Clinical Utility of SARS-CoV-2 Whole Genome Sequencing in Deciphering Source of Infection.
Clinical Utility of SARS-CoV-2 Whole Genome Sequencing in Deciphering Source of Infection.
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SARS-CoV-2全基因组测序在破译感染源中的临床应用
DOI：
10.1016/j.jhin.2020.10.014
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发表时间：
2020-10-24
期刊：
影响因子：
--
通讯作者：
Keio Donner Project
中科院分区：
文献类型：
--
作者：
Takenouchi T;Iwasaki YW;Harada S;Ishizu H;Uwamino Y;Uno S;Osada A;Abe K;Hasegawa N;Murata M;Takebayashi T;Fukunaga K;Saya H;Kitagawa Y;Amagai M;Siomi H;Kosaki K;Keio Donner Project
由人类严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）引起的2019冠状病毒病（COVID-19）是一个世界性问题。从医院感染控制的角度来看，确定感染源至关重要。我们进行了本研究，以评估使用全基因组测序来确定没有明确感染接触史的住院患者的感染源的有效性。最近，我们在一家三级医院遇到了两个看似独立的COVID-19集群。全病毒基因组测序根据病毒单倍型区分两个簇。然而，在临床上与第1或第2簇无关的14名COVID-19患者中，感染源尚不清楚。这些患者在医院内没有明确的感染性接触史（“未确定的感染源”），其单倍型与簇2中的单倍型相似，但不具有用于表征簇2的两个突变，这表明这14例“未确定的感染源”病例不是来自簇2。全病毒基因组测序可用于确认感染源不明的散发性COVID-19病例确实不是机构层面集群的一部分。
Coronavirus disease 2019 (COVID-19) caused by human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a worldwide problem. From the standpoint of hospital infection control, determining the source of infection is critical. We conducted the present study to evaluate the efficacy of using whole genome sequencing to determine the source of infection in hospitalized patients who do not have a clear infectious contact history. Recently, we encountered two seemingly separate COVID-19 clusters in a tertiary hospