Detection of B.1.351 SARS-CoV-2 Variant Strain — Zambia, December 2020

Mwenda, Mulenga; Saasa, Ngonda; Sinyange, Nyambe; Busby, George B.J.; Chipimo, Peter J.; Hendry, Jason A.; Kapona, Otridah; Yingst, Samuel L.; Hines, Jonas Z; Minchella, P.; Simulundu, Edgar; Changula, Katendi; Nalubamba, King S.; Sawa, Hirofumi; Kajihara, Masahiro; Yamagishi, Junya; Kapina, Muzala; Kapata, Nathan; Fwoloshi, Sombo; Zulu, Paul Msanzya; Mulenga, Lloyd; Agolory, Simon; Mukonka, Victor; Bridges, Daniel J.

doi:10.15585/mmwr.mm7008e2

Cited by 126 publications

(89 citation statements)

References 2 publications

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“…At the time of writing, Zambia was experiencing a second wave of SARS-CoV-2 infections that began in mid-December, 2020, which coincided with detection of the more transmissible SARS-CoV-2 501Y.V2 (B.1.351) variant, first detected in South Africa. 24 56•5% of reported confirmed cases in Zambia to July 31, 2020, were in Lusaka District (ZNPHI). However, no significant differences in SARS-CoV-2 prevalence estimates were identified between the six districts in our study.…”

Section: Discussionmentioning

confidence: 99%

Prevalence of SARS-CoV-2 in six districts in Zambia in July, 2020: a cross-sectional cluster sample survey

Mulenga¹,

Hines²,

Fwoloshi³

et al. 2021

The Lancet Global Health

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128

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Background Between March and December, 2020, more than 20 000 laboratory-confirmed cases of SARS-CoV-2 infection were reported in Zambia. However, the number of SARS-CoV-2 infections is likely to be higher than the confirmed case counts because many infected people have mild or no symptoms, and limitations exist with regard to testing capacity and surveillance systems in Zambia. We aimed to estimate SARS-CoV-2 prevalence in six districts of Zambia in July, 2020, using a population-based household survey. Methods Between July 4 and July 27, 2020, we did a cross-sectional cluster-sample survey of households in six districts of Zambia. Within each district, 16 standardised enumeration areas were randomly selected as primary sampling units using probability proportional to size. 20 households from each standardised enumeration area were selected using simple random sampling. All members of selected households were eligible to participate. Consenting participants completed a questionnaire and were tested for SARS-CoV-2 infection using real-time PCR (rtPCR) and anti-SARS-CoV-2 antibodies using ELISA. Prevalence estimates, adjusted for the survey design, were calculated for each diagnostic test separately, and combined. We applied the prevalence estimates to census population projections for each district to derive the estimated number of SARS-CoV-2 infections. Findings Overall, 4258 people from 1866 households participated in the study. The median age of participants was 18•2 years (IQR 7•7-31•4) and 50•6% of participants were female. SARS-CoV-2 prevalence for the combined measure was 10•6% (95% CI 7•3-13•9). The rtPCR-positive prevalence was 7•6% (4•7-10•6) and ELISA-positive prevalence was 2•1% (1•1-3•1). An estimated 454 708 SARS-CoV-2 infections (95% CI 312 705-596 713) occurred in the six districts between March and July, 2020, compared with 4917 laboratory-confirmed cases reported in official statistics from the Zambia National Public Health Institute. Interpretation The estimated number of SARS-CoV-2 infections was much higher than the number of reported cases in six districts in Zambia. The high rtPCR-positive SARS-CoV-2 prevalence was consistent with observed community transmission during the study period. The low ELISA-positive SARS-CoV-2 prevalence might be associated with mitigation measures instituted after initial cases were reported in March, 2020. Zambia should monitor patterns of SARS-CoV-2 prevalence and promote measures that can reduce transmission. Funding US Centers for Disease Control and Prevention.

