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Review
. 2006 Jan;19(1):63-79.
doi: 10.1128/CMR.19.1.63-79.2006.

Diagnosis of hepatitis a virus infection: a molecular approach

Omana V Nainan  1 , Guoliang Xia, Gilberto Vaughan, Harold S Margolis
Affiliations
Review

Diagnosis of hepatitis a virus infection: a molecular approach

Omana V Nainan et al. Clin Microbiol Rev. 2006 Jan.

Abstract

Current serologic tests provide the foundation for diagnosis of hepatitis A and hepatitis A virus (HAV) infection. Recent advances in methods to identify and characterize nucleic acid markers of viral infections have provided the foundation for the field of molecular epidemiology and increased our knowledge of the molecular biology and epidemiology of HAV. Although HAV is primarily shed in feces, there is a strong viremic phase during infection which has allowed easy access to virus isolates and the use of molecular markers to determine their genetic relatedness. Molecular epidemiologic studies have provided new information on the types and extent of HAV infection and transmission in the United States. In addition, these new diagnostic methods have provided tools for the rapid detection of food-borne HAV transmission and identification of the potential source of the food contamination.

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Figures

FIG. 1.
FIG. 1.
Virologic, immunologic and biochemical events during the course of experimental hepatitis A virus infection in chimpanzees inoculated intravenously with human HAV, strain HLD2. ALT, alanine aminotransferase. (Adapted from reference with permission of the publisher.)
FIG. 2.
FIG. 2.
Schematic representation of the HAV genome organization, translation products, and regions used for amplification. The area encoding the polyprotein is represented by solid box and the proposed cleavage sites by vertical lines. Regions commonly used for PCR amplifications are as follows: region 1, C terminus of VP3 region (nt 2,020 to nt 2,226); region 2, N terminus of VP1 region (nt 2,172 to nt 2,415); region 3, VP1/P2A junction region (nt 2,984 to nt 3,217); region 4, VP1-P2B region (nt 2,896 to nt 3,289); region 5, entire VP1 region (nt 2,172 to nt 3,125); and region 6, VP3-P2B region (nt 2,133 to nt 3,289). Nucleotide position numbering is according to the HM175 sequence (46).
FIG. 3.
FIG. 3.
Phylogenetic analysis of 3,582 HAV isolates in the VP1/P2B region (315-bp fragment). The dendrogram (unweighted-pair group method using average linkages) was created by using Kimura's two-parameter model. Isolates were obtained from the United States (n = 2,190) and other parts of the world. The U.S. specimens included specimens from hepatitis A cases from CDC's Sentinel Counties Study of Acute Viral Hepatitis (11, 170), published and unpublished outbreak investigations (30, 63, 112), and others submitted to CDC for investigation. Specimens from the U.S.-Mexico Border Infectious Disease Surveillance (BIDS) project (258) were also included and represented cases primarily from the United States. Specimens from other countries include those from Mexico, Brazil, Israel, Jordan, Egypt, Moldova, and Kazakhstan and were submitted to CDC as part of outbreak or epidemiologic investigations. Sequences from GenBank (Italy, Norway, Spain, Tunisia, and Japan) were also included in the analysis. Only unique sequence patterns are shown in the tree. Genotypes and subgenotypes are indicated on the branches, and the geographical locations of case patients are indicated in different colors.
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