Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa.

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection

Retraction.

This is a retraction of 'Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa' 10.1126/science.add873

Recovery of enteroviruses and poliovirus in Harare sewage using the bag-mediated filtration system at the introduction of the inactivated polio vaccine in Zimbabwe

Environmental surveillance is a sensitive method for detecting circulating virus in the absence of clinical cases and is important for monitoring progress for poliovirus (PV) eradication. This study used the bag-mediated filtration system (BMFS) to determine PV and enterovirus (EV) prevalence in sewage at the transition from oral polio vaccine type 2 (OPV2) use to inactivated polio vaccine (IPV) use in Zimbabwe, and examined the correlation between environmental surveillance results and vaccination coverage of OPV. A total of 18 BMFS samples from 6 sampling sites were analysed for the presence of EV and PV via direct RT-qPCR, direct ITD (intratypic differentiation), and the WHO algorithm. EV prevalence in Harare wastewater was 88.9% (16/18) using direct RT-PCR, 61.1% (11/18) using direct ITD, and 77.8% (14/18) using the WHO algorithm. Of the 18 samples analysed using the WHO algorithm, 10 samples (55.6%) were positive for Sabin-like PV type 3 (SL3). Of these 10 samples, 2 were also positive for non-polio enteroviruses (NPEV), resulting in a total of 6 (33.3%) samples positive for NPEV and 4 negative. The sensitivity of isolation in detecting EVs in sewage was 92.9% when comparing direct RT-qPCR results to the WHO algorithm. Using direct ITD, two high-density, low-income sampling sites were negative for SL3 and one low-density, high-income sampling point was negative for SL3 using the WHO algorithm. There was a strong association between relative EV concentration and the number of OPV3 vaccine recipients (r = 0.8590; p = 0.0284) in sampled areas. This study demonstrated the ability of BMFS to detect PVs circulating in Harare wastewater at the beginning of the OPV–IPV switch and can be used to monitor potential reintroduction of wild PV or vaccine-derived PVs from endemic areas