Whole genome detection of rotavirus mixed infections in human, porcine and bovine samples co-infected with various rotavirus strains collected from sub-Saharan Africa

Abstract

Group A rotaviruses (RVA) are among the main global causes of severe diarrhea in children under the age of 5 years. Strain diversity, mixed infections and untypeable RVA strains are frequently reported in Africa. We analysed rotavirus-positive human stool samples (n=13) obtained from hospitalised children under the age of 5 years who presented with acute gastroenteritis at sentinel hospital sites in six African countries, as well as bovine and porcine stool samples (n=1 each), to gain insights into rotavirus diversity and evolution. Polyacrylamide gel electrophoresis (PAGE) analysis and genotyping with G- (VP7) and P-specific (VP4) typing primers suggested that 13 of the 15 samples contained more than 11 segments and/or mixed G/P genotypes. Full-length amplicons for each segment were generated using RVA-specific primers and sequenced using the Ion Torrent and/or Illumina MiSeq next-generation sequencing platforms. Sequencing detected at least one segment in each sample for which duplicate sequences, often having distinct genotypes, existed. This supported and extended the PAGE and RT-PCR genotyping findings that suggested these samples were collected from individuals that had mixed rotavirus infections. The study reports the first porcine (MRC-DPRU1567) and bovine (MRC-DPRU3010) mixed infections. We also report a unique genome segment 9 (VP7), whose G9 genotype belongs to lineage VI and clusters with porcine reference strains. Previously, African G9 strains have all been in lineage III. Furthermore, additional RVA segments isolated from humans have a clear evolutionary relationship with porcine, bovine and ovine rotavirus sequences, indicating relatively recent interspecies transmission and reassortment. Thus, multiple RVA strains from sub-Saharan Africa are infecting mammalian hosts with unpredictable variations in their gene segment combinations. Whole-genome sequence analyses of mixed RVA strains underscore the considerable diversity of rotavirus sequences and genome segment combinations that result from a complex evolutionary history involving multiple host species.

Comparative In Vitro and In Vivo Studies of Porcine Rotavirus G9P[13] and Human Rotavirus Wa G1P[8]

“…Viral RNA was then extracted by using the RNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. Complete genome sequencing of PRV G9P [13] was conducted as previously described (39).…”

Porcine Rotaviruses: Epidemiology, Immune Responses and Control Strategies

“…The presence of group A, B, C and H porcine RVs has been confirmed in several African countries [65,117,121,122,123]. The prevalence of porcine RVA in Kenya and Uganda reported in the recent study by Amimo et al of 26.2% [65] was higher compared to the prevalence rates of 6.5%–25.7% reported for samples collected in 2004–2011 in the USA [65], several European countries [75,84,85], Thailand [89], and India [124], but however, lower (32.7%–38.3%) to those observed in Vietnam [74], Brazil [80] and Korea [76].…”

Unexpected detection of porcine rotavirus C strains carrying human origin VP6 gene

“…Among domesticated animals, the swine population witnesses infection by RVs such as RVA, RVB, RVC, RVE and RVH (Estes and Kapikian 2007;Wakuda et al 2011). Hitherto reports mention co-infection of different RV genotypes in pigs (Nyaga et al 2015). Hence, a chance for re-assortment in swine cannot be overlooked until the extensive screening of pig population for the presence of re-assorted or new RV types across the globe (Steyer et al 2007;Medici et al 2011;Sharma et al 2013;Navarro et al 2017).…”