Variants in ABCB1, TGFB1, and XRCC1 genes and susceptibility to viral hepatitis A infection in Mexican Americans§


  • Lyna Zhang,

    Corresponding author
    1. Office of Public Health Genomics, Office of Surveillance, Epidemiology, and Laboratory Services
    2. Division of Viral Hepatitis, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention
    • Division of Viral Hepatitis, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Diseases Control and Prevention, 1600 Clifton Road NE, MS A33, Atlanta, GA 30333===

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    • fax: 404-639-1563

  • Ajay Yesupriya,

    1. Office of Public Health Genomics, Office of Surveillance, Epidemiology, and Laboratory Services
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  • Dale J. Hu,

    1. Division of Viral Hepatitis, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention
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  • Man-huei Chang,

    1. Office of Public Health Genomics, Office of Surveillance, Epidemiology, and Laboratory Services
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  • Nicole F. Dowling,

    1. Office of Public Health Genomics, Office of Surveillance, Epidemiology, and Laboratory Services
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  • Renée M. Ned,

    1. Office of Public Health Genomics, Office of Surveillance, Epidemiology, and Laboratory Services
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  • Venkatachalam Udhayakumar,

    1. Division of Parasitic Diseases and Malaria, Center for Global Health
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  • Mary Lou Lindegren,

    1. Division of HIV/AIDS Prevention Surveillance and Epidemiology, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
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  • Yury Khudyakov

    1. Division of Viral Hepatitis, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention
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  • Potential conflict of interest: Nothing to report.

  • Supported by the Centers for Disease Control and Prevention, Atlanta, GA.

  • The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention.

  • §

    Mary Lou Lindegren is currently affiliated with the Department of Pediatrics, University of Vanderbilt, Nashville, TN.


Hepatitis A vaccination has dramatically reduced the incidence of hepatitis A virus (HAV) infection, but new infections continue to occur. To identify human genetic variants conferring a risk for HAV infection among the three major racial/ethnic populations in the United States, we assessed associations between 67 genetic variants (single nucleotide polymorphisms [SNPs]) among 31 candidate genes and serologic evidence of prior HAV infection using a population-based, cross-sectional study of 6,779 participants, including 2,619 non-Hispanic whites, 2,095 non-Hispanic blacks, and 2,065 Mexican Americans enrolled in phase 2 (1991-1994) of the Third National Health and Nutrition Examination Survey. Among the three racial/ethnic groups, the number (weighted frequency) of seropositivity for antibody to HAV was 958 (24.9%), 802 (39.2%), and 1540 (71.5%), respectively. No significant associations with any of the 67 SNPs were observed among non-Hispanic whites or non-Hispanic blacks. In contrast, among Mexican Americans, variants in two genes were found to be associated with an increased risk of HAV infection: TGFB1 rs1800469 (adjusted odds ratio [OR], 1.38; 95% confidence interval [CI], 1.14-1.68; P value adjusted for false discovery rate [FDR-P] = 0.017) and XRCC1 rs1799782 (OR, 1.57; 95% CI, 1.27-1.94; FDR-P = 0.0007). A decreased risk was found with ABCB1 rs1045642 (OR, 0.79; 95% CI, 0.71-0.89; FDR-P = 0.0007). Conclusion: Genetic variants in ABCB1, TGFB1, and XRCC1 appear to be associated with susceptibility to HAV infection among Mexican Americans. Replication studies involving larger population samples are warranted. (HEPATOLOGY 2012)

Hepatitis A is a highly contagious liver infection caused by the hepatitis A virus (HAV) that is usually spread by fecal-oral contact or by ingestion of contaminated food or water.1 Lifelong immunity is conferred by infection or vaccination.2 Antibody to HAV (anti-HAV) seroprevalence studies have been used to identify susceptible populations and high-prevalence localities.3 Tens of millions of people worldwide are estimated to become infected with HAV each year. Disease patterns vary in areas of differing endemicity and correlate with socioeconomic status and access to clean water and sanitation. In many parts of the world, economic development and improved sanitation and living standards have resulted in significant shifts in the acquisition of HAV infection from infancy and childhood to older ages.4 In developing countries, where infection is endemic, most persons are infected in early childhood when asymptomatic infection is likely. In developed countries, where the incidence rate is lower, infection typically occurs at older ages when clinical symptoms become more apparent.5 Community-wide epidemics contribute significantly to the burden of disease in developed countries. In these settings, disease tends to occur in circumscribed groups, such as travelers to hepatitis A endemic areas, or as outbreaks among high-exposure groups such as intravenous drug users or men who have sex with men.5-7

Prior to the introduction of vaccines against HAV in the United States, hepatitis A occurred as large nationwide epidemics approximately every 10 years. The last epidemic occurred during the mid-1990s and affected particularly adolescents and young adults,8 causing substantial morbidity and economic losses estimated at $489 million annually.9 Since the introduction of an HAV vaccine in 1995, the incidence of hepatitis A has decreased markedly for all age groups; however, an estimated 25,000 new infections still occurred in 2007.10 Approximately 50% of all reported hepatitis A cases have no specific risk factors identified.11 In cases where risk factors have been identified, the majority of adults are international travelers, men who have sex with men, or intravenous drug users.6, 7

Host genetic factors have played an important role in determining the differential susceptibility to infectious diseases such as hepatitis B and C, malaria, HIV/AIDS, tuberculosis, and invasive pneumococcal disease.12 In outbreaks of hepatitis A, some people are infected while others remain uninfected after exposure, suggesting that people vary in their susceptibility to HAV infection.5, 6 However, to date, the number of studies of human genetic variation and HAV infection are few, except for two small candidate gene studies,13, 14 and twin studies showing that genetic factors accounted for ≈36% of the total variability in HAV-specific immune response to vaccination.15, 16 There are no reports investigating host genetic factors for hepatitis A in the United States population, though many public health researchers have focused on behavior, environment, and viral factors. Examining host factors may provide insight into pathogenesis and susceptibility to HAV infection and also help to identify and target high-risk populations for vaccination.

