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

Engelbrecht, Susan; Delaney, Kayla Eileen; Kleinhans, Bronwyn; Wilkinson, Eduan; Tegally, Houriiyah; Stander, Tania; Zyl, Gert van; Preiser, Wolfgang; Oliveira, Túlio de

doi:10.3390/v13030526

Cited by 25 publications

(23 citation statements)

References 36 publications

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“…In other studies, lineage B.1.1.29 was reported to have been commonly identified in Europe, particularly the UK [36,64]; this is supported by the findings of our study, in which the majority of the migration events of the B.1.1.x clade originated from the UK (Table 2, Figure 8). Interestingly, this lineage was also reported in March-April of 2020 in Cape Town, South Africa, and it was estimated to have been imported from the Netherlands [64]. However, the B.1.1.29 lineage was identified much less frequently in Cyprus after June 2020.…”

Section: Discussionsupporting

confidence: 92%

A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic

Chrysostomou

Vrancken

Koumbaris³

et al. 2021

Viruses

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The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial outbreak on the island. In this study, we performed a comprehensive retrospective molecular epidemiological analysis (genetic, phylogenetic, phylodynamic and phylogeographic analyses) of SARS-CoV-2 isolates in Cyprus from April 2020 to January 2021, covering the first ten months of the SARS-CoV-2 infection epidemic on the island. The primary aim of this study was to assess the transmissibility of SARS-CoV-2 lineages in Cyprus. Whole SARS-CoV-2 genomic sequences were generated from 596 clinical samples (nasopharyngeal swabs) obtained from community-based diagnostic testing centers and hospitalized patients. The phylogenetic analyses revealed a total of 34 different lineages in Cyprus, with B.1.258, B.1.1.29, B.1.177, B.1.2, B.1 and B.1.1.7 (designated a Variant of Concern 202012/01, VOC) being the most prevalent lineages on the island during the study period. Phylodynamic analysis showed a highly dynamic epidemic of SARS-CoV-2 infection, with three consecutive surges characterized by specific lineages (B.1.1.29 from April to June 2020; B.1.258 from September 2020 to January 2021; and B.1.1.7 from December 2020 to January 2021). Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, ΔH69/V70, S898F, ΔY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. Phylogeographic analysis indicated that the majority of imports and exports were to and from the United Kingdom (UK), although many other regions/countries were identified (southeastern Asia, southern Europe, eastern Europe, Germany, Italy, Brazil, Chile, the USA, Denmark, the Czech Republic, Slovenia, Finland, Switzerland and Pakistan). Taken together, these findings demonstrate that the SARS-CoV-2 infection epidemic in Cyprus is being maintained by a continuous influx of lineages from many countries, resulting in the establishment of an ever-evolving and polyphyletic virus on the island.

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Section: Discussionsupporting

confidence: 92%

A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic

Chrysostomou

Vrancken

Koumbaris³

et al. 2021

Viruses

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“…Note that the African country which has been stricken the most by the disease is South Africa where the prevalence of AC is much higher. It has been observed (Engelbrecht et al, 2021) that in this country COVID-19 clusters have occurred there in closed supermarkets, most often equipped with AC .…”

Section: Viii4 Airborne Close Contactmentioning

confidence: 94%

Increased airborne transmission of COVID-19 with new variants, Implications for health policies

Rowe¹,

Canosa

Meslem

et al. 2022

Preprint

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The aim of the present paper is to highlight that new variants, either of higher viral load such as delta or higher contagiousness like omicron, lead to an even higher airborne transmission than historical strains. We first review the question of the route of contamination and of the dose following exposure, and the importance of the counting unit for pathogens, itself linked to the dose-response law. Using the counting unit of Wells, i.e. the quantum of contagium, we develop the conservation equation of quanta which allows deriving the value of the quantum concentration at steady state for a well-mixed room. With the choice of an exponential response function, this leads to the famous Wells-Riley equation. The analysis points out the importance of a number of parameters such as the time of exposure, the quantum production rate, mask wearing and the incidence rate in the population in order to evaluate the risk. The link with the monitoring concentration of carbon dioxide is made and used for a risk analysis of a variety of situations for which we have made concrete CO2 time monitoring. The main conclusion of these observations is that the present norms of ventilation, already insufficient, are not respected, especially in a variety of public premises, leading to high risk of contamination. Finally, we insist that public health policy in the field of airborne transmission should be based on a multi parameter analysis, considering the whole complexity of dose evaluation.

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“…Coronavirus Disease 2019 (COVID-19), 2021 ). In December 2020, new variants of concerns (VOC) were detected in other countries, including the UK and South Africa ( Cella et al., 2021 ; Engelbrecht et al., 2021 ; Fiorentini et al., 2021 ; Voloch et al., 2021 ). These strains were related to increased transmissibility and posed higher public health concerns.…”

Section: Introductionmentioning

confidence: 99%

One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar

Benslimane

Al-Khatib

Al-Jamal

et al. 2021

Front. Cell. Infect. Microbiol.

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Qatar, a country with a strong health system and a diverse population consisting mainly of expatriate residents, has experienced two large waves of COVID-19 outbreak. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population’s genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number of mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. These findings raise the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor the SARS-CoV-2 profile and re-emergence in Qatar.

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

Cited by 25 publications

References 36 publications

A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic

A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic

Increased airborne transmission of COVID-19 with new variants, Implications for health policies

One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar

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