Data_Sheet_1_Genetic diversity of murine norovirus populations less susceptible to chlorine.pdf

High genetic diversity in RNA viruses contributes to their rapid adaptation to environmental stresses, including disinfection. Insufficient disinfection can occur because of the emergence of viruses that are less susceptible to disinfection. However, understanding regarding the mechanisms underlying the alteration of viral susceptibility to disinfectants is limited. Here, we performed an experimental adaptation of murine norovirus (MNV) using chlorine to understand the genetic characteristics of virus populations adapted to chlorine disinfection. Several MNV populations exposed to an initial free chlorine concentration of 50 ppm exhibited reduced susceptibility, particularly after the fifth and tenth passages. A dominant mutation identified using whole-genome sequencing did not explain the reduced susceptibility of the MNV populations to chlorine. Conversely, MNV populations with less susceptibility to chlorine, which appeared under higher chlorine stress, were accompanied by significantly lower synonymous nucleotide diversity (πS) in the major capsid protein (VP1). The nonsynonymous nucleotide diversity (πN) in VP1 in the less-susceptible populations was higher than that in the susceptible populations, although the difference was not significant. Therefore, the ability of MNV populations to adapt to chlorine was associated with the change in nucleotide diversity in VP1, which may lead to viral aggregate formation and reduction in chlorine exposure. Moreover, the appearance of some nonsynonymous mutations can also contribute to the alteration in chlorine susceptibility by influencing the efficiency of viral replication. This study highlights the importance of understanding the genetic characteristics of virus populations under disinfection, which can contribute to the development of effective disinfection strategies and prevent the development of virus populations less susceptible to disinfectants.</p

Identification of Novel Ghanaian G8P[6] Human-Bovine Reassortant Rotavirus Strain by Next Generation Sequencing

<div><p>Group A rotaviruses (RVAs) are the most important etiological agent of acute gastroenteritis in children <5 years of age worldwide. The monovalent rotavirus vaccine Rotarix was introduced into the national Expanded Programme on Immunization (EPI) in Ghana in May 2012. However, there is a paucity of genetic and phylogenetic data on the complete genomes of human RVAs in circulation pre-vaccine introduction. The common bovine rotavirus VP7 genotype G8 has been sporadically detected in Ghanaian children, usually in combination with the VP4 genotype P[6]. To investigate the genomic constellations and phylogeny of RVA strains in circulation prior to vaccine introduction, the full genomes of two unusual G8P[6] strains, GH018-08 and GH019-08, detected during burden of disease surveillance, were characterized by Illumina MiSeq sequencing. The Ghanaian isolates, GH018-08 and GH019-08, exhibited the unusual, previously unreported genotype constellation G8-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H3. Phylogenetic analyses confirmed that 10 out of the 11 genes of GH018-08 and GH019-08 were identical/nearly identical, with significant variation detected only in their VP1 genes, and clearly established the occurrence of multiple independent interspecies transmission and reassortment events between co-circulating bovine/ovine/caprine rotaviruses and human DS-1-like RVA strains. These findings highlight the contribution of reassortment and interspecies transmission events to the high rotavirus diversity in this region of Africa, and justify the need for simultaneous monitoring of animal and human rotavirus strains.</p></div

Phylograms based on the full-length open reading frame (ORF) nucleotide sequences of VP6, VP1, VP2 and VP3 encoding genome segments of RVA strains GH018-08 and GH019-08 indicating genetic relationships with cognate RVA genes.

<p>See Legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100699#pone-0100699-g001" target="_blank">Figure 1</a>.</p

Genotype constellation of GH018-08 and GH019-08 with selected reference RVA strains of known genomic constellation.

a<p>RVA strain names according to proposed nomenclature of new classification system. <b>Boldface</b> font indicates RVA strains sequenced in this study. GenBank accession numbers for reference strains are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100699#pone.0100699.s003" target="_blank">Table S2</a>.</p>b<p>DS-1-like genotypes indicated by <b>boldface</b> font;</p>†<p>Typical bovine-like RVA genotypes.</p>‡<p>AU-1-like genotype.</p

Phylograms based on the full-length open reading frame (ORF) nucleotide sequences of VP7 and VP4 encoding genome segments of RVA strains GH018-08 and GH019-08 indicating genetic relationships with cognate RVA genes.