To our knowledge, this study is the first to use data from a large, population-based, national representative sample of three major racial/ethnic groups (non-Hispanic white, non-Hispanic black, and Mexican American) in the United States to assess a number of human genetic variants and their possible associations with susceptibility to HAV infection. We obtained genotyping data for 67 single nucleotide polymorphisms (SNPs) across 31 candidate genes and evaluated statistical associations of these variants with total anti-HAV seropositivity (as an indication of prior infection) using DNA samples from 6,779 participants in the Third National Health and Nutrition Examination Survey (NHANES III).17


anti-HAV, antibody to HAV; CDC, Centers for Disease Control and Prevention; CI, confidence interval; CYP, cytochrome P450 enzyme; FDR, false discovery rate; FDR-P, P value adjusted for false discovery rate; HAV, hepatitis A virus; NCHS, National Center for Health Statistics; NHANES III, Third National Health and Nutrition Examination Survey; OR, odds ratio; SNP, single nucleotide polymorphism.

Materials and Methods

Ethics Statement.

All procedures were approved by the Centers for Disease Control and Prevention (CDC) Ethics Review Board, and written informed consent was obtained from all participants. In 2001, the CDC and the National Center for Health Statistics (NCHS) Ethics Review Board approved a revised plan that allows linkage of genetic data to NHANES information through NCHS Research Data Centers to ensure confidentiality of the study participants' identities. More information on the DNA bank is available online.18 The current study was approved by the CDC Ethics Review Board.

Study Population.

NHANES III was conducted between 1988 and 1994, and the survey design, population, and DNA bank have been described elsewhere.19, 20 Briefly, NHANES III used a stratified, multistage probability design to provide nationally representative estimates of the health and nutritional status of the civilian, noninstitutionalized population aged ≥2 months in the United States. NHANES III oversampled minorities (non-Hispanic blacks, Mexican Americans), the young, and the elderly. Data were collected from household interviews and physical examinations. A DNA bank was created from blood samples collected during the second phase (1991-1994) from 7,159 participants aged ≥12 years, 62% of whom originated from households containing multiple family members (mean, 1.59 members per household; range, 1-11 members per household). Genetic data were combined with behavioral, environmental, and clinical information available in NHANES III. Analyses included only those who were tested for anti-HAV antibodies and who self-reported as non-Hispanic white (n = 2,619), non-Hispanic black (n = 2,095), or Mexican American (excluding Hispanic persons of other origin [n = 2,065]). Persons who did not self-report as one of these three groups were classified as “other” (n = 348) and were excluded because of concerns about their small numbers and a mix of race/ethnicities not fitting the three main race/ethnicities that were categorized.

Laboratory Measures and Phenotype Definition.

Serum specimens were stored at −20°C prior to serologic testing. Testing for total anti-HAV was conducted at the Hepatitis Reference Laboratory, Division of Viral Hepatitis, CDC, using a commercially available enzyme immunoassay (HAVAB-EIA, Abbott Laboratories, Abbott Park, IL). Testing was performed on specimens from persons who completed the medical examination component of NHANES III.17 An anti-HAV–positive person was considered to have been infected with HAV.

Region was defined by standard Census Bureau groupings as Northeast, Midwest, South, and West. Persons who were born outside of the United States were considered foreign-born. Poverty income ratio was calculated by dividing the total family income by the poverty threshold adjusted for family size for the year of the interview. Values <1 were considered below the poverty line.

Selection of Polymorphisms and Genotyping.

Acute HAV infection is typically accompanied by substantial hepatic inflammation, hepatocellular necrosis, periportal infiltrates of immune cells, oxidative stress, and altered expression of cytochrome P450 enzymes (CYPs) activated by the innate immune response in the liver.21-23 Genes were included in our analysis based on their involvement in inflammation, innate and adaptive immune responses, oxidative stress, apoptosis, and DNA repair as determined by information gathered from GeneCards24 and published literature. The included candidate genes are listed in Table 1, with detailed rationale for selection of each gene included in Supporting Table 1. All variants included in this analysis were genotyped for previous NHANES III studies and are available in a restricted access database through the NCHS Research Data Center.18, 20, 25 Detailed genotyping methods and quality control criteria have been described.20, 25

Table 1. Weighted Allele Frequencies of Genetic Variants Tested for Associations With Anti-HAV Seropositivity in Participants From the NHANES III DNA Bank (1991-1994) and Corresponding Allele Frequencies From HapMap (Release 28)
Gene Symbol*SNP No.HGVS NameAllele§Non-Hispanic Whites, %||Non-Hispanic Blacks, %Mexican Americans, %PCEU %#ASW %**MEX %††
  • Abbreviations: HGVS, Human Genome Variation Society; NA, not available.

  • *

    Official gene symbols are from the HUGO Gene Nomenclature Committee (

  • Unique reference SNP identifier in the Entrez SNP database at the National Center for Biotechnology information (

  • HGVS names refer to the official nomenclature at:

  • §

    The major allele (determined by the frequency in the total population) is given in parentheses.

  • ||

    The minor allele frequencies were adjusted using NHANES III genetic sample weights.

  • Calculated using polytomous logistic regression models that included the three racial/ethnic subpopulations of NHANES III.

  • #

    Allele frequencies from Utah residents with northern and western European ancestry from the CEPH collection (n = 113) in the HapMap (

  • **

    Allele frequencies from persons of African ancestry in the southwest United States (n = 56) in the HapMap.

  • ††

    Allele frequencies from persons of Mexican ancestry in Los Angeles, California (n = 58) in the HapMap.

