Phylogenetic analysis of human parvovirus B19, indicating two subgroups of genotype 1 in Vietnamese patients

Abstract

Recently, three distinct genotypes (1, 2 and 3) of human parvovirus B19 (B19) have been identified. However, the characteristics and distribution of B19 genotypes in Vietnam have not been investigated. Phylogenetic analysis using 49 subgenomic NS1/VP1u regions and two coding NS1-VP1/VP2 regions has been applied to investigate the prevalence of B19 genotypes in Vietnamese patients co-infected with Hepatitis B virus. Genetic analysis of the subgenomic NS1/ VP1u region of B19 revealed that two genotypes of B19 were identified in these populations, with predominance of genotype 1 (47/49, 96 %) followed by genotype 2 (2/49, 4 %), but not genotype 3. Further, phylogenetic analysis of subgenomic B19 genomes revealed two major subgroups within genotype 1 (B19-1A and B19-1B) with an estimated nucleotide difference of >5 % between each subgroup, forming different branches. The mean percentage of amino acid variation between subgroup B19-1A and B19-1B was >2 % of the NS1, VP1 and VP2 proteins. Our results indicated that two of the three known genotypes of B19 were present in Vietnamese patients, with genotype 1 predominating, and that this genotype can be classified into at least two subgroups, B19-1A and B19-1B. INTRODUCTIONHuman parvovirus B19 (B19) is a member of the genus Erythrovirus within the family Parvoviridae . Parvoviruses are non-enveloped and are amongst the smallest DNA-containing viruses that are capable of infecting mammalian cells . B19 has a diverse spectrum of clinical manifestations, including erythema infectiosum, hydrops fetalis, aplastic anaemia (Anderson et al., 1983;Young & Brown, 2004), arthritis (Takahashi et al., 1998;Moore, 2000), myocarditis (Bültmann et al., 2003;Bock et al., 2005; Tschöpe et al., 2005;Bock, 2006), vasculitic syndromes (Finkel et al., 1994;Dingli et al., 2000), neurological disorders (Barah et al., 2001) and hepatic inflammation (Naides et al., 1996;Yoto et al., 1996;Hillingsø et al., 1998;Karetnyi et al., 1999; He et al., 2003).The genome of B19 consists of a linear, single-stranded DNA molecule of about 5600 nt (Morinet, 1992;Zhi et al., 2004), which contains three open reading frames encoding the non-structural protein NS1 (77 kDa) and the two structural proteins VP1 (84 kDa) and VP2 (58 kDa) (Cotmore et al., 1986). Genetic diversity among B19 strains has been shown to be very low, with <1-2 % nucleotide divergence of the full-length sequences. Partial sequence data from different coding regions of the viral genome have confirmed a slightly higher degree of variability with a larger number of strains from distinct epidemiological settings and geographical areas (Erdman et al., 1996). However, some B19 strainsThe GenBank/EMBL/DDBJ accession numbers for the nucleotide sequences of B19 samples determined in this study are DQ357064 (V147) and DQ357065 (V115). obtained from patients with persistent infection show a higher degree of variability, particularly in the VP1-unique (VP1u) region, demonstrating 4 and 8 % divergence at the DNA and protein levels, respectively (Hemaue...

Phylogenetic Analysis of Human Parvovirus B19 Sequences from Eleven Different Countries Confirms the Predominance of Genotype 1 and Suggests the Spread of Genotype 3b

“…Genotype 1 dominated in 9 of the 11 countries investigated here. Thus, our results further confirm the predominance of genotype 1 in most parts of the world (15). The mean genetic distance among all genotype 1 sequences within the 994-nt region was 0.91%, and the maximal genetic distance was 4.70% (DQ357065 and DQ293995).…”

Biological and Immunological Relations among Human Parvovirus B19 Genotypes 1 to 3

“…However, after recognition of the variant strains V9 (44, 45), A6 (46), and LaLi (27), the human erythroviruses are now classified into genotypes 1 (prototype), 2 (LaLi-like), and 3 (V9-like) (57). Furthermore, phylogenetic analyses have revealed two subgroups within genotypes 1 and 3 (52,57,67).…”

Keeping Pace with Parvovirus B19 Genetic Variability: a Multiplex Genotype-Specific Quantitative PCR Assay

“…On the whole, the genetic diversity of genotype 1a remains low, and primers and probes are expected to recognize targets with high expectation values. The distance of genotype 1b is about 4% from genotype 1a, but the circulation of this subgenotype, and of additional rarer variants still within the genotype 1 cluster, seems to be geographically restricted (5,8). Genotypes 2 and 3 pose different problems.…”

“…However, the advantage to perform B19V detection with a validated qPCR methodology able to discriminate and quantitate different genotypes derives from two considerations. First, variant genotypes are known to circulate at higher frequencies in areas other than Europe or the United States, and in addition the changing demographic and epidemiological scenario will probably lead to a more global circulation of genotype 3 (5,6,8,9). Second, a reliable viral diagnosis should be able to detect variant genotypes even in particular sporadic clinical situations when standard assays, focused on genotype 1, may fail in B19V detection (7,10,23,24).…”

“…Specifically, B19 viruses are now formally subdivided into three genotypes, the prototype genotype 1 and the two variant genotypes 2 and 3, and further subtypes (3,4). In particular, within genotype 1, the majority of isolates are referred to as genotype 1a, while a few isolates from Asia show separate clustering and are referred to as genotype 1b (5). Within genotype 3, two distinct subtypes are usually referred to as genotypes 3a and 3b (6).…”