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Section: Discussionmentioning

confidence: 99%

Prevalence of SARS-CoV-2 in six districts in Zambia in July, 2020: a cross-sectional cluster sample survey

Mulenga¹,

Hines²,

Fwoloshi³

et al. 2021

The Lancet Global Health

Self Cite

128

111

View full text Add to dashboard Cite

show abstract

“…The SARS-CoV-2 lineage B.1.351 (also known as 501Y.V2) was first identified in October 2020 in South Africa—Eastern Cape Province and quickly spread throughout the country [ 45 , 46 ]. Detection of the B.1.351 variant occurred simultaneously with a rapid increase of confirmed COVID-19 cases in Zambia.…”

Section: Variant Of Concernmentioning

confidence: 99%

“…Among the 23 individuals’ samples collected during one week in December 2020, 96% were the B.1.351 variant. Among 245 formerly sequenced genomes, none were from this lineage [ 45 ]. In the European Union/European Economic Area (EU/EEA), approximately 350 cases have been detected in 16 countries.…”

Section: Variant Of Concernmentioning

confidence: 99%

The Emerging Concern and Interest SARS-CoV-2 Variants

et al. 2021

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for coronavirus disease 2019 (COVID-19) was discovered in December 2019 in Wuhan, China. Since that time, the virus has spread around the world, which resulted in an announcement of the World Health Organization (WHO), dated in March 2020, that COVID-19 was a worldwide pandemic, and since then, the world has been struggling with this disease. SARS-CoV-2, similar to other RNA viruses, continually mutates, and new variants are appearing. Among large numbers of detected SARS-CoV-2 variants, only an insignificant amount of them are able to pose a risk to public health, as they are more contagious and cause more severe conditions. The emerged variants were classified by the Centers for Disease Control and Prevention (CDC) in collaboration with SARS-CoV-2 Interagency Group (SIG) according to strictly defined pattern. Variants were classified as variants of concern, variants of interest, and variants of high consequence. In the last few months, three variants of concern (B.1.1.7, B.1.351, and P.1) and four variants of interests (B.1.526, B.1.525, B.1.427/B.1.429, and P.2) were distinguished and are essential for close monitoring. This analysis summarizes the principal information concerning SARS-CoV-2 variants, such as their infectivity, severity, mutations, and immune susceptibility.

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“…The growing lineage B.1.1.7 16 carrying N501Y (N501Y.v1) is identified to be with increased infectivity and capability to reduce the activity of neutralization 17 . Following B.1.1.7, another lineage B.1.351 18 was identified and considered the second version of N501Y variants (N501Y.v2). This lineage includes another S mutation E484K, which is capable of evading the neutralization of most monoclonal antibodies 19 .…”

Section: Introductionmentioning

confidence: 99%

Nucleocapsid mutation R203K/G204R increases the infectivity, fitness and virulence of SARS-CoV-2

Xing

Meng

et al. 2021

Preprint

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In addition to the mutations on the spike protein (S), co-occurring mutations on nucleocapsid (N) protein are also emerging in SARS-CoV-2 world widely. Mutations R203K/G204R on N, carried by high transmissibility SARS-CoV-2 lineages including B.1.1.7 and P.1, has a rapid spread in the pandemic during the past year. In this study, we performed comprehensive population genomic analyses and virology experiment concerning on the evolution, causation and virology consequence of R203K/G204R mutations. The global incidence frequency (IF) of 203K/204R has rose up from nearly zero to 76% to date with a shrinking from August to November in 2020 but bounced later. Our results show that the emergence of B.1.1.7 is associated with the second growth of R203K/G204R mutants. We identified positive selection evidences that support the adaptiveness of 203K/204R variants. The R203K/G204R mutant virus was created and compared with the native virus. The virus competition experiments show that 203K/204R variants possess a replication advantage over the preceding R203/G204 variants, possibly in relation to the ribonucleocapsid (RNP) assemble during the virus replication. Moreover, the 203K/204R virus increased the infectivity in a human lung cell line and induced an enhanced damage to blood vessel of infected hamsters' lungs. In consistence, we observed a positive association between the increased severity of COVID-19 and the IF of 203K/204R from in silicon analysis of global clinical and epidemic data. In combination with the informatics and virology experiment, our work suggested the contribution of 203K/204R to the increased transmission and virulence of the SARS-CoV-2. In addition to mutations on the S protein, the mutations on the N protein are also important to virus spread during the pandemic.

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Detection of B.1.351 SARS-CoV-2 Variant Strain — Zambia, December 2020

Cited by 126 publications

References 2 publications

Prevalence of SARS-CoV-2 in six districts in Zambia in July, 2020: a cross-sectional cluster sample survey

Prevalence of SARS-CoV-2 in six districts in Zambia in July, 2020: a cross-sectional cluster sample survey

The Emerging Concern and Interest SARS-CoV-2 Variants

Nucleocapsid mutation R203K/G204R increases the infectivity, fitness and virulence of SARS-CoV-2

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