ABCB1rs1045642NM_000927.3:c.3435T>CT (C)51.620.944.7<.00157.120.545.7
CATrs769214NG_013339.1:g.4246G>AG (A)33.941.250.3<.00133.639.551.8
CCL5rs2280788NG_015990.1:g.4973C>GG (C)<.0010.08NANA
CCR2rs1799864NM_001123396.1:c.190G>A;A (G)9.514.521.7<.001NANANA
CRPrs1205NM_000567.2:c.*1082G>AA (G)34.721.235.5<.00134.126.337.1
 rs1417938NM_000567.2:c.61+29A>TT (A)12.034.523.6<.00132.0NANA
 rs1800947NM_000567.2:c.552G>CC (G)<.0010.07NANA
 rs2808630NG_013007.1:g.8512G>AG (A)28.615.721.1<.00129.913.221.6
 rs3093058NG_013007.1:g.4065A>TT (A)<.0010.0NANA
 rs3093066NM_000567.2:c.*216C>AA (C)0.523.01.6<.0010.0NANA
CXCL12rs169097NM_000609.4:c.*693C>TT (C)0.317.21.0<.0010.0NANA
CYP1A2rs2472299NG_008431.1:g.23518A>GT (C)28.238.526.7<0.00127.431.626.7
 rs2606345NM_000499.3:c.-27+606G>TG (T)33.884.161.7<.001NANANA
CYP1A2rs11854147NT_010194.17:g.45843328T>CT (C)31.472.161.3<.00129.665.861.2
 rs2069514NT_010194.17:g.45828777G>AA (G)1.626.333.7<.001NANANA
 rs4886406NT_010194.17:g.45847760G>TG (T)27.838.326.5<.00125.931.626.7
CYP1B1rs1056836NM_000104.3:c.1294C>G;G (C)<.00144.775.031.0
 rs1056837NM_000104.3:c.1347T>A;T (C)45.072.726.3<.00144.774.630.7
 rs162557NG_008386.1:g.2873T>CT (C)23.221.613.1<.001NANANA
CYP2A6rs1801272NM_000762.5:c.479T>A;A (T)<.0010.5NANA
CYP2C19rs4986893NM_000769.1:c.636G>A;A (G)<.001NANANA
 rs4986894NG_008384.1:g.4903T>CC (T)13.718.311.0<.00112.410.512.9
CYP2E1rs2031920NG_008383.1:g.3979C>TT (C)2.20.810.7<.0016.2NA12.9
CYP3A4rs2740574NT_007933.15:g.37414939C>TG (A)<.001NANANA
FCGR2Ars1801274NM_021642.3:c.497A>G;A (G)49.447.448.6<.00149.153.557.0
IL10rs1800871NG_012088.1:g.4206T>CT (C)24.239.638.1<.00117.9NANA
 rs1800872NG_012088.1:g.4433A>CA (C)24.339.337.9<.00121.236.837.7
 rs1800896NG_012088.1:g.3943A>GG (A)46.935.630.5<.00153.135.131
IL1Brs1143623NG_008851.1:g.3528G>CC (G)28.511.242.9<.00133.3NANA
IL4rs2243248NT_034772.6:g.40322516T>GG (T)7.515.712.0<.0018.418.49.5
 rs2243250NT_034772.6:g.40323026C>TT (C)<.00113.756.139.5
 rs2243270NM_172348.1:c.136-1297A>GG (A)16.463.741.8<.00114.255.337.8
IL4Rrs1801275NM_000418.2:c.1727A>G;G (A)20.867.128.6<.00119.9NA24.1
 rs1805015NM_000418.2:c.1507T>C;C (T)15.736.715.7<.00115.029.812.1
ITGA2rs1126643NM_002203.3:c.759C>TT (C)41.229.644.6<.00136.327.747.4
MBL2rs11003125NG_008196.1:g.4447C>GG (C)36.412.851.0<.001NANANA
 rs1800450NM_000242.2:c.161G>A;A (G)<.00115.03.515.5
 rs1800451NM_000242.2:c.170G>A;A (G)<.0011.818.43.4
 rs5030737NM_000242.2:c.154C>T;T (C)<.0017.20.91.8
 rs7096206NG_008196.1:g.4776C>GC (G)22.415.111.4<.00121.720.213.8
NOS2Ars1800482NG_011470.1:g.4047G>CC (G)<.0010NANA
 rs9282799NG_011470.1:g.3828C>TT (C)<.0010NANA
NOS3rs1799983NM_000603.4:c.894T>G;T (G)32.513.119.6<.00134.6NANA
 rs2070744NM_000603.4:c.-51-762C>TC (T)<.0010NANA
NQO1rs10517NM_000903.2:c.*1119T>CT (C)<.0019.510.59.8
 rs1800566NM_000903.2:c.559C>T;T (C)19.418.836.8<.00118.621.135.3
 rs34755915NM_000903.2:c.303+20G>AA (G)<.001NANANA
 rs689452NM_000903.2:c.8-27G>CG (C)11.913.76.3<.0018.5NANA
 rs689453NM_000903.2:c.72G>AA (G)<.0017.66.14.3
OGG1rs1052133NM_016820.3:c.994C>G;G (C)21.516.433.0<.00120.6NANA
PON1rs662NM_000446.5:c.575A>G;G (A)31.567.146.5<.00133.262.350.0
 rs854560NM_000446.5:c.163T>A;A (T)35.617.923.0<.001NANANA
PPARGrs1801282NM_015869.4:c.34C>G;G (C)13.22.512.4<.0019.72.611.2
TGFB1rs1800468NM_030578.2:c.*18G>AA (G)<.001NANANA
 rs1800469NG_013091.1:g.14783T>CT (C)31.423.844.8<.00128.819.637.1
 rs1982073NM_000660.3:c.29C>T;C (T)38.544.050.3<.0010NANA
TLR4rs4986790NM_138554.3:c.896A>G;G (A)<.0013.55.33.5
TNFrs1800629XM_002342635.1:c.-233+8274C>TT (C)<.00117.36.16.0
 rs1800750XM_002342635.1:c.-233+8342C>TT (C)
 rs361525XM_002342635.1:c.-233+8204C>TT (C)
VDRrs2239185NM_000376.2:c.756-3968C>TC (T)47.842.958.2<.001NANANA
 rs731236NM_000376.2:c.1056T>C;C (T)<.00143.825.022.8
XRCC1rs1001581NM_006297.2:c.145-216G>AA (G)39.936.730.2<.00138.543.938.8
 rs1799782NM_006297.2:c.580C>T;T (C)<.001NANANA
 rs25486NM_006297.2:c.1083-59G>AG (A)<.00136.723.731.9
 rs25487NM_006297.2:c.1196A>G;A (G)36.115.925.6<.00136.617.530.7
 rs25489NM_006297.2:c.839G>A;A (G)4.03.512.4<.0014.42.77.9

Statistical Analysis.

