Table of Contents

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 other types (e.g., HPV 6, 11) with genital warts. No national surveillance system exists to measure the full burden of HPV infection, and no reliable national population estimate of HPV exists. 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 2010 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 girls and women. 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 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 and older were eligible. The public data file includes data for persons aged 18-59 years. Please see Analytic Notes about the release of data for adolescents aged 14-17 years.

Description of Laboratory Methodology

Roche Cobas HPV DNA Test

LBXHP2C (Cobas HPV Swab High Risk Result)

DNA extraction is performed with a modified protocol and the commercial QIAamp kit (Qiagen, Valencia, CA). Presence of high-risk HPV in the extracted patient DNA is determined with the Cobas Human Papillomavirus (HPV) Test. This qualitative in-vitro diagnostics test uses oligonucleotide probes labeled with four different fluorescent dyes. The primers target a DNA region of approximately 200 nucleotides within the polymorphic L1 region of the HPV genome to detect 14 high-risk HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68) in a single analysis. The test reports concurrently the presence of one or more of these types at clinically relevant infection levels, however the test has been modified from the FDA approved format (sample type and extraction) and results cannot be used clinically.

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, 89, and IS39) 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.

Laboratory Method Files

HPV Vaginal Swab Linear Array Laboratory Procedure Manual (December 2016)

HPV Vaginal Swab Cobas High Risk Laboratory Procedure Manual (December 2016)

Laboratory Quality Assurance and Monitoring

Vaginal swab specimens are processed, stored, and shipped to 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 are stored at room temperature until they are shipped to Chronic Viral Diseases Branch, Division of High-Consequence Pathogens and Pathology for analysis.

The NHANES quality assurance and quality control (QA/QC) protocols meet the 1988 Clinical Laboratory Improvement Act mandates. 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 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 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 on “dry run” sessions. In addition, contract laboratories randomly perform repeat testing on 2% of all specimens.

NCHS developed and distributed a quality control protocol for all the contract laboratories which outlined the use of Westgard rules when running NHANES 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 2013 - 2014 Laboratory Data Overview for general information on NHANES laboratory data.

Sample Weights

MEC exam sample weights should be used for analyses.

NHANES 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 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. Certain sensitive data on respondents under 18 years of age (e.g. HPV typing results, sexual behavior variables) are not included in the public use files. These data may be requested as described in the NHANES guidelines.

Roche Cobas HPV DNA Test

The Roche Cobas HPV test is qualitative and only determines the presence or absence of high-risk HPV. If any analyte HPV 16, HPV 18 or Other High-risk is indicated as positive (POS) in the Cobas result file the result for the sample ID will be recorded as positive. If all of the HPV analytes are negative (NEG) in the Cobas result file the result for the sample ID will be recorded as negative. If any of the analytes are indicated as invalid in the Cobas result file, the DNA from that sample will be re-tested one time to obtain valid results. If the repeated result are still invalid the final result will be recorded as invalid.

HPV PCR Assay

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.

Detection Limits

 Since this data is reported as qualitative data the use of lower LLODs is not applicable.

Data Access

The public release data file includes HPV data for participants aged 18–59. Data for youth aged 14–17 years are available through the NCHS Research Data Center (RDC).

References

Codebook and Frequencies

SEQN - Respondent sequence number

Variable Name:
SEQN
SAS Label:
Respondent sequence number
English Text:
Respondent sequence number.
Target:
Females only 14 YEARS - 17 YEARS

LBXHP2C - Cobas HPV Swab High Risk

Variable Name:
LBXHP2C
SAS Label:
Cobas HPV Swab High Risk
English Text:
Cobas HPV Swab High Risk
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 23 23
2 Negative 225 248
3 Inadequate 32 280
. Missing 77 357

LBDRPCR - Roche HPV linear array summary result

Variable Name:
LBDRPCR
SAS Label:
Roche HPV linear array summary result
English Text:
Roche HPV linear array (LA) summary result
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 34 34
2 Negative 236 270
3 Inadequate 10 280
. Missing 77 357

LBDRHP - Roche LA high positive globin control

Variable Name:
LBDRHP
SAS Label:
Roche LA high positive globin control
English Text:
Roche LA high positive globin control
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 268 268
2 Negative 2 270
. Missing 87 357

