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

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.

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Simultaneous persistence of multiple genome variants of human parvovirus B19

Journal of General Virology ◽

10.1099/vir.0.83053-0 ◽

2008 ◽

Vol 89 (1) ◽

pp. 164-176 ◽

Cited By ~ 25

Author(s):

Beate Schneider ◽

Andrea Höne ◽

René H. Tolba ◽

Hans-Peter Fischer ◽

Johannes Blümel ◽

...

Keyword(s):

Parvovirus B19 ◽

Acute Infection ◽

Human Parvovirus B19 ◽

Genotype 1 ◽

Genotype 3 ◽

Viral Dna ◽

Antiviral Immune Response ◽

Sequence Heterogeneity ◽

Genotype 2 ◽

Genome Variants

The species human parvovirus B19 (B19V) can be divided into three genotypes. In this study, we addressed the question as to whether infection of an individual is restricted to one genotype. As viral DNA is detectable in tissue for long times after acute infection, we examined 87 liver specimens from adults for the presence of B19V DNA. Fifty-nine samples were found to be positive, 32 of them for genotype 1, 27 for genotype 2 and four for genotype 3. In four samples, DNA of two genotypes was detected; samples from three individuals were positive for genotypes 1 and 2 and a sample from one individual was positive for genotypes 1 and 3. Surprisingly, significant sequence heterogeneity was observed at approximately 1 % of the nucleotides of the genotype 1 genomes from individuals with double genotype 1 and 2 infection. Controls using different enzymes for genome amplification and dilutions of the template verified that nucleotide heterogeneity was due to the presence of three or more genome variants of genotype 1. In summary, the evidence shows that individuals can be infected with two different genotypes, and B19V DNA can persist as a population of different genomes. The results may have implications for the understanding of the antiviral immune response and the development of vaccines against B19V.

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Contamination of coagulation factor concentrates with human parvovirus B19 genotype 1 and 2

Thrombosis and Haemostasis ◽

10.1160/th04-04-0229 ◽

2004 ◽

Vol 92 (10) ◽

pp. 838-845 ◽

Cited By ~ 35

Author(s):

Beate Schneider ◽

Maria Becker ◽

Hans-Hermann Brackmann ◽

Anna Eis-Hübinger

Keyword(s):

Parvovirus B19 ◽

Simultaneous Detection ◽

Coagulation Factor ◽

Nucleic Acid Amplification ◽

Clotting Factor ◽

Human Parvovirus B19 ◽

Genotype 1 ◽

Viral Inactivation ◽

Genotype 2 ◽

Coagulation Factor Concentrates

SummaryHuman parvovirus B19 (B19) DNA has frequently been detected in plasma-derived coagulation factor concentrates. Furthermore, transmission of B19 infection was observed, indicating presence of the infectious virus despite routine viral inactivation/removal procedures during the manufacturing process. Recently, human parvovirus DNA isolates, variant from B19, have been identified resulting in classification of B19 virus into three distinct genotypes, with all viruses previously classified as B19 belonging to genotype 1. So far, there is no information available on contamination of clotting factor concentrates with genotype 2. Therefore, we analysed 202 different factor concentrate lots for genotype 1 and 2 DNA by PCR. Analysis of one hundred eighty-one lots representing 13 different products, administered over the last three years, was compared to 21 lots (8 products) used until the early 1980s which had not been treated by viral inactivation procedures. Genotype 1 DNA was detected in 77/181 (42.5%) currently administered lots, and 17/21 (81%) previously used lots. The level of genotype 1 DNA contamination was similar in currently and previously administered concentrates. Genotype 2 DNA was found in 5/202 (2.5%) lots, all of which were co-contaminated with genotype 1 DNA. DNA sequence analysis showed that the PCR-double positive concentrates contained typical genotype 1 and genotype 2 DNA. Because genotype 2 appears to cause a similar spectrum of diseases as genotype 1, simultaneous detection of genotype 2 by nucleic acid amplification testing (NAT), now widely applied to plasma pools for genotype 1, would give an added level of safety to blood products.

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Co-infection of human parvovirus B19 in Vietnamese patients with hepatitis B virus infection

Journal of Hepatology ◽

10.1016/j.jhep.2006.03.013 ◽

2006 ◽

Vol 45 (3) ◽

pp. 361-369 ◽

Cited By ~ 20

Author(s):

Nguyen L. Toan ◽

Le H. Song ◽

Peter G. Kremsner ◽

Dinh N. Duy ◽

Vu Q. Binh ◽

...