All statistical analyses accounted for sample weights and the survey design to produce unbiased national estimates using SAS-Callable SUDAAN 9.01 (Research Triangle Institute, Research Triangle Park, NC) and SAS 9.1 (SAS Institute, Cary, NC). Weighted allele frequencies and their 95% confidence intervals were calculated using NHANES III genetic sample weights for the 7159 DNA bank participants.20 The Taylor series linearization approach,26, 27 which derives a linear approximation of variance estimates to develop corrected standard errors and confidence intervals, was implemented to correct for correlations within sampled clusters, including the possible genetic relatedness of persons sampled from the same household. Tests of the difference in allele frequencies among the three racial/ethnic groups were performed by using polytomous logistic regression. Nei's distance (DA) was calculated to compare genetic differentiation between the racial/ethnic groups using the formula 1 − [(p1p2)1/2 + (q1q2)1/2], where p1 and q1 are frequencies of the major and minor alleles, respectively, in the first population, while p2 and q2 represent the corresponding frequencies in the second population.28

For each genetic variant, univariate and multivariable regression models were used to test for genetic associations with anti-HAV status and stratified by self-reported race/ethnicity. An additive genetic model (AA versus Aa versus aa) was assumed in regression analyses to test the null hypothesis that anti-HAV status did not differ by an increasing number of minor alleles. Interaction between each variant and race/ethnicity was examined to test racial/ethnic differences in the genetic effects. Age and country of origin were included in multivariable regression models. The P value from Satterthwaite statistics was adjusted for each genetic variant to control for the false discovery rate (FDR) as estimated by PROC MULTTEST in SAS using the linear step-up method of Benjamini and Hochberg.29 A significant association was defined at an FDR adjusted P value (FDR-P) < 0.05, implying that less than 5% of these significant associations can be expected to be false-positive. Interaction between age and each variant associated with anti-HAV seropositivity was examined to test age differences in the genetic effects.

Power calculations were determined using Quanto.30 The effective sample sizes (sample sizes adjusted by a design effect of 1.2) of three race/ethnic groups were used to account for the complex survey design of NHANES III. Assuming additive genetic models and using anti-HAV prevalence for the three different racial/ethnic groups reported here, we calculated power to detect SNP associations with an odds ratio of 1.3, which is consistent with significant genetic associations observed in other studies.31, 32 For the three SNPs that were only significantly associated with anti-HAV seroprevalence in Mexican Americans, we also assessed if the study was adequately powered to detect these associations in other two racial/ethnic groups.


Population Characteristics.

Characteristics of the included participants (n = 6,779) are shown in Table 2. Overall prevalence of HAV infection was 29.6%. The anti-HAV seropositivity rate was significantly higher among Mexican Americans (71.5%) compared with non-Hispanic whites (24.9%) and non-Hispanic blacks (39.2%). Age was most strongly associated with infection prevalence, rising steadily with increasing age across all three subpopulations (P < 0.0001), reaching 92.8% among Mexican Americans, 87.3% among non-Hispanic blacks, and 66.1% among non-Hispanic whites aged ≥65 years. Anti-HAV prevalence differed substantially between US- and foreign-born participants across all racial/ethnic groups (P < 0.0001), particularly among Mexican Americans. Foreign-born Mexican Americans had higher seroprevalence (93.8%) than US-born Mexican Americans (48.1%). Low education level was also associated with high anti-HAV seropositivity across all three racial/ethnic groups (P = 0.0001, 0.03, and 0.003 for non-Hispanic whites, non-Hispanic blacks, and Mexican Americans, respectively). Poverty income ratio and geographic region were not significantly associated with anti-HAV prevalence in any race/ethnicity (P > 0.05).

Table 2. Characteristics of Included Participants in NHANES III DNA Bank (1991-1994)
CharacteristicsNon-Hispanic Whites (n = 2,619)Non-Hispanic Blacks (n = 2,095)Mexican Americans (n = 2,065)
Anti-HAV +veAnti-HAV −vePAnti-HAV +veAnti-HAV −vePAnti-HAV +veAnti-HAV −ve 
nWeighted % (SE)*nWeighted % (SE)nWeighted % (SE)nWeighted % (SE)nWeighted % (SE)nWeighted % (SE)
  • Abbreviations: ALT, alanine aminotransferase; AST, aspartate aminotransferase; HBV, hepatitis B virus; HCV, hepatitis C virus; SE, standard error.

  • *

    Frequencies were adjusted using NHANES III genetic sample weights.

  • P value was calculated using the Wald chi-square test based on the log odds ratio.

  • Poverty income ratio was calculated by dividing the total family income by the poverty threshold adjusted for family size for the year of the interview.

