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.
