Global Co-Existence of Two Evolutionary Lineages of Parvovirus B19 1a, Different in Genome-Wide Synonymous Positions

<div><p>Parvovirus B19 (B19V) can cause infection in humans. To date, three genotypes of B19V, with subtypes, are known, of which genotype 1a is the most prevalent genotype in the Western world. We sequenced the genome of B19V strains of 65 asymptomatic, recently infected Dutch blood donors, to investigate the spatio-temporal distribution of B19V strains, in the years 2003–2009. The sequences were compared to B19V sequences from Dutch patients with fifth disease, and to global B19V sequences as available from GenBank. All Dutch B19V strains belonged to genotype 1a. Phylogenetic analysis of the strains from Dutch blood donors showed that two groups of genotype 1a co-exist. A clear-cut division into the two groups was also found among the B19V strains from Dutch patients, and among the B19V sequences in GenBank. The two groups of genotype 1a co-exist around the world and do not appear to differ in their ability to cause disease. Strikingly, the two groups of B19V predominantly differ in synonymous mutations, distributed throughout the entire genome of B19V. We propose to call the two groups of B19V genotype 1a respectively subtype 1a1 and 1a2.</p> </div

Nucleotide diversity between B19V subtype 1a1 and 1a2.

<p>Shown are the variable nucleotides in B19V strains from Dutch blood donors, patients and global GenBank sequences (>4 kb), when a 51% consensus level was used. Along the top of the graph, the position of synonymous mutations (in grey) and the position of nonsynonymous mutations (in white) are depicted, along the B19V genome. In the coloured part each row represents a B19V strain. Strains in the upper part belong to B19V subtype 1a1, strains in the lower part are subtype 1a2. Position 3535–3544 and 4192–4216 are possible substitution hotspots. n.d. = not determined and Y = C or T. green = adenine, black = guanine, blue = cytosine, and red = thymine.</p

GenBank sequences used in this study.

<p>GenBank sequences used in this study.</p

Phylogenetic analysis of Dutch and global B19V 1a strains by Maximum Likelihood method.

<p>The tree with the highest log likelihood (−13872,9929) is shown. The bootstrap value for the B19V 1a1 cluster is shown. B19V sequences from blood donors are shown in blue, while global GenBank sequences are shown in black.</p

Phylogenetic relationship between the consensus sequences of B19V-1a subtypes found in blood donors (shown in pink) and the sequences found in patients with fifth disease (shown in black).

<p>The nucleotide distance relationship is shown for the 652 bp NS1-VP1u region (A) and the 669 bp VP2 (B) region.</p

Distribution of intra- and inter-group genetic distances.

<p>Distribution of intra- and inter-group genetic distances.</p

Primers used for PCR and sequencing of B19V in Dutch blood donors.

1<p>Numbering according to B19V GenBank sequence M13178. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043206#pone.0043206-Shade1" target="_blank">[9]</a></p

Graph showing the spatial distribution of B19V 1a1 and 1a2 in Dutch blood donors (A) and patients (B) fragment VP2.

<p>Graph showing the spatial distribution of B19V 1a1 and 1a2 in Dutch blood donors (A) and patients (B) fragment VP2.</p

Non-synonymous nucleotide sequence variations of HPV-18 L1.

<p>Non-synonymous nucleotide sequence variations of HPV-18 L1.</p

Maximum parsimony tree based on nucleotide sequences of L1 HPV-16 gene.

<p>Study sequences of 241 HPV-16 positive samples collected in 2009 and 2011 are shown in blue. Reference sequences of European/A lineages (GenBank reference AF536179 K02718 = NC001526, HQ644236, AF534061) are shown in green, African/B lineages (GenBank references AF472508, HQ644298 and AF536180) in brown. African-2/C lineage GenBank reference AF472509 is shown in pink. References sequences from lineage D are shown in purple HQ644257 (sublineage D1-North American), AY686579-(sublineage D2, Asian-American) AF402678 (sublineage D3, Asian-American). HPV-16 variant used in the vaccine (GenBank reference AF043286) is shown in red. The number given in each circle indicates the number of viral strains with the same sequence.</p