Total95824.9 (1.4)1,66175.1 (1.4) 80239.2 (1.8)1,29360.8 (1.8) 1,54071.5 (2.1)52528.5 (2.1) 
 Male38122.9 (2.0)66677.1 (2.0).1534838.4 (2.0)54461.6 (2.0).4577171.8 (2.6)25128.2 (2.6).80
 Female57726.8 (1.8)99573.2 (1.8) 45439.8 (2.0)74960.2 (2.0) 76971.2 (2.4)27428.8 (2.4) 
Age, years               
 12-19186.9 (1.7)24893.1 (1.7)<.0001347.4 (1.5)44992.6 (1.5)<.000115740.6 (2.8)23659.4 (2.8)<.0001
 20-29236.6 (1.5)30993.4 (1.5) 6115.3 (1.9)34584.7 (1.9) 36574.0 (2.4)12926.0 (2.4) 
 30-447413.7 (2.2)47986.3 (2.2) 30244.2 (2.7)35555.8 (2.7) 45077.9 (3.0)11922.1 (3.0) 
 45-6423232.5 (2.8)37267.5 (2.8) 22563.8 (3.1)11836.2 (3.1) 33987.4 (2.8)2912.6 (2.8) 
 ≥6561166.1 (2.9)25333.6 (2.9) 18087.3 (3.7)2612.7 (3.7) 22992.8 (2.4) 12 7.2 (2.4) 
Country of origin               
 United States88323.7 (1.5)1,60076.3 (1.5).00268136.5 (1.5)1,24363.5 (1.5).00260748.1 (2.3)47051.9 (2.3)<.0001
 Outside United States7550.4 (4.9)5449.6 (4.9) 11168.6 (5.0)4831.4 (5.0) 93293.8 (1.2)556.25 (1.2) 
Region of residence               
 Northeast20923.9 (1.1)53772.6 (1.1).2315240.9 (1.5)23659.2 (1.5).461668.5 (12.0)731.5 (12.0).42
 Midwest35127.4 (3.0)53772.6 (3.0) 14537.6 (1.0)26962.4 (1.0) 17978.8 (2.2)4521.2 (2.2) 
 West11920.3 (3.9)32879.7 (3.9) 6337.0 (7.1)9563.0 (7.1) 62670.3 (3.4)22829.7 (3.4) 
 South27927.0 (1.3)46973.0 (1.3) 44240.0 (2.7)69360.3 (2.7) 71970.8 (2.5)24529.1 (2.5) 
Poverty income ratio               
 <19125.4 (4.4)12674.6 (4.4).8026438.8 (2.3)43961.3 (2.3).9754876.6 (2.9)15123.4 (2.9).04
 ≥177824.1 (1.5)1,46075.9 (1.5) 47038.7 (2.0)76261.3 (2.0) 82867.7 (2.5)34132.3 (2.5) 
Education, years               
 <1238733.1 (2.2)40466.9 (2.2)<.000138142.9 (2.9)57357.1 (2.9).031,06877.4 (2.4)28122.6 (2.4).003
 ≥1256722.1 (1.2)1,25577.9 (1.2) 40836.0 (1.4)71964.0 (1.4) 46161.3 (2.5)24338.7 (2.5) 
C-reactive protein, mg/dL               
 >19641.4 (5.4)9358.6 (5.4).000310250.3 (3.9)10049.7 (3.9).00612875.7 (4.9)3024.3 (4.9).35
 ≤186024.0 (1.3)1,56776.0 (1.3) 70038.1 (1.9)1,19161.9 (1.9) 1,41071.2 (2.1)49528.8 (2.1) 
ALT, U/L               
 <4393924.8 (1.3)1,62475.2 (1.3).6776938.9 (1.8)1,25261.1 (1.8).161,44670.7 (2.1)50229.3 (2.1).12
 ≥431827.8 (7.5)3572.2 (7.5) 3346.6 (5.2)3953.4 (5.2) 8982.9 (5.9)2317.1 (5.9) 
AST, U/L               
 <4092925.3 (1.4)1,58274.7 (1.4).0476340.0 (1.9)1,23761.0 (1.9).411,35670.4 (2.2)47229.6 (2.2).16
 ≥402817.8 (3.7)7782.2 (3.7) 3943.7 (5.5)5456.3 (5.5) 17978.7 (4.6)5321.3 (4.6) 
Coinfection with HBV               
 Yes5852.6 (5.3)3747.4 (5.3).00216864.0 (3.8)8736.0 (3.8).00016987.4 (5.4)812.6 (5.4).03
 No90024.0 (1.4)1,62376.0 (1.4) 63335.4 (1.7)1,20664.6 (1.7) 1,47170.9 (2.1)51729.1 (2.1) 
Coinfection with HCV               
 Yes1829.5 (9.7)2570.5 (9.7).612950.1 (5.1)3249.9 (5.1).092867.5 (7.6)1232.5 (7.6).54
 No93824.8 (1.4)1,63675.3 (1.4) 77338.8 (1.9)1,26061.2 (1.9) 1,51171.6 (2.1)51328.4 (2.1) 

Furthermore, in all three racial/ethnic groups, coinfection with HBV (indicated by positivity to antibody to hepatitis B core antigen) was significantly higher among participants who were anti-HAV–positive than those who were anti-HAV-negative (P = 0.002, 0.0001, and 0.03 for non-Hispanic whites, non-Hispanic blacks, and Mexican Americans, respectively).

Genetic Associations with Anti-HAV Seropositivity.

Allele frequencies of the selected candidate gene polymorphisms were similar to those reported in comparable HapMap populations33 (Table 1). For 65 of the 67 variants (97%), allele frequencies were significantly different (P < 0.001) across racial/ethnic groups. The extent of this differentiation varied greatly between SNPs and between racial/ethnic populations (Table 1 and Supporting Table 2). As several SNPs differed substantially between populations (e.g., DA = 0.250 for CYP3A4 rs2740574 between non-Hispanic whites and non-Hispanic blacks), each genetic variant was tested for associations with anti-HAV seropositivity in univariate and multivariable regression models stratified by the three racial/ethnic groups.

This study identified significant genetic associations with anti-HAV seropositivity among Mexican Americans, but not among non-Hispanic whites or non-Hispanic blacks, under an additive genetic model using both univariate (data not shown) and multivariable regression models (Table 3). Since age and birthplace were the most important determinants of HAV infection between 1988 and 1994 in the United States,17 and since both were significantly associated in each racial/ethnic group (Table 2), we adjusted for age and country of origin (birthplace) in multivariable regression models. Two variants were found associated with susceptibility to anti-HAV seropositivity among Mexican Americans (Table 3 and Supporting Table 3). Specifically, for TGFB1 rs1800469 and XRCC rs1799782, the T allele was associated with an increased risk of anti-HAV seropositivity (FDR-P = 0.017 and 0.0007, respectively). The prevalence odds ratio of seropositivity calculated by multivariable regression was 1.38 (95% CI, 1.14-1.68) for TGFB1 rs1800469 and 1.57 (95% CI, 1.27-1.94) for XRCC1 rs1799782. These two minor alleles are common in the Mexican American population (TGFB1 rs1800469 [44.8%] and XRCC1 rs1799782 [14.8%]), but are less frequent among non-Hispanic whites (TGFB1 rs1800469 [31.4%] and XRCC1 rs1799782 [5.0%]) and non-Hispanic blacks (TGFB1 rs1800469 [44.0%] and XRCC1 rs1799782 [6.2%]) (P < 0.001) (Table 1). CYP2E1 rs2031920 was marginally associated with increased odds of anti-HAV seropositivity (OR, 1.46; 95% CI, 1.12-1.91; FDR-P = 0.043) (Table 3).

Table 3. Associations* of Genetic Variants and Anti-HAV Seropositivity by Race/Ethnicity in the NHANES III DNA Bank (1991-1994)
Gene SymbolVariantAlleleNon-Hispanic WhitesNon-Hispanic BlacksMexican Americans
OR (95% CI)Raw PFDR-P§OR (95% CI)Raw PFDR-POR (95% CI)Raw PFDR-P
  • *

    Additive genetic model adjusted for age and country of origin.

  • The major allele (determined by the frequency in the total population) is given in parentheses.

  • Based on multivariable logistic regression analysis within each race/ethnicity group.

  • §

    Adjusted for multiple comparisons using false discovery rate in PROC MULTTEST (SAS 9.1).

