Full genomic characterization of a porcine rotavirus strain detected in an asymptomatic piglet in Accra, Ghana

Abstract

Background The introduction of rotavirus A vaccination across the developing world has not proved to be as efficacious as first hoped. One cause of vaccine failure may be infection by zoonotic rotaviruses that are very variable antigenically from the vaccine strain. However, there is a lack of genomic information about the circulating rotavirus A strains in farm animals in the developing world that may be a source of infection for humans. We therefore screened farms close to Accra, Ghana for animals sub-clinically infected with rotavirus A and then sequenced the virus found in one of these samples. Results 6.1% of clinically normal cows and pigs tested were found to be Rotavirus A virus antigen positive in the faeces. A subset of these (33.3%) were also positive for virus RNA. The most consistently positive pig sample was taken forward for metagenomic sequencing. This gave full sequence for all open reading frames except segment 5 (NSP1), which is missing a single base at the 5′ end. The virus infecting this pig had genome constellation G5-P[7]-I5-R1-C1-M1-A8-N1-T7-E1-H1, a known porcine genotype constellation. Conclusions Farm animals carry rotavirus A infection sub-clinically at low frequency. Although the rotavirus A genotype discovered here has a pig-like genome constellation, a number of the segments most closely resembled those isolated from humans in suspected cases of zoonotic transmission. Therefore, such viruses may be a source of variable gene segments for re-assortment with other viruses to cause vaccine breakdown. It is recommended that further human and pig strains are characterized in West Africa, to better understand this dynamic.

Effect of rotavirus genetic diversity on vaccine impact

“…Initially, rotaviruses were assumed to be host specific, and it was believed that this specificity was correlated with specific genotypes. 27 The discovery of genotypes in humans that have previously been identified in animals now indicates that RVA is capable of undergoing adaptations that enable interspecies transmission. 28 The increased risk of zoonotic RV transmission in developing countries could be explained by an insufficient supply of potable water, the absence of proper medical facilities and cohabitation with farm animals.…”

“…Initially, rotaviruses were assumed to be host specific, and it was believed that this specificity was correlated with specific genotypes 27 . The discovery of genotypes in humans that have previously been identified in animals now indicates that RVA is capable of undergoing adaptations that enable interspecies transmission 28 .…”

Emergence of human-porcine reassortment G9P[19] porcine rotavirus A strain in Guangdong Province, China

“…Phylogenetic analysis showed that the NSP1–NSP5 genes of GDJM1 were clustered into branches of A8, N1, T1, E1 and H1, respectively ( Figure 3 ). The NSP1 segment clustered with the A8 clade, and it is likely that GDJM1 segment has a porcine origin, as porcine isolates dominate this cluster ( 23 ). The NSP1 and NSP3 segments of GDJM1 were closely related to the human strains NT0077 and UFS-NGS-MRC-DPRU4723, with nucleotide identities of 95.63% and 96.69%, respectively.…”

Group A rotavirus gastroenteritis in orphaned Leopardus tigrinus and Leopardus pardalis (Carnivora: Felidae) in the Eastern Amazon

“…Although pigs and cattle may harbor group A RV infection sub-clinically at low frequency, further studies are urgently needed to better understand the dynamic of zoonotic risk involving transmission to humans 60,61 . Of note, the porcine genogroup E RVs are considered uncommon and its pathogenesis is not yet well elucidated.…”