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Countries globally are affected by the COVID-19 pandemic, with nearly two million cases and 120 000 deaths occurring within 4 months of the discovery of the severe acute respiratory syndrome coronavirus-2 in December 2019 in China. Accurate diagnoses of cases is key in managing the pandemic by identification, isolation and treatment of patients and defining the epidemiology of the virus. By mid-January 2020, a scientist from China published the full genome of the virus, which facilitated the development of accurate molecular diagnostic assays. By the end of January 2020, the WHO, in collaboration with laboratories in Asia, Europe and the USA, published several real-time reverse transcriptase PCR (rtRT-PCR) protocols that allowed identification of cases and development of commercial assays. Clinical investigations facilitated development of accurate case definition and guidance for laboratories on the optimum specimens and procedures for diagnoses. Currently, laboratory-based rtRT-PCR is the recommended test for diagnoses of acute cases to ensure patients can be identified and isolated and to facilitate the public health response. However, due to delays in diagnoses, severe shortage of tests and laboratory capacity, point-of-care molecular or antigen tests are becoming more attractive. Although serological tests are not suitable for diagnoses of acute cases, they are important to define epidemiological questions, including attack rate in the population, and to identify immune individuals. This review aimed to summarise the current available information for diagnoses of cases and to aid laboratories and healthcare workers to select the best assays and procedures.

We describe Shuni virus (SHUV) detection in human neurologic disease cases in South Africa. SHUV RNA was identified in 5% of cerebrospinal fluid specimens collected during the arbovirus season from public sector hospitals. This finding suggests that SHUV may be a previously unrecognized cause of human neurologic infections in Africa.

Reverse-zoonotic infections of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) from humans to wildlife species internationally raise concern over the emergence of new variants in animals. A better understanding of the transmission dynamics and pathogenesis in susceptible species will mitigate the risk to humans and wildlife occurring in Africa. Here we report infection of an exotic puma (July 2020) and three African lions (July 2021) in the same private zoo in Johannesburg, South Africa. One Health genomic surveillance identified transmission of a Delta variant from a zookeeper to the three lions, similar to those circulating in humans in South Africa. One lion developed pneumonia while the other cases had mild infection. Both the puma and lions remained positive for SARS-CoV-2 RNA for up to 7 weeks.

We detected Shuni virus in horses and ovine fetuses and Shamonda virus in a caprine fetus in South Africa. We identified a Shuni/Shamonda virus reassortant in a horse and Shuni/Caimito, Shamonda/Caimito, and Shamonda/Sango virus reassortants in Culicoides midges. Continued genomic surveillance will be needed to detect orthobunyavirus infections in Africa.

We collected >40,000 mosquitoes from 5 provinces in South Africa during 2011-2018 and screened for zoonotic flaviviruses. We detected West Nile virus in mosquitoes from conservation and periurban sites and potential new mosquito vectors; Banzi virus was rare. Our results suggest flavivirus transmission risks are increasing in South Africa.

Global genomic surveillance of SARS-CoV-2 has identified variants associated with increased transmissibility, neutralization resistance and disease severity. Here we report the emergence of the PANGO lineage C.1.2, detected at low prevalence in South Africa and eleven other countries. The initial C.1.2 detection is associated with a high substitution rate, and includes changes within the spike protein that have been associated with increased transmissibility or reduced neutralization sensitivity in SARS-CoV-2 variants of concern or variants of interest. Like Beta and Delta, C.1.2 shows significantly reduced neutralization sensitivity to plasma from vaccinees and individuals infected with the ancestral D614G virus. In contrast, convalescent donors infected with either Beta or Delta show high plasma neutralization against C.1.2. These functional data suggest that vaccine efficacy against C.1.2 will be equivalent to Beta and Delta, and that prior infection with either Beta or Delta will likely offer protection against C.1.2.

Collaboration and openness are essential to minimize the risks of future pandemics, says the World Health Organization’s scientific advisory group, SAGO. Collaboration and openness are essential to minimize the risks of future pandemics, says the World Health Organization’s scientific advisory group, SAGO. A team of researchers wearing full PPE catch bats at dusk

Background Next generation sequencing (NGS) has expanded virus detection capabilities beyond the limitations of sequence-specific methods. While mosquito collections in South Africa (SA) have been investigated for the major arbovirus genera ( Alpha -, Orthobunya-, and Orthoflavivirus ), research on insect-specific viruses (ISVs) is limited. Methods Here we used an RNA-sequencing viral-metagenomics approach to investigate arboviruses and ISVs in mosquitoes collected in SA. Ten archived mosquito pools, representing up to 50 mosquitoes per pool, previously tested for the major arbovirus genera were investigated for the presence of additional viruses using NGS. These pools included known arbovirus mosquito vectors from the Aedes , Anopheles , Culex , and Mansonia genera, collected from wildlife areas in the Kruger National Park (Mpumalanga/Limpopo) and rural areas of Jozini (KwaZulu-Natal). Extracted RNA was DNA-depleted, subjected to Sequence Independent Single Primer Amplification (SISPA), and sequenced on the Illumina MiSeq platform. Results Although no mammalian arboviruses were detected, bioinformatic analysis detected several ISVs in pools of Aedes aegypti , Ae.ochraceus , and Anopheles squamosus mosquitoes. These ISVs included the cell fusing agent-, Tesano aedes-, Fako-, formosus-, verdadero-, Aedes partiti-like virus 1 and the Kwale mosquito virus and several novel ISVs within the Iflavivirus genus as well as some unclassified viruses. Conclusion This study confirms the value of sequence independent metagenomics approaches to detect novel viruses in mosquito pools. Such studies provide insight into viral diversity and mosquito-virus interactions, supporting the future evaluation of ISVs as biological control agents. This in turn can contribute to protecting the health of animals and humans within a One Health approach.

Shuni virus is associated with neurologic and febrile illness in animals and humans. To determine potential vectors, we collected mosquitoes in South Africa and detected the virus in species of the genera Mansonia, Culex, Aedes, and Anopheles. These mosquitoes may be associated with Shuni virus outbreaks in Africa and emergence in other regions.