ABCB1rs1045642T (C)1.03 (0.91-1.16)0.630.991.01 (0.86-1.18)0.900.990.79 (0.71-0.89)0.000020.0007
CATrs769214G (A)1.09 (0.93-1.29)0.260.941.01 (0.81-1.25)0.96>0.990.82 (0.71-0.94)0.0030.043
CCL5rs2280788G (C)0.89 (0.65-1.21)0.420.960.46 (0.14-1.45)0.160.852.18 (0.75-6.33)0.130.55
CCR2rs1799864A (G)0.86 (0.66-1.11)0.210.900.88 (0.65-1.18)0.360.941.14 (0.93-1.40)0.180.60
CRPrs1205A (G)1.00 (0.78-1.28)>0.99>0.991.01 (0.84-1.22)0.870.991.09 (0.90-1.34)0.360.80
 rs1417938T (A)0.82 (0.62-1.10)0.160.850.85 (0.71-1.02)0.070.590.98 (0.73-1.31)0.88>0.99
 rs1800947C (G)0.81 (0.54-1.22)0.290.940.82 (0.33-2.05)0.660.991.23 (0.59-2.57)0.560.88
 rs2808630G (A)1.19 (0.96-1.47)0.090.701.10 (0.88-1.36)0.380.940.94 (0.60-1.45)0.760.96
 rs3093058T (A)0.49 (0.09-2.58)0.370.941.08 (0.87-1.35)0.460.971.16 (0.42-3.17)0.770.96
 rs3093066A (C)1.46 (0.42-5.15)0.530.991.03 (0.85-1.25)0.740.990.65 (0.28-1.51)0.290.75
CXCL12rs169097T (C)2.45 (0.50-12.03)0.240.941.12 (0.91-1.40)0.260.941.55 (0.54-4.48)0.390.80
CYP1A1rs2472299T (C)1.07 (0.87-1.33)0.500.991.09 (0.89-1.33)0.390.941.06 (0.83-1.36)0.610.91
 rs2606345G (T)1.06 (0.86-1.31)0.590.991.34 (1.01-1.78)0.030.311.16 (0.95-1.42)0.120.54
CYP1A2rs11854147T (C)1.06 (0.87-1.30)0.550.991.43 (1.13-1.81)0.0020.091.15 (0.93-1.43)0.160.60
 rs2069514A (G)1.01 (0.63-1.60)0.981.001.21 (1.05-1.40) (0.89-1.40)0.330.77
 rs4886406G (T)1.11 (0.88-1.42)0.350.941.09 (0.87-1.37)0.440.971.00 (0.78-1.28)0.991.00
CYP1B1rs1056836T (C)1.00 (0.82-1.23)0.97>0.991.14 (0.86-1.53)0.340.940.84 (0.64-1.11)0.200.60
 rs1056837G (C)0.96 (0.77-1.19)0.690.991.11 (0.81-1.51)0.500.990.81 (0.61-1.07)0.120.54
 rs162557T (C)0.88 (0.67-1.17)0.360.941.23 (1.01-1.49)0.030.311.11 (0.83-1.48)0.460.83
CYP2A6rs1801272A (T)1.13 (0.61-2.08)0.680.990.73 (0.20-2.67)0.620.990.65 (0.34-1.22)0.160.60
CYP2C19rs4986893A (G)6.01 (0.52-70.09)0.130.791.74 (0.03-117.59)0.790.991.21 (0.05-31.55)0.90>0.99
 rs4986894C (T)0.99 (0.77-1.27)0.930.990.98 (0.76-1.27)0.880.991.00 (0.72-1.39)>0.99>0.99
CYP2E1rs2031920T (C)1.33 (0.61-2.90)0.450.970.97 (0.38-2.45)0.940.991.46 (1.12-1.91)0.0030.043
CYP3A4rs2740574G (A)0.91 (0.62-1.32)0.590.991.01 (0.83-1.22)0.940.991.16 (0.87-1.56)0.280.75
FCGR2Ars1801274A (G)1.02 (0.86-1.22)0.810.990.99 (0.83-1.18)0.900.991.11 (0.85-1.46)0.420.81
IL10rs1800871T (C)1.15 (0.93-1.42)0.180.870.92 (0.77-1.10)0.310.941.11 (0.89-1.39)0.310.77
 rs1800872A (C)1.13 (0.90-1.40)0.260.940.93 (0.78-1.11)0.400.941.10 (0.88-1.37)0.380.80
 rs1800896G (A)0.81 (0.65-1.03)0.070.591.20 (1.05-1.38) (0.68-1.29)0.680.94
IL1Brs1143623C (G)0.95 (0.82-1.11)0.540.990.83 (0.58-1.17)0.260.941.00 (0.81-1.23)0.96>0.99
IL4rs2243248G (T)1.32 (1.00-1.75)0.040.400.95 (0.76-1.17)0.600.991.03 (0.79-1.34)0.820.97
 rs2243250T (C)0.98 (0.86-1.12)0.750.991.01 (0.85-1.19)0.940.991.26 (1.02-1.56)0.020.11
 rs2243270G (A)0.92 (0.80-1.05)0.190.871.07 (0.83-1.37)0.580.991.26 (1.02-1.55)0.020.11
IL4Rrs1801275G (A)0.98 (0.82-1.16)0.760.991.00 (0.86-1.15)0.981.001.12 (0.88-1.42)0.330.77
 rs1805015C (T)0.94 (0.74-1.21)0.620.991.01 (0.87-1.16)0.940.991.00 (0.75-1.34)0.99>0.99
ITGA2rs1126643T (C)0.90 (0.74-1.10)0.280.940.99 (0.80-1.24)0.96>0.991.01 (0.83-1.23)0.90>0.99
MBL2rs11003125G (C)1.05 (0.90-1.22)0.520.990.97 (0.71-1.33)0.860.991.09 (0.73-1.64)0.640.92
 rs1800450A (G)0.78 (0.66-0.93)0.0030.090.91 (0.55-1.52)0.720.991.11 (0.83-1.47)0.460.83
 rs1800451A (G)1.29 (0.78-2.15)0.300.940.83 (0.68-1.01)0.050.460.89 (0.45-1.73)0.710.94
 rs5030737T (C)0.78 (0.58-1.06)0.100.731.08 (0.50-2.35)0.830.991.08 (0.53-2.20)0.820.97
 rs7096206C (G)1.15 (0.96-1.39)0.110.781.07 (0.77-1.51)0.660.990.89 (0.59-1.35)0.560.88
NOS2Ars1800482C (G)1.44 (0.19-10.95)0.710.991.47 (1.07-2.02) (0.20-0.84)0.010.08
 rs9282799T (C)1.23 (0.21-7.36)0.810.991.03 (0.61-1.74)0.910.991.47 (0.40-5.45)0.550.88
NOS3rs1799983T (G)1.01 (0.86-1.19)0.910.990.90 (0.68-1.20)0.460.970.83 (0.72-0.95)0.0040.05
 rs2070744C (T)1.03 (0.77-1.39)0.830.990.89 (0.69-1.14)0.330.940.75 (0.59-0.96)0.020.11
NQO1rs10517T (C)0.90 (0.67-1.22)0.480.980.96 (0.78-1.19)0.720.990.78 (0.49-1.25)0.270.75
 rs1800566T (C)0.98 (0.78-1.24)0.860.990.93 (0.75-1.17)0.530.990.90 (0.70-1.16)0.400.80
 rs34755915A (G)1.12 (0.57-2.21)0.730.991.14 (0.44-2.94)0.780.991.08 (0.15-7.60)0.941.00
 rs689452G (C)0.85 (0.61-1.19)0.330.940.95 (0.77-1.17)0.630.990.75 (0.48-1.18)0.190.60
 rs689453A (G)0.95 (0.66-1.35)0.740.991.14 (0.71-1.84)0.560.990.88 (0.52-1.49)0.620.91
OGG1rs1052133G (C)1.17 (0.88-1.55)0.270.940.97 (0.78-1.21)0.770.991.18 (0.87-1.62)0.260.75
PON1rs662G (A)0.96 (0.76-1.20)0.690.991.09 (0.92-1.28)0.290.941.06 (0.86- 1.31)0.550.88
 rs854560A (T)1.04 (0.83-1.31)0.720.990.95 (0.74-1.23)0.700.990.82 (0.70-0.96)0.010.08
PPARGrs1801282G (C)0.85 (0.65-1.10)0.190.870.63 (0.34-1.18)0.130.790.97 (0.76-1.24)0.810.97
TGFB1rs1800468A (G)1.19 (0.89-1.59)0.220.910.98 (0.61-1.59)0.940.990.72 (0.43-1.21)0.200.60
 rs1800469T (C)1.06 (0.91-1.25)0.420.961.07 (0.91-1.26)0.370.941.38 (1.14-1.68)0.00070.017
 rs1982073C (T)1.06 (0.93-1.21)0.390.941.04 (0.88-1.24)0.610.991.28 (1.06-1.55)0.010.08
TLR4rs4986790G (A)1.07 (0.73-1.57)0.720.990.74 (0.51-1.07)0.090.701.03 (0.52-2.06)0.92>0.99
TNFrs1800629T (C)0.98 (0.79-1.22)0.880.990.87 (0.67-1.15)0.300.941.12 (0.77-1.64)0.520.88
 rs1800750T (C)1.40 (0.84-2.33)0.180.870.92 (0.49-1.72)0.780.991.13 (0.68-1.88)0.620.91
 rs361525T (C)0.98 (0.69-1.39)0.910.990.93 (0.56-1.56)0.790.991.25 (0.70-2.24)0.430.81
VDRrs2239185C (T)1.02 (0.82-1.28)0.850.991.06 (0.85-1.32)0.580.991.06 (0.80-1.39)0.690.94
VDRrs731236C (T)1.03 (0.85-1.24)0.770.991.11 (0.87-1.40)0.380.940.92 (0.71-1.19)0.500.88
XRCC1rs1001581A (G)1.00 (0.82-1.22)0.991.001.06 (0.89-1.27)0.480.980.94 (0.82-1.09)0.380.80
 rs1799782T (C)1.13 (0.75-1.70)0.550.991.31 (0.89-1.92)0.150.851.57 (1.27-1.94)0.000010.0007
 rs25486G (A)1.07 (0.88-1.31)0.450.971.07 (0.88-1.29)0.470.981.01 (0.83-1.24)0.90>0.99
 rs25487A (G)1.04 (0.85-1.26)0.710.991.04 (0.80-1.36)0.740.991.03 (0.85-1.25)0.730.94
 rs25489A (G)0.86 (0.48-1.54)0.590.991.52 (0.90-2.57)0.100.730.76 (0.58-0.99)0.030.15

