Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan.
Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan.
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DOI：
10.1016/j.meegid.2021.105003
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发表时间：
2021-10
期刊：
影响因子：
--
通讯作者：
Mehmood N
中科院分区：
文献类型：
--
作者：
Tamim S;Trovao NS;Thielen P;Mehoke T;Merritt B;Ikram A;Salman M;Alam MM;Umair M;Badar N;Khurshid A;Mehmood N
严重急性呼吸道综合征冠状病毒2型（SARS-CoV-2）的基因组流行病学为COVID-19大流行提供了全球流行病学见解。该病毒的测序已经大规模进行，许多国家将数据存入开放获取的数据库，以便进行深入的全球系统发育分析。为了促进这些努力，我们在巴基斯坦国立卫生研究院（NIH）建立了牛津纳米孔技术（ONT）测序能力。这项研究强调了在巴基斯坦第二波COVID-19高峰期间（2020年11月至2021年2月）共同传播的多种SARS-CoV-2谱系，病毒起源追溯到美利坚合众国和沙特阿拉伯。将10份SARS-CoV-2阳性样品用于ONT文库制备。序列和系统发育分析确定，这些患者感染的是谱系B.1.1.250，最初于2020年3月和4月在英国和孟加拉国发现，并在欧洲、美国和澳大利亚流行，直到本研究进行时。血统B.1.261最初在沙特阿拉伯被发现，并在巴基斯坦广泛传播。一个样品与亲本B.1谱系聚类，另一个与来自新加坡的谱系B.6聚类。未来，监测巴基斯坦流行谱系的演变动态将有助于更好地追踪病毒传播、其扩张轨迹的变化趋势、持久性、其人口动态的变化，并为更好地实施控制措施提供指导。
Genomic epidemiology of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has provided global epidemiological insight into the COVID-19 pandemic since it began. Sequencing of the virus has been performed at scale, with many countries depositing data into open access repositories to enable in-depth global phylogenetic analysis. To contribute to these efforts, we established an Oxford Nanopore Technologies (ONT) sequencing capability at the National Institutes of Health (NIH), Pakistan. This study highlights multiple SARS-CoV-2 lineages co-circulating during the peak of a second COVID-19 wave in Pakistan (Nov 2020-Feb 2021), with virus origins traced to the United States of America and Saudi Arabia. Ten SARS-CoV-2 positive samples were used for ONT library preparation. Sequence and phylogenetic analysis determined that the patients were infected with lineage B.1.1.250, originally identified in the United Kingdom and Bangladesh during March and April of 2020, and in circulation until the time of this study in Europe, USA and Australia. Lineage B.1.261 was originally identified in Saudi Arabia with widespread local dissemination in Pakistan. One sample clustered with the parental B.1 lineage and the other with lineage B.6 originally from Singapore. In the future, monitoring the evolutionary dynamics of circulating lineages in Pakistan will enable improved tracing of the viral spread, changing trends of their expansion trajectories, persistence, changes in their demographic dynamics, and provide guidance for better implementation of control measures.
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DOI：
10.1016/j.lanwpc.2021.100104
发表时间：
2021-03
期刊：
The Lancet regional health. Western Pacific
影响因子：
--
作者：
Nabeshima T;Takazono T;Ashizawa N;Miyazaki T;Inoue S;Ngwe Tun MM;Izumikawa K;Mukae H;Moi ML;Morita K
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DOI：
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发表时间：
2011-08-09
期刊：
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影响因子：
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影响因子：
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Andersen KG
DOI：
10.1016/j.jhin.2016.10.008
发表时间：
2017-03
期刊：
The Journal of hospital infection
影响因子：
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通讯作者：
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