First influenza D virus full-genome sequence retrieved from livestock in Namibia, Africa.

Influenza D virus (IDV) was first isolated in 2011 in the USA and has since been shown to circulate in cattle, pigs, sheep, wild boar, and camels. In Africa, there is limited data on the epidemiology of IDV and, so, we investigated the presence of IDV among domestic ruminants and wild animals in Namibia by screening nasal swabs using an IDV-specific molecular assay. IDV RNA was detected in bovines (n=2), giraffes (n=2) and wildebeest (n=1). The hemagglutinin-esterase-fusion (HEF) gene from one of the bovine and the wildebeest samples was successfully sequenced as well as the full genome for the second bovine sample. Phylogenetic analysis of the HEF gene positioned the African virus variants within the D/OK lineage but with a long branch. The African variant had an amino acid diversity of 2.41% and most likely represents a distinct genotype within the lineage. Notably, the polymerase acidic protein gene (PA) was more closely related to a different lineage (D/660), indicative of potential reassortment. This is the first genetic characterization of IDV in Africa and it adds important data to our understanding of the global IDV distribution.

The Oryx Antelope (Oryx gazella): An Unexpected Host for Porcine Circovirus-2 (PCV-2).

For several years after its discovery, Porcine circovirus 2 (PCV-2) represented a major threat to the swine industry through economic losses due to the associated clinical syndromes, decreased production performances in both symptomatic and asymptomatic animals and disease management costs. Widespread vaccination administration has largely reduced the impact of this infection and represents the most effective control measure. The efficacy of vaccination is threatened by the emergence of novel (or uncommon) PCV-2 genotypes. In addition to domestic pigs, PCV-2 has been detected in several other species, a fact which could have an impact on new variant emergence and maintenance. Considering this, the present study assessed the distribution of the minor PCV-2c genotype in non-Suidae ungulates in Namibia. Red hartebeests (Alcelaphus buselaphus caama) (n = 44), kudus (Tragelaphus strepsiceros) (n = 10) and oryxes (Oryx gazella) (n = 54), whose mediastinal lymph nodes were sampled after slaughtering during the period 2019-2021, were included in the study. Two oryxes (3.7%; 95% CI = 0.45-12.75%) were PCV-2-positive by PCR. Complete genome sequence was obtained for the two samples identifying them as PCV-2c genotype. The sequences were identical and shared a high percentage of identity (~99.9%) with those recently obtained from warthogs living in the same area. The present study confirms the presence of the PCV-2c genotype (previously considered extinct) in Namibian wild animal populations and demonstrates greater than expected PCV-2 host plasticity. Because of the role these niches can have in the maintenance and evolution of minor PCV-2 genotypes, more extensive and dedicated studies should be performed to prepare authorities to promptly react to potential emerging threats from these viruses.

The prevalence of non-O157:H7 Shiga toxin-producing Escherichia coli (STEC) in Namibian game meat.

Large game animals play an important role as carriers and transmitters of O157:H7 and non-O157:H7 Shiga toxin-producing Escherichia coli (STEC) in nature. Fresh meat obtained from game animals has been identified as an important source of food-borne STEC infections. The aim of this study was to evaluate the incidence of the top 6 non-O157 STEC strains (serogroups O26, O45, O103, O111, O121, and O145) in Namibian game meat based on testing for stx, eae, and O-group-specific genes. Meat samples from gemsboks (Oryx gazella) (n = 75), springboks (Antidorcas marsupialis) (n = 41), greater kudus (Tragelaphus strepsiceros) (n = 5), and wildebeests (Connochaetes taurinus) (n = 5) were collected from 2 Namibian abattoirs and tested for STEC using real-time PCR techniques. Both Shiga toxin (stx) and intimin (eae) virulence genes were detected in 94 out of 126 samples (74.6%). Five of the top 6 STEC serogroup-specific genes were also detected in samples that were positive for both the stx and eae genes. The results of this study show a high incidence of non-O157 STEC O-group genes in Namibian game meat, which suggests that further scrutiny and testing may be necessary to avoid foodborne outbreaks.