In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild birds in Lesotho and Botswana. In this study, the complete or partial genomes of 117 viruses from the SA outbreaks in 2021–2022 were analyzed to decipher the sub-regional spread of the disease. Our analysis showed that seven H5N1 sub-genotypes were associated with the initial outbreaks, but by late 2022 only two sub-genotypes still circulated. Furthermore, SA poultry was not the source of Lesotho’s outbreaks, and the latter was most likely an introduction from wild birds. Similarly, SA and Botswana’s outbreaks in 2021 were unrelated, but viruses of Botswana’s unique sub-genotype were introduced into SA later in 2022 causing an outbreak in ostriches. At least 83% of SA’s commercial poultry cases in 2021–2022 were point introductions from wild birds. Like H5N8 HPAI in 2017–2018, a coastal seabird-restricted sub-lineage of H5N1 viruses emerged in the Western Cape province in 2021 and spread to Namibia, causing mortalities in Cape Cormorants. In SA ~24,000 of this endangered species died, and the loss of >300 endangered African penguins further threatens biodiversity.

DNA samples from 74 patients with non-malarial acute febrile illness (AFI), 282 rodents, 100 cattle, 56 dogs and 160 Rhipicephalus sanguineus ticks were screened for the presence of Anaplasma phagocytophilum DNA using a quantitative PCR (qPCR) assay targeting the msp2 gene. The test detected both A. phagocytophilum and Anaplasma sp. SA/ZAM dog DNA. Microbiome sequencing confirmed the presence of low levels of A. phagocytophilum DNA in the blood of rodents, dogs and cattle, while high levels of A. platys and Anaplasma sp. SA/ZAM dog were detected in dogs. Directed sequencing of the 16S rRNA and gltA genes in selected samples revealed the presence of A. phagocytophilum DNA in humans, dogs and rodents and highlighted its importance as a possible contributing cause of AFI in South Africa. A number of recently described Anaplasma species and A. platys were also detected in the study. Phylogenetic analyses grouped Anaplasma sp. SA/ZAM dog into a distinct clade, with sufficient divergence from other Anaplasma species to warrant classification as a separate species. Until appropriate type-material can be deposited and the species is formally described, we will refer to this novel organism as Anaplasma sp. SA dog.

Migratory birds carried clade 2.3.4.4B H5Nx highly pathogenic avian influenza (HPAI) viruses to South Africa in 2017, 2018 and 2021, where the Gauteng Province is a high-risk zone for virus introduction. Here, we combined environmental faecal sampling with sensitive rRT-PCR methods and direct Ion Torrent sequencing to survey wild populations between February and May 2022. An overall IAV incidence of 42.92% (100/231) in water bird faecal swab pools or swabs from moribund or dead European White Storks (Ciconia ciconia) was detected. In total, 7% of the IAV-positive pools tested H5-positive, with clade 2.3.4.4B H5N1 HPAI confirmed in the storks; 10% of the IAV-positive samples were identified as H9N2, and five complete H9N2 genomes were phylogenetically closely related to a local 2021 wild duck H9N2 virus, recent Eurasian LPAI viruses or those detected in commercial ostriches in the Western and Eastern Cape Provinces since 2018. H3N1, H4N2, H5N2 and H8Nx subtypes were also identified. Targeted surveillance of wild birds using environmental faecal sampling can thus be effectively applied under sub-Saharan African conditions, but region-specific studies should first be used to identify peak prevalence times which, in southern Africa, is linked to the peak rainfall period, when ducks are reproductively active.

Background: Schistosomiasis, also known as bilharzia, is a chronic parasitic blood fluke infection acquired through contact with contaminated surface water. The illness may be mild or can cause significant morbidity with potentially serious complications. Children and those living in rural areas with limited access to piped water and services for healthcare are the most commonly infected. To address the prevalence of the disease in parts of South Africa (SA) effective national control measures are planned, but have not yet been implemented. This study aimed to estimate the prevalence and trends of public sector laboratory-confirmed schistosomiasis cases in SA over an eight-year (2011–2018) period, to inform future control measures. Methodology & principal findings: This is a descriptive analysis of secondary data from the National Health Laboratory Service (NHLS). The study included all records of patients for whom microscopic examination detected Schistosoma species eggs in urine or stool specimens from January 2011 to December 2018. Crude estimates of the prevalence were calculated using national census mid-year provincial population estimates as denominators, and simple linear regression was used to analyse prevalence trends. A test rate ratio was developed to describe variations in testing volumes among different groups and to adjust prevalence estimates for testing variations. A total number of 135 627 schistosomiasis cases was analysed with the highest prevalence observed among males and individuals aged 5–19 years. We describe ongoing endemicity in the Eastern Cape Province, and indicate important differences in the testing between population groups. Conclusion: While there was no overall change in the prevalence of schistosomiasis during the analysis period, an average of 36 people per 100 000 was infected annually. As such, this represents an opportunity to control the disease and improve quality of life of affected people. Laboratory-based surveillance is a useful method for reporting occurrence and evaluating future intervention programs where resources to implement active surveillance are limited.

Since 2012, outbreaks of African swine fever (ASF) in domestic pigs have increased outside of South Africa's ASF control zone. This study describes the epidemiological investigation and findings of an ASF outbreak in a small-scale pig unit in Gauteng Province and makes recommendations to prevent future outbreaks. Polymerase chain reaction testing and molecular analysis were performed on pig tissue samples. Veterinary services conducted epidemiological investigations, forward and backward tracing and surveillance. Farm management and biosecurity practices were assessed. Quarantine, culling, carcass disposal and disinfection were implemented. ASF virus genotype I was detected. A concurrent ASF outbreak in neighbouring Mpumalanga Province was identified as a possible source. Inadequate biosecurity measures probably facilitated viral transmission. Potential mechanisms for the introduction of the ASF virus include swill feeding practices, free roaming of pigs, scavenging, illegal slaughter and trade of pig products within the community. Molecular typing of the ASF virus linked the outbreak with an ongoing ASF outbreak in Mpumalanga Province. Pig enterprises with poor biosecurity practices may face greater risk of ASF introduction. Small-scale pig keepers should be targeted for ASF awareness and education campaigns. Innovative and cost-effective biosecurity solutions are needed in this resource-poor setting.

Abattoir workers may contract Q fever by inhalation of Coxiella burnetii bacteria in aerosols generated by slaughtering livestock, or in contaminated dust. We estimated the seroprevalence of C. burnetii and examined the associated factors in a survey of South African abattoir workers. Coxiella burnetii seropositivity was determined by detection of IgG antibodies against C. burnetii phase II antigen. Logistic regression, adjusted for clustering and sampling fraction, was employed to analyze risk factors associated with C. burnetii seropositivity. Among 382 workers from 16 facilities, the overall seroprevalence was 33% (95% confidence interval (CI): 28–38%) and ranged from 8% to 62% at the facility level. Prolonged contact with carcasses or meat products (odds ratio (OR): 4.6, 95% CI: 1.51–14.41) and prior abattoir or butchery work experience (OR: 1.9, 95% CI: 1.13–3.17) were associated with C. burnetii seropositivity. In contrast, increasing age and livestock ownership were inversely associated. Precautions to protect abattoir personnel from Q fever are discussed.