High detection frequency and genetic diversity of porcine circovirus 3 (PCV-3) in Namibian backyard farms and warthogs

Since its first identification in 2015, porcine circovirus 3 (PCV-3) has been reported worldwide with a high frequency and in the presence of several clinical conditions, although its impact on pig health and productivity is still debated. Data on the presence of PCV-3 in Africa are, however, limited. A previous study performed on commercial pigs in Namibia failed to identify the pathogen. In the present study, the viral circulation in backyard farms, characterised by lower biosecurity measures and frequent animal exchange between farms, was assessed. The susceptibility of warthogs to PCV-3 infection and their potential epidemiological role were also evaluated. Tonsils from 77 pigs from backyard piggeries and 55 warthogs were collected in different regions of Namibia and tested by PCR. Positive samples were sequenced and compared to PCV-3 strains circulating globally. Forty-two out of 77 pigs (54.54 %) and 12 out of 55 warthogs (21.82 %) tested positive, demonstrating the presence of PCV3 in the country and suggesting that the high biosecurity measures implemented in the commercial farms that previously tested negative for PCV-3 probably prevented viral introduction. The partial ORF2 gene was successfully sequenced in samples from 27 pigs and 6 warthogs. Genetically, the identified strains were part of 3 distinct groups which included both backyard pigs and warthogs from different regions of Namibia. There is also evidence for the occurrence of multiple introduction events most likely from Asian countries, either directly into Namibia or through other African countries. Considering the strict Namibian regulations on live animal importation, understanding the source of viral introduction is challenging, although semen importation or the habit of feeding backyard pigs with human food waste might have played a role. Pig exchanges between farms for breeding purposes or wildlife movements could also have been involved in PCV-3 dispersal within Namibia. Despite the significant advances in the field, further studies should be undertaken to properly understand PCV-3 epidemiology in Namibia and its impact on pig productivity and wildlife health.