LBDRLP - Roche LA low positive globin control

Variable Name:
LBDRLP
SAS Label:
Roche LA low positive globin control
English Text:
Roche LA low positive globin control
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 254 254
2 Negative 16 270
. Missing 87 357

LBDR06 - HPV type 6

Variable Name:
LBDR06
SAS Label:
HPV type 6
English Text:
HPV type 6
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 268 270
3 Inadequate 10 280
. Missing 77 357

LBDR11 - HPV type 11

Variable Name:
LBDR11
SAS Label:
HPV type 11
English Text:
HPV type 11
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 270 270
3 Inadequate 10 280
. Missing 77 357

LBDR16 - HPV type 16

Variable Name:
LBDR16
SAS Label:
HPV type 16
English Text:
HPV type 16
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 3 3
2 Negative 267 270
3 Inadequate 10 280
. Missing 77 357

LBDR18 - HPV type 18

Variable Name:
LBDR18
SAS Label:
HPV type 18
English Text:
HPV type 18
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 1 1
2 Negative 269 270
3 Inadequate 10 280
. Missing 77 357

LBDR26 - HPV type 26

Variable Name:
LBDR26
SAS Label:
HPV type 26
English Text:
HPV type 26
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 270 270
3 Inadequate 10 280
. Missing 77 357

LBDR31 - HPV type 31

Variable Name:
LBDR31
SAS Label:
HPV type 31
English Text:
HPV type 31
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 270 270
3 Inadequate 10 280
. Missing 77 357

LBDR33 - HPV type 33

Variable Name:
LBDR33
SAS Label:
HPV type 33
English Text:
HPV type 33
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 270 270
3 Inadequate 10 280
. Missing 77 357

LBDR35 - HPV type 35

Variable Name:
LBDR35
SAS Label:
HPV type 35
English Text:
HPV type 35
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 268 270
3 Inadequate 10 280
. Missing 77 357

LBDR39 - HPV type 39

Variable Name:
LBDR39
SAS Label:
HPV type 39
English Text:
HPV type 39
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 8 8
2 Negative 262 270
3 Inadequate 10 280
. Missing 77 357

LBDR40 - HPV type 40

Variable Name:
LBDR40
SAS Label:
HPV type 40
English Text:
HPV type 40
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 268 270
3 Inadequate 10 280
. Missing 77 357

LBDR42 - HPV type 42

Variable Name:
LBDR42
SAS Label:
HPV type 42
English Text:
HPV type 42
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 3 3
2 Negative 267 270
3 Inadequate 10 280
. Missing 77 357

LBDR45 - HPV type 45

Variable Name:
LBDR45
SAS Label:
HPV type 45
English Text:
HPV type 45
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 1 1
2 Negative 269 270
3 Inadequate 10 280
. Missing 77 357

LBDR51 - HPV type 51

Variable Name:
LBDR51
SAS Label:
HPV type 51
English Text:
HPV type 51
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 7 7
2 Negative 263 270
3 Inadequate 10 280
. Missing 77 357

LBDR52 - HPV type 52

Variable Name:
LBDR52
SAS Label:
HPV type 52
English Text:
HPV type 51
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 3 3
2 Negative 267 270
3 Inadequate 10 280
. Missing 77 357

LBDR53 - HPV type 53

Variable Name:
LBDR53
SAS Label:
HPV type 53
English Text:
HPV type 53
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 268 270
3 Inadequate 10 280
. Missing 77 357

LBDR54 - HPV type 54

Variable Name:
LBDR54
SAS Label:
HPV type 54
English Text:
HPV type 54
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 7 7
2 Negative 263 270
3 Inadequate 10 280
. Missing 77 357

LBDR55 - HPV type 55

Variable Name:
LBDR55
SAS Label:
HPV type 55
English Text:
HPV type 55
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 3 3
2 Negative 267 270
3 Inadequate 10 280
. Missing 77 357

LBDR56 - HPV type 56

Variable Name:
LBDR56
SAS Label:
HPV type 56
English Text:
HPV type 56
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 3 3
2 Negative 267 270
3 Inadequate 10 280
. Missing 77 357