<p>Neighbour-Joining trees were constructed and rooted with cognate genes of the avian RVA strain PO-13 using MEGA v6.06 software. Only the genotypes in which study strains cluster are shown completely. GH018-08 and GH019-08 are shown in boldface and indicated by a blue, closed circle, animal strains by a black closed box, reported human-artiodactyl reassortant strains by a closed pink box, multiple reassortant bovine-feline/canine-human strains by an open pink circle, and African human strains by an open red triangle. Significant bootstrap values (2000 replicates) of ≥80% are shown. Bar: nucleotide substitutions per site. GenBank Accession numbers for all strains are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100699#pone.0100699.s003" target="_blank">Table S2</a>.</p

Summary of partial characterization data for GH018-08 and GH019-08.

<p>N/A: Not available; EIA: Enzyme Immunoassay; Neg: Negative; +: positive; L: Long electropherotype by PAGE; H: hospitalization as a measure of severity of rotavirus infection, G?: G-type not available</p

Emergence and Characterization of Unusual DS-1-Like G1P[8] Rotavirus Strains in Children with Diarrhea in Thailand

<div><p>The emergence and rapid spread of unusual DS-1-like G1P[8] rotaviruses in Japan have been recently reported. During rotavirus surveillance in Thailand, three DS-1-like G1P[8] strains (RVA/Human-wt/THA/PCB-180/2013/G1P[8], RVA/Human-wt/THA/SKT-109/2013/G1P[8], and RVA/Human-wt/THA/SSKT-41/2013/G1P[8]) were identified in stool specimens from hospitalized children with severe diarrhea. In this study, we sequenced and characterized the complete genomes of strains PCB-180, SKT-109, and SSKT-41. On whole genomic analysis, all three strains exhibited a unique genotype constellation including both genogroup 1 and 2 genes: G1-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. This novel genotype constellation is shared with Japanese DS-1-like G1P[8] strains. Phylogenetic analysis revealed that the G/P genes of strains PCB-180, SKT-109, and SSKT-41 appeared to have originated from human Wa-like G1P[8] strains. On the other hand, the non-G/P genes of the three strains were assumed to have originated from human DS-1-like strains. Thus, strains PCB-180, SKT-109, and SSKT-41 appeared to be derived through reassortment event(s) between Wa-like G1P[8] and DS-1-like human rotaviruses. Furthermore, strains PCB-180, SKT-109, and SSKT-41 were found to have the 11-segment genome almost indistinguishable from one another in their nucleotide sequences and phylogenetic lineages, indicating the derivation of the three strains from a common origin. Moreover, all the 11 genes of the three strains were closely related to those of Japanese DS-1-like G1P[8] strains. Therefore, DS-1-like G1P[8] strains that have emerged in Thailand and Japan were assumed to have originated from a recent common ancestor. To our knowledge, this is the first report on whole genome-based characterization of DS-1-like G1P[8] strains that have emerged in an area other than Japan. Our observations will provide important insights into the evolutionary dynamics of emerging DS-1-like G1P[8] rotaviruses.</p></div

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15 mars 19401940/03/15 (A69).Appartient à l’ensemble documentaire : PoitouCh

Genomic dsRNA profiles of strains PCB-180, SKT-109, and SSKT-41.

<p>Lanes 1–2, dsRNAs of strains KU (G1P[8]) (lane 1) and DS-1 (G2P[4]) (lane 2) extracted from the cell cultures; and lanes 3–5, dsRNAs of strains PCB-180 (lane 3), SKT-109 (lane 4), and SSKT-41 (lane 5) extracted from stool samples. The numbers on the left indicate the order of the genomic dsRNA segments of strain KU.</p

Phylogenetic tree constructed from the nucleotide sequences of the VP2 genes of strains PCB-180, SKT-109, and SSKT-41, and representative RVA strains.

<p>See legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141739#pone.0141739.g003" target="_blank">Fig 3</a>. Scale bar: 0.02 substitutions per nucleotide.</p