A genomics network established to respond rapidly to public health threats in South Africa

Msomi, Nokukhanya; Mlisana, Koleka; Oliveira, Túlio de; Willianson, Carolyn; Bhiman, Jinal N.; Goedhals, Dominique; Engelbrecht, Susan; Zyl, Gert van; Preiser, Wolfgang; Hardie, Diana; Hsiao, Marvin; Mulder, Nicola; Martin, Darren; Christoffels, Alan; York, Denis; Giandhari, Jennifer; Wilkinson, Eduan; Pillay, Sureshnee; Tegally, Houriiyah; James, San Emmanuel; Kanzi, Aquilah; Lessells, Richard

doi:10.1016/s2666-5247(20)30116-6

Cited by 54 publications

(45 citation statements)

References 8 publications

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“…We detected this new variant through intensified genomic surveillance in response to a rapid resurgence of cases in the Eastern Cape Province 20 . However, both before and after the detection of 501Y.V2, our genomic surveillance involved regular sequencing of a random selection of residual samples from routine diagnostic services.…”

Section: Discussionmentioning

confidence: 99%

“…As part of the Network for Genomic Surveillance in South Africa (NGS-SA) 42 , five sequencing hubs receive randomly selected samples for sequencing every week according to approved protocols at each site. These samples include remnant nucleic acid extracts or remnant nasopharyngeal and oropharyngeal swab samples from routine diagnostic SARS-CoV-2 PCR testing from public and private laboratories in South Africa.…”

Section: Sampling Of Sars-cov-2mentioning

confidence: 99%

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Detection of a SARS-CoV-2 variant of concern in South Africa

Tegally

Wilkinson

Giovanetti

et al. 2021

Nature

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This is a PDF file of a peer-reviewed paper that has been accepted for publication. Although unedited, the content has been subjected to preliminary formatting. Nature is providing this early version of the typeset paper as a service to our authors and readers. The text and figures will undergo copyediting and a proof review before the paper is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

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Section: Discussionmentioning

confidence: 99%

Section: Sampling Of Sars-cov-2mentioning

confidence: 99%

Detection of a SARS-CoV-2 variant of concern in South Africa

Tegally

Wilkinson

Giovanetti

et al. 2021

Nature

Self Cite

1,582

1,533

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“…Keeping track of unique mutations like this will allow us to understand how the virus spreads between different locations in the city, the surrounding countryside and throughout the country. This is the primary objective of Network for Genomic Surveillance in South Africa (NGS-SA) [ 35 ].…”

Section: Discussionmentioning

confidence: 99%

Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa

Engelbrecht

Delaney

Kleinhans

et al. 2021

Viruses

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Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9–17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town.

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“…All sequence data are freely available in the GISAID database (Supplementary Table 1 and Supplementary Table 2). Sequence data of SARS-CoV-2 from South Africa was reported previously (Msomi et al ., 2020).…”

Section: Methodsmentioning

confidence: 78%

“…The first COVID-19 case in Africa was recorded in Egypt on the 14th of February, 2020 (Lone and Ahmad, 2020), and on 27 th February, the sub-Saharan African region recorded its first case in Nigeria. Further cases in sub-Saharan Africa were recorded in South Africa and Zimbabwe, on March 5 th and 20 th , respectively (Msomi et al ., 2020). The initial cases identified in Africa were mostly introduced from Europe, the Middle East and the United States of America (Hâncean et al ., 2020; Lone and Ahmad, 2020; Mehtar et al ., 2020).…”

Section: Introductionmentioning

confidence: 99%

Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread

Mashe

Takawira

Martins³

et al. 2021

Preprint

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Zimbabwe reported its first case of SARS-Cov-2 infection in March 2020, and case numbers increased to more than 8,099 to 16th October 2020. An understanding of the SARS-Cov-2 outbreak in Zimbabwe will assist in the implementation of effective public health interventions to control transmission. Nasopharyngeal samples from 92,299 suspected and confirmed COVID-19 cases reported in Zimbabwe between 20 March and 16 October 2020 were obtained. Available demographic data associated with those cases identified as positive (8,099) were analysed to describe the national breakdown of positive cases over time in more detail (geographical location, sex, age and travel history). The whole genome sequence (WGS) of one hundred SARS-CoV-2-positive samples from the first 120 days of the epidemic in Zimbabwe was determined to identify their relationship to one another and WGS from global samples. Overall, a greater proportion of infections were in males (55.5%) than females (44.85%), although in older age groups more females were affected than males. Most COVID-19 cases (57 %) were in the 20-40 age group. Eight lineages, from at least 25 separate introductions into the region were found using comparative genomics. Of these, 95% had the D614G mutation on the spike protein which was associated with higher transmissibility than the ancestral strain. Early introductions and spread of SARS-CoV-2 were predominantly associated with genomes common in Europe and the United States of America (USA), and few common in Asia at this time. As the pandemic evolved, travel-associated cases from South Africa and other neighbouring countries were also recorded. Transmission within quarantine centres occurred when travelling nationals returning to Zimbabwe. International and regional migration followed by local transmission were identified as accounting for the development of the SARS-CoV-2 epidemic in Zimbabwe. Based on this, rapid implementation of public health interventions are critical to reduce local transmission of SARS-CoV-2. Impact of the predominant G614 strain on severity of symptoms in COVID-19 cases needs further investigation.

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A genomics network established to respond rapidly to public health threats in South Africa

Cited by 54 publications

References 8 publications

Detection of a SARS-CoV-2 variant of concern in South Africa

Detection of a SARS-CoV-2 variant of concern in South Africa

Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa

Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread

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