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1.
Nat Med ; 2022 Jun 27.
Article in English | MEDLINE | ID: covidwho-1908212

ABSTRACT

Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.

2.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-335264

ABSTRACT

South Africa’s fourth COVID-19 wave was driven predominantly by three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern. We have now identified two new lineages, BA.4 and BA.5. The spike proteins of BA.4 and BA.5 are identical, and comparable to BA.2 except for the addition of 69-70del, L452R, F486V and the wild type amino acid at Q493. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure with the TaqPath™ COVID-19 qPCR assay. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa from the first week of April 2022 onwards. Using a multinomial logistic regression model, we estimate growth advantages for BA.4 and BA.5 of 0.08 (95% CI: 0.07 - 0.09) and 0.12 (95% CI: 0.09 - 0.15) per day respectively over BA.2 in South Africa.

3.
Interdiscip Perspect Infect Dis ; 2022: 2663174, 2022.
Article in English | MEDLINE | ID: covidwho-1789041

ABSTRACT

The Princess Marina Hospital in Gaborone, Botswana, had an outbreak of COVID-19 from early August 2020. The aim of this paper was to describe the outbreak investigation. The investigation's specific objectives were to describe the COVID-19 cases in terms of person, place, and time (PPT) and to determine measures to prevent further transmission of the infection. The data reported herein were collected over a 3-month period from beginning of August to end of October 2020. The investigation included all COVID-19 cases i.e. both patients and healthcare workers. It followed the steps of an outbreak investigation. These included assembling an investigation team comprising both the hospital and DHMT staff. All the wards reported their confirmed cases to the infection control team who in turn prepared line lists and case reports. Epicurves were produced from date of positive result. A total of 193 cases were reported, of which 110 (57.0%) were patients and 83 (43.0%) were healthcare workers. The median age was 35 years. Females accounted for 154 (79.8%) participants. Most of the wards were affected. The wards with the highest numbers of cases were female medical ward (39), emergency department (24), gynecology ward (17), and pediatric medical ward (10). Control measures included restricting movement into the hospital as well as clinical screening at all entry points. Furthermore, all patients were tested before admission into the wards. Surveillance of COVID-19 cases was continued beyond the 3 months reported in this paper. COVID-19 can spread rapidly in hospital settings affecting both patients and healthcare workers. Outbreak investigations including describing cases in terms of person, place, and time are critical if the most effective and efficient control measures are to be implemented.

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