Keyword(s):

Hepatitis B Virus ◽

Virus Infection ◽

Hepatitis B ◽

Parvovirus B19 ◽

Hepatitis B Virus Infection ◽

Human Parvovirus B19 ◽

B Virus

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

Journal of Clinical Microbiology ◽

10.1128/jcm.01201-09 ◽

2009 ◽

Vol 47 (11) ◽

pp. 3735-3738 ◽

Cited By ~ 44

Author(s):

J. M. Hubschen ◽

Z. Mihneva ◽

A. F. Mentis ◽

F. Schneider ◽

Y. Aboudy ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Parvovirus B19 ◽

Human Parvovirus B19 ◽

Genotype 1

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Incidence of positive DNA from Cytomegalovirus, Human Parvovirus B19 and Hepatitis B virus, at birth

Salud Pública de México ◽

10.1590/s0036-36342012000200004 ◽

2012 ◽

Vol 54 (2) ◽

pp. 105-106

Author(s):

Víctor Javier Lara-Díaz ◽

Víctor Arízaga-Ballesteros ◽

Adriana Garrido-Rodríguez ◽

Rolando Ruiz-de la Garza ◽

Jorge Eugenio Moreno-Cuevas

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Parvovirus B19 ◽

Human Parvovirus B19 ◽

B Virus

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Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1804921115 ◽

2018 ◽

Vol 115 (29) ◽

pp. 7557-7562 ◽

Cited By ~ 28

Author(s):

Barbara Mühlemann ◽

Ashot Margaryan ◽

Peter de Barros Damgaard ◽

Morten E. Allentoft ◽

Lasse Vinner ◽

...

Keyword(s):

Common Ancestor ◽

Parvovirus B19 ◽

Recent Common Ancestor ◽

Human Parvovirus B19 ◽

Genotype 1 ◽

Most Recent Common Ancestor ◽

Genotype 2 ◽

Order Of Magnitude ◽

The 1960S

Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to ∼70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9–99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from ∼0.5 to ∼6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed ∼12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to ∼5.0–6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.

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Identification and genetic diversity of two human parvovirus B19 genotype 3 subtypes

Journal of General Virology ◽

10.1099/vir.0.82496-0 ◽

2007 ◽

Vol 88 (2) ◽

pp. 428-431 ◽

Cited By ~ 48

Author(s):

Armen Parsyan ◽

Camille Szmaragd ◽

Jean-Pierre Allain ◽

Daniel Candotti

Keyword(s):

Genetic Diversity ◽

Parvovirus B19 ◽

Divergence Time ◽

Mutation Rates ◽

Human Parvovirus B19 ◽

Genotype 1 ◽

Genotype 3 ◽

Nucleotide Substitutions ◽

The Family

Three genotypes (1–3) of human parvovirus B19 have been identified. Analysis of 13 nearly full-length genotype 3 sequences from Ghana, Europe and Brazil identified two genetically distinct clusters. The classification of genotype 3 strains into two subtypes (B19/3a and B19/3b) is proposed. The rate of evolutionary change of B19 genotype 3 strains (2×10−4 nucleotide substitutions per site per year) was similar to those of B19 genotype 1 and carnivore parvoviruses, supporting the hypothesis that high mutation rates are characteristic of members of the family Parvoviridae. The estimated divergence time between B19/3a and B19/3b is 525 years. In Ghana, subtype B19/3a is predominant.

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Origin and Evolution of Emerging Liaoning Virus（genus Seadornavirus, family Reoviridae)

10.21203/rs.2.20915/v1 ◽

2020 ◽

Author(s):

Jun Zhang ◽

Hong Liu ◽

Jiahui Wang ◽

Jiheng Wang ◽

Jianming Zhang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Population Variation ◽

Central China ◽

Liaoning Province ◽

Western China ◽

Shanxi Province ◽

Genotype 1 ◽

Genotype 3 ◽

Long Distance ◽

Genotype 2

Abstract Background:Liaoning virus(LNV) is a member of the genus Seadornavirus, family Reoviridae and has been isolated from kinds of sucking insects in Asia and Australia. However, there are no systematic studies describe the molecular genetic evolution and migration of LNVs isolated from different time, regions and vectors.Methods:Here, a phylogenetic analysis using Bayesian Markov chain Monte Carlo simulations was conducted on the LNVs isolated from a variety of vectors during 1990-2014,worldwide. Results:The phylogenetic analysis demonstrated that the LNV could be divided into 3 genotypes, of which genotype 1 mainly composed of LNVs isolated from Australia during 1990 to 2014 as well as the original LNV strain(LNV-NE97-31) isolated from Liaoning province in northern China in 1997,genotype 2 comprised of the isolates all from Xinjiang province in western China and genotype 3 consisted the isolates from Qinghai and Shanxi province of central China. LNVs emerged about 272 years ago in Australia and gradually evolved into three LNV lineages in the order genotype1(at 73.0 years ago),genotype2(at 46.5 years ago)and genotype 3(at 25.3 years ago). Following further phylogeographic analysis, we proposed that Australia (113°E-153°E,10°S-42°S) was the source of LNVs and the genotype 1 LNVs transmitted from this region to Liaoning province(118°E-125°E,38°N-43°N) in Northeast Asian continent then further spread across the central part of China to Xinjiang province in western China(75°E-95°E,35°N-50°N).Conclusion: LNVs were initially isolated from Liaoning province of China in the Northeast Asia, however, the present study demonstrated that LNVs were originated from Australia in the South Pacific region and transmitted to mainland China then rapidly spread across China and evolved three different genotypes.The above results suggested that LNV had the characteristics of long-distance transmission and there were great genetic diversity existed in the LNV population. Therefore, it is of great importance to strengthen the monitoring of the population variation of LNV and maintain vigilance to avoid LNV breaking through the species barrier and further clarify its relationship to human and animal infection.

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