The minor allele (T) of ABCB1 rs1045642 was associated with lower risk for anti-HAV seropositivity among Mexican Americans (OR, 0.79; 95% CI, 0.71-0.89; FDR-P = 0.0007) (Table 3 and Supporting Table 3). Another variant, CAT rs769214, was marginally associated with decreased odds of anti-HAV seropositivity (OR, 0.82; 95% CI, 0.71-0.94; FDR-P = 0.043) (Table 3).

To test age differences in the genetic effects, we examined interactions between age and each polymorphism associated with anti-HAV seropositivity. No significant interactions between age and genetic associations of ABCB1 rs1045642 or XRCC1 rs1799782 were found (P = 0.08 and 0.34, respectively). A weak interaction was detected with TGFB1 rs1800469 (P = 0.02), but the trend of the odds of infection prevalence was not increased with age as expected (Supporting Table 4). Therefore, age appears to be an independent determinant of HAV infection.


This is the first study assessing associations between human genetic variants and HAV infection among a nationally representative sample of the three major race/ethnicities in the United States. Variants in ABCB1, TGFB1, and XRCC1 were significantly associated with the prevalence of HAV infection in Mexican Americans.

We observed that individuals carrying the functional T allele of TGFB1 rs1800469 are more prone to have been infected with HAV. TGFB1 is a multifunctional cytokine that regulates proliferation and differentiation of a wide variety of cell types. It plays a crucial role in the pathogenesis of liver injury during acute hepatitis A infection.34 The TT genotype of TGFB1 rs1800469 (C-509T), located at nucleotide −509 in the TGFB1 promoter, is associated with higher plasma levels of TGFB1, which have been shown to be under genetic control (heritability estimate, 0.54), with C-509T responsible for 8.2% of additive genetic variance in a twin study.35 The T allele of C-509T alters TGFB1 transcription activity by influencing affinity of transcription factor Yin Yang 1 for its promoter.36 Excessive release of TGFB1 in serum during acute hepatitis A infection can markedly inhibit antigen-specific T cell activation and proliferation as well as humoral response.37 This may explain why carriers of the TGFB1 rs1800469 T allele (the high TGFB1 producers) are more susceptible to HAV infection.

