Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.
Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.
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DOI：
10.1016/j.ijid.2020.11.128
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发表时间：
2021-03
期刊：
影响因子：
--
通讯作者：
de Oliveira T
中科院分区：
文献类型：
--
作者：
Giandhari J;Pillay S;Wilkinson E;Tegally H;Sinayskiy I;Schuld M;Lourenço J;Chimukangara B;Lessells R;Moosa Y;Gazy I;Fish M;Singh L;Sedwell Khanyile K;Fonseca V;Giovanetti M;Carlos Junior Alcantara L;Petruccione F;de Oliveira T
成立了南非基因组监测网络(NGS-SA)，以调查SARS-CoV-2疫情在南非的传入情况并了解其早期传播动态。本文介绍了该小组的第一个结果，这是对疫情第一个月期间在第一个入境口岸夸祖鲁-纳塔尔(KZN)采集的第一批21个SARS-CoV-2全基因组的分子流行病学研究。通过将其与有效繁殖数(R)的计算相结合，它的目的是阐明南非的感染模式。最大的两个省--豪登省和KZN省--发现的病例数量增长缓慢，而疫情在西开普省和东开普省传播得更快。对传播潜力的估计表明，自第一批病例和死亡病例以来，R=1下降，但随后在2020年5月6日至18日期间估计的R平均值为1.39。还证明，KZN的早期传播与多次国际传入有关，并以血统B1和B为主。还提供了在疫情第一个月内在德班一家医院发生的当地感染的证据。南非的新冠肺炎大流行在空间维度上非常不同，KZN有许多不同的SARS-CoV2病毒介绍和医院传播的证据，这推高了KZN的早期死亡率。地方一级的疫情仍在发展中，南非疫情监测系统的目标是澄清南非的动态，并随着疫情的演变制定最有效的措施。
The Network for Genomic Surveillance in South Africa (NGS-SA) was formed to investigate the introduction and understand the early transmission dynamics of the SARS-CoV-2 epidemic in South-Africa. This paper presents the first results from this group, which is a molecular epidemiological study of the first 21 SARS-CoV-2 whole genomes sampled in the first port of entry – KwaZulu-Natal (KZN) – during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), it aimed to shed light on the patterns of infections in South Africa. Two of the largest provinces – Gauteng and KZN – had a slow growth rate for the number of detected cases, while the epidemic spread faster in the Western Cape and Eastern Cape. The estimates of transmission potential suggested a decrease towards R = 1 since the first cases and deaths, but a subsequent estimated R average of 1.39 between 6–18 May 2020. It was also demonstrated that early transmission in KZN was associated with multiple international introductions and dominated by lineages B1 and B. Evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic was also provided. The COVID-19 pandemic in South Africa was very heterogeneous in its spatial dimension, with many distinct introductions of SARS-CoV2 in KZN and evidence of nosocomial transmission, which inflated early mortality in KZN. The epidemic at the local level was still developing and NGS-SA aimed to clarify the dynamics in South Africa and devise the most effective measures as the outbreak evolved.
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