to 59 years. See Analytic Notes
for information on participants aged 14-17 years.
Description of Laboratory
DNA from the self-collected penile swab is extracted for use in the test
below: Roche Linear Array.
Roche Linear Array Assay
This assay uses 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 amplifies essentially all HPV types found
in the genital tract along with the human β-globin gene. After amplification the
samples are 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, and 89) and for the
positive β-globin control as well. Types are read by comparing the reaction
pattern to the typing template. Samples that are negative for HPV and the
β-globin control indicate lack of a suitable sample and are considered
inadequate for interpretation.
Please refer to the Laboratory Method Files section for detailed laboratory
procedure manual(s) of the methods used.
Laboratory Method Files
HPV Penile Swab Linear Array Laboratory Procedure Manual
(Updated November 2018)
Assurance and Monitoring
Penile swab specimens are processed, stored and shipped to the Division
of High-Consequence Pathogens and Pathology, National Center for Emerging and
Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC),
Atlanta, GA for analysis.
Detailed instructions on specimen collection and processing are discussed in
the NHANES Laboratory
Procedures Manual (LPM). Vials are stored under appropriate refrigerated
(2-8°C) conditions until they are shipped to the CDC for testing.
The NHANES quality control and quality assurance protocols (QA/QC) meet the
1988 Clinical Laboratory Improvement Act (CLIA) mandates. Detailed QA/QC
instructions are discussed in the NHANES
Mobile Examination Centers (MECs)
performance is monitored using several techniques. NCHS and contract consultants
use a structured quality assurance evaluation during unscheduled visits to
evaluate both the quality of the laboratory work and the quality-control
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 are maintained.
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 on “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 are submitted to NCHS. The reports are reviewed and the
laboratories are required to explain any identified areas of concern.
The HPV PCR tests are research tests. The HPV laboratory followed strict
research QC/QA and has been CLIA certified since August 2008. Detailed quality
control and quality assurance instructions are discussed in the NHANES
Laboratory Procedures Manual (LPM). The analytical methods are described in the
Description of the Laboratory Methodology section.
Data Processing and Editing
The data were reviewed. Incomplete data or improbable values were sent to the
performing laboratory for confirmation.
Refer to the 2013-2014
Laboratory Data Overview for general information on NHANES Laboratory
MEC exam sample weights should be used
Demographic and Other Related Variables
The analysis of
NHANES laboratory data must be conducted using the appropriate survey design and
demographic variables. The NHANES
2013-2014 Demographics File contains demographic data, health indicators,
and other related information collected during household interviews as well as
the sample weight variables. This laboratory data file can be linked to the
other NHANES data files using the unique survey participant identifier (i.e.,
HPV PCR Assay Summary Variable
HPV PCR Summary variable
(LBDRPCR) indicates the following: if at least one type is positive (LBDRPCR=1);
if the sample is negative (LBDRPCR=2); if the sample is inadequate (LBDRPCR=3);
or if the sample is missing (LBDRPCR=.).
If Beta globin is not present in the sample (both LBDRHP and LBDRLP are
negative) and HPV type is not 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 that are
positive for the XR probe and 33, 35, or 58 require specific testing to confirm
the presence of HPV 52.
Since this data is reported as
qualitative data the use of lower LLODs is not applicable.
The public release data file includes HPV
DNA data for males aged 18-59 years. HPV DNA data for youth aged 14–17 years are
available through the NCHS Research Data