We found that Mexican American carriers of the T allele of XRCC1 rs1799782 have a higher prevalence of HAV infection. XRCC1 is a major DNA repair gene involved in efficient repairs of single-strand DNA breaks and base excision to correct DNA damage caused by oxidative stress and inflammation.38 Genetic variants in DNA repair genes can be associated with differences in the ability to repair DNA damage, which may be a requisite for risk of many diseases, including HIV and HBV-related hepatocellular carcinoma.39, 40 HAV induces oxidative stress that alters base excision repair pathways and increases apoptotic response in acute hepatitis A.23, 41 The Arg194Trp variant (rs1799782) of XRCC1 resides in a microRNA-binding site and alters microRNA-target interaction to affect gene and protein expression, in turn influencing the risk of certain human diseases. The rs1799782 T allele is associated with increased binding with microRNA-138.42 Mexican American carriers of this functional T allele showed increased susceptibility to HAV infection, suggesting that XRCC1 rs1799782 may play a role in susceptibility to HAV infection through its indirect effects on inflammation, oxidative stress, and apoptosis pathways.

The ABCB1 gene (formerly MDR1) encodes one member of the ATP-binding cassette super family of membrane transporters that actively effluxes a wide range of compounds from cells. It is involved in multidrug resistance and antiapoptosis.43 Up-regulated expression of ABCB1 in human hepatocytes and bile ductules in viral hepatitis may offer protection against the accumulation of toxic bile constituents and render these cells resistant to oxidative stress.44 The 3435C>T (I1145I) variant (rs1045642) represents a main functional polymorphism, leading to changes in ABCB1 messenger RNA level, protein expression, protein folding, and substrate specificity.45, 46 This variant accounts for approximately two-fold changes in ABCB1 messenger RNA expression in liver tissue in vitro.47 In the Mexican American population studied here, individuals with one or two copies of T allele are less prone to HAV infection, suggesting that ABCB1 rs1045642 may affect the individual's susceptibility to HAV infection via the protective effect of ABCB1 in liver during viral hepatitis.

Serologic evidence of hepatitis A infection was more prevalent among Mexican Americans (71.5%) compared with non-Hispanic whites (24.9%) and blacks (39.2%). Hepatitis A is endemic in Mexico and in Central and South America.48 The higher infection prevalence and hepatitis A incidence in Hispanic communities may be due to more opportunities for exposure arising from higher levels of circulating virus in the community or more frequent travel to HAV-endemic countries. Host genetic variation may explain, at least in part, the marked increase in the prevalence of HAV infection in Mexican Americans compared with other racial/ethnic groups. It is striking that the high seroprevalence of HAV infection in Mexican Americans displayed such close associations with high frequencies of the TGFB1, ABCB1, and XRCC1 functional alleles. Alternatively, these differences in the loci found associated with HAV infection across racial/ethnic groups may be caused by varying linkage disequilibrium patterns (Supporting Fig. 1) or by gene-environment interactions that have not been identified or measured.49, 50

While the genetic associations observed from this large population-based survey may be representative and generalizable to the United States population, there are several limitations to discuss. Overly conservative P values may be generated by FDR, which may decrease our ability to identify true associations. Unlike unadjusted P values expressing the probability of a false-positive result for a single test, the FDR gives a conservative estimate of the proportion of false-positives among variants with significant association.29 Also, this study is prone to potential confounding from population substructure, though we stratified all analyses according to self-reported race/ethnicity. There is a considerable body of literature reporting on genetic admixture in non-Hispanic black and Hispanic populations,51, 52 with substantially less among non-Hispanic whites.53 We were not able to assess population substructure in our analysis, because ancestry-informative markers are not yet available for NHANES III. There is little clinical or epidemiological evidence that some individuals or populations may be biologically more resistant or susceptible to HAV infections. It is possible that the three SNPs identified in our study may simply be markers of population subgroups who have higher exposure to HAV or who migrated to the United States from a region where HAV is highly endemic. Additionally, the statistical power to detect significant associations with uncommon genetic variants was limited. This study had 80% power to detect associations in odds ratio ≥1.3 among variants with a minor allele frequency ≥12% in non-Hispanic whites, ≥16% in non-Hispanic blacks, and ≥24% in Mexican Americans (Supporting Table 5). It did appear that this study was adequately powered to detect in each racial/ethnic group the three associations that were significant in the Mexican American population (Supporting Table 6). The implicated markers are suggested to be functional by epidemiological, in vitro, or in vivo studies,35, 36, 42, 45-47 but it is possible that they may be proxies for the true causal variants. If this is the case, then differences in linkage disequilibrium (Supporting Fig. 1) may hamper our ability to detect associations across all three racial/ethnic groups, if they exist.54 The relatively small number of variants that we examined for each gene also served as a limitation. Further fine mapping in all three racial/ethnic subpopulations may be warranted. Finally, this study is cross-sectional, allowing us to test for disease susceptibility but not incidence or severity. Therefore, it will be important to examine these findings in additional populations and to assess whether these variants are also associated with other factors or characteristics associated with increased risk of hepatitis A infection, some of which may be unrelated to biological susceptibility. For example, some variants may simply be of higher prevalence among Mexican Americans who are of lower socioeconomic status (a risk factor for hepatitis A infection itself) or those who have a higher proportion of Native American ancestry.

In conclusion, this study is the first to examine genetic associations with risk of HAV infection using a population-based and nationally representative sample of the United States population. We found significant associations between susceptibility to HAV infection and variants in TGFB1, XRCC1, and ABCB1 among Mexican Americans. It would be prudent to examine these findings in diverse populations. Furthermore, NHANES can be used to facilitate the population-level assessment of new and validated genetic variants for viral hepatitis susceptibility.


We sincerely thank all the study subjects who participated in NHANES III. We also thank Muin J. Khoury for oversight of the project, Chong-Gee Teo and Scott Holmberg for critical review, and the staff at the Research Data Center, National Center for Health Statistics, for data support and assistance in disclosure review.