Prevalence and diversity of NoV in environmental samples from Africa.

<p>Prevalence and diversity of NoV in environmental samples from Africa.</p

Summary of NoV prevalence and diversity data from 19 studies conducted in 1976–1979, and between 1997 and 2013 in 14 African countries.

<p>Summary of NoV prevalence and diversity data from 19 studies conducted in 1976–1979, and between 1997 and 2013 in 14 African countries.</p

Map of Africa indicating the countries from which prevalence and diversity data was obtained (light blue) and countries where only NoV genotype data was available (dark blue).

<p>BF—Burkina Faso, BW—Botswana, CF—Central African Republic, CM—Cameroon, DJ—Djibouti, EG—Egypt, ET—Ethiopia, GH—Ghana, KE—Kenia, LY—Libya, MA—Morocco, MW—Malawi, NG—Nigeria, SN—Senegal, TN—Tunisia, TZ—Tanzania, ZA—South Africa. Reprinted from d-maps.com under a CC BY license, with permission from Daniel Dalet, original copyright 2007–2015 (<a href="http://d-maps.com/carte.php?num_car=737&lang=en" target="_blank">http://d-maps.com/carte.php?num_car=737&lang=en</a>).</p

Circulation of NoV GII.4 variants between 1998 and 2013 in 12 African countries.

<p>Circulation of NoV GII.4 variants between 1998 and 2013 in 12 African countries.</p

Additional NoV genotyping data from African studies which did not meet the inclusion criteria for prevalence estimates or only reported genotyping data.

<p>Additional NoV genotyping data from African studies which did not meet the inclusion criteria for prevalence estimates or only reported genotyping data.</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

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

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