LBDR58 - HPV type 58

Variable Name:
LBDR58
SAS Label:
HPV type 58
English Text:
HPV type 58
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 4 4
2 Negative 266 270
3 Inadequate 10 280
. Missing 77 357

LBDR59 - HPV type 59

Variable Name:
LBDR59
SAS Label:
HPV type 59
English Text:
HPV type 59
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 268 270
3 Inadequate 10 280
. Missing 77 357

LBDR61 - HPV type 61

Variable Name:
LBDR61
SAS Label:
HPV type 61
English Text:
HPV type 61
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 7 7
2 Negative 263 270
3 Inadequate 10 280
. Missing 77 357

LBDR62 - HPV type 62

Variable Name:
LBDR62
SAS Label:
HPV type 62
English Text:
HPV type 62
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 1 1
2 Negative 269 270
3 Inadequate 10 280
. Missing 77 357

LBDR64 - HPV type 64

Variable Name:
LBDR64
SAS Label:
HPV type 64
English Text:
HPV type 64
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 270 270
3 Inadequate 10 280
. Missing 77 357

LBDR66 - HPV type 66

Variable Name:
LBDR66
SAS Label:
HPV type 66
English Text:
HPV type 66
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 4 4
2 Negative 266 270
3 Inadequate 10 280
. Missing 77 357

LBDR67 - HPV type 67

Variable Name:
LBDR67
SAS Label:
HPV type 67
English Text:
HPV type 67
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 5 5
2 Negative 265 270
3 Inadequate 10 280
. Missing 77 357

LBDR68 - HPV type 68

Variable Name:
LBDR68
SAS Label:
HPV type 68
English Text:
HPV type 68
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 268 270
3 Inadequate 10 280
. Missing 77 357

LBDR69 - HPV type 69

Variable Name:
LBDR69
SAS Label:
HPV type 69
English Text:
HPV type 69
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 270 270
3 Inadequate 10 280
. Missing 77 357

LBDR70 - HPV type 70

Variable Name:
LBDR70
SAS Label:
HPV type 70
English Text:
HPV type 70
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 1 1
2 Negative 269 270
3 Inadequate 10 280
. Missing 77 357

LBDR71 - HPV type 71

Variable Name:
LBDR71
SAS Label:
HPV type 71
English Text:
HPV type 71
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 270 270
3 Inadequate 10 280
. Missing 77 357

LBDR72 - HPV type 72

Variable Name:
LBDR72
SAS Label:
HPV type 72
English Text:
HPV type 72
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 1 1
2 Negative 269 270
3 Inadequate 10 280
. Missing 77 357

LBDR73 - HPV type 73

Variable Name:
LBDR73
SAS Label:
HPV type 73
English Text:
HPV type 73
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 268 270
3 Inadequate 10 280
. Missing 77 357

LBDR81 - HPV type 81

Variable Name:
LBDR81
SAS Label:
HPV type 81
English Text:
HPV type 81
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 2 2
2 Negative 268 270
3 Inadequate 10 280
. Missing 77 357

LBDR82 - HPV type 82

Variable Name:
LBDR82
SAS Label:
HPV type 82
English Text:
HPV type 82
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 1 1
2 Negative 269 270
3 Inadequate 10 280
. Missing 77 357

LBDR83 - HPV type 83

Variable Name:
LBDR83
SAS Label:
HPV type 83
English Text:
HPV type 83
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 3 3
2 Negative 267 270
3 Inadequate 10 280
. Missing 77 357

LBDR84 - HPV type 84

Variable Name:
LBDR84
SAS Label:
HPV type 84
English Text:
HPV type 84
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 5 5
2 Negative 265 270
3 Inadequate 10 280
. Missing 77 357

LBDR89 - HPV type 89

Variable Name:
LBDR89
SAS Label:
HPV type 89
English Text:
HPV type 89
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 8 8
2 Negative 262 270
3 Inadequate 10 280
. Missing 77 357

LBDRPI - HPV type IS39

Variable Name:
LBDRPI
SAS Label:
HPV type IS39
English Text:
HPV type IS39
Target:
Females only 14 YEARS - 17 YEARS
Code or Value Value Description Count Cumulative Skip to Item
1 Positive 0 0
2 Negative 270 270
3 Inadequate 10 280
. Missing 77 357