Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern

Mashe, Tapfumanei; Takawira, Faustinos Tatenda; Gumbo, Hlanai; Juru, Agnes; Nyagupe, Charles; Maeka, Kenneth K; Mtapuri-Zinyowera, Sekesai; Gudza-Mugabe, Muchaneta; Martins, Leonardo de Oliveira; O’Grady, Justin; Kingsley, Robert A.; Page, Andrew J.; Simbi, Raiva

doi:10.1016/s2666-5247(21)00061-6

Cited by 10 publications

(9 citation statements)

References 2 publications

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“…With the emergence of multiple VOCs, the WHO has encouraged genomic surveillance worldwide. Rapid genome sequencing has been used widely in public health, in investigation of outbreaks [14], identification of novel VOCs [15,16], and tracking the source and spread of variants [17].…”

Section: Introductionmentioning

confidence: 99%

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

et al. 2022

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The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 % of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks.

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Section: Introductionmentioning

confidence: 99%

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

et al. 2022

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“…The lockdown introduced a 6am – 6pm curfew and a ban on public gatherings and intercity travel with the exception of essential travel including commercial cargo. The second wave in Zimbabwe was associated with the emergence of a new SARS-CoV-2 variant B.1.351 (beta variant) in South Africa [3] , which was subsequently also detected in Zimbabwe [4] . Prior to the ongoing third wave, a traveller returning from India was found to have a SARS-CoV-2 infection with the delta variant (B.1.617.2), which is thought to be more transmissible and likely driving the current third wave in Zimbabwe [5] .…”

Section: Introductionmentioning

confidence: 99%

Community SARS-CoV-2 seroprevalence before and after the second wave of SARS-CoV-2 infection in Harare, Zimbabwe

et al. 2021

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Background By the end of July 2021 Zimbabwe, has reported over 100,000 SARS-CoV-2 infections. The true number of SARS-CoV-2 infections is likely to be much higher. We conducted a seroprevalence survey to estimate the prevalence of past SARS-CoV-2 in three high-density communities in Harare, Zimbabwe before and after the second wave of SARS-CoV-2. Methods Between November 2020 and April 2021 we conducted a cross-sectional study of randomly selected households in three high-density communities (Budiriro, Highfield and Mbare) in Harare. Consenting participants answered a questionnaire and a dried blood spot sample was taken. Samples were tested for anti-SARS-CoV-2 nucleocapsid antibodies using the Roche e801 platform. Findings A total of 2340 individuals participated in the study. SARS-CoV-2 antibody results were available for 70·1% (620/885) and 73·1% (1530/2093) of eligible participants in 2020 and 2021. The median age was 22 (IQR 10-37) years and 978 (45·5%) were men. SARS-CoV-2 seroprevalence was 19·0% (95% CI 15·1-23·5%) in 2020 and 53·0% (95% CI 49·6-56·4) in 2021. The prevalence ratio was 2·47 (95% CI 1·94-3·15) comparing 2020 with 2021 after adjusting for age, sex, and community. Almost half of all participants who tested positive reported no symptoms in the preceding six months. Interpretation Following the second wave, one in two people had been infected with SARS-CoV-2 suggesting high levels of community transmission. Our results suggest that 184,800 (172,900-196,700) SARS-CoV-2 infections occurred in these three communities alone, greatly exceeding the reported number of cases for the whole city. Further seroprevalence surveys are needed to understand transmission during the current third wave despite high prevalence of past infections. Funding GCRF, Government of Canada, Wellcome Trust, Bavarian State Ministry of Sciences, Research, and the Arts

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“…Funding and training from the African Centre for Disease Control and Prevention (Africa CDC) and Quadram Biosciences Institute (QIB, United Kingdom) has boosted SARS-CoV-2 sequencing in Zimbabwe. A report of the first data on SARS-CoV-2 sequencing in Zimbabwe revealed that the B.1.351 VOC, originally identified in South Africa was present in 74 (69%) of 107 sequenced cases in December 2020, and 99 (95%) of 104 sequenced cases in January 2021 ( Mashe, T., Takawira, F. T., Gumbo, H., Juru, A., Nyagupe, C., Maeka, K. K., et al., 2021 ). As of 18 July 2021, Zimbabwe has submitted a total of 558 SARS-CoV-2 sequences to the GISAID database.…”

Section: What Efforts Have Been Made For Sequencing In Zimbabwe?mentioning

confidence: 99%

Inadequate SARS-CoV-2 Genetic Sequencing capacity in Zimbabwe: A call to urgently address this key gap to control current and future waves

Dzobo¹,

Musuka²,

Mashe³

et al. 2021

IJID Regions

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Zimbabwe continues to confront the COVID-19 pandemic; there is an urgent need for the rapid scale-up of genomic surveillance efforts. In this piece, we express concern on the limited capacity for SARS-CoV-2 genomic surveillance in Zimbabwe due to limited skillsets and laboratory infrastructural deficiencies. We call for an urgent need for funding from the government of Zimbabwe to set up a robust genomic surveillance program to detect SARS-CoV-2 variants of concern in Zimbabwe and guide public health responses accordingly.

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Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern

Cited by 10 publications

References 2 publications

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

Community SARS-CoV-2 seroprevalence before and after the second wave of SARS-CoV-2 infection in Harare, Zimbabwe

Inadequate SARS-CoV-2 Genetic Sequencing capacity in Zimbabwe: A call to urgently address this key gap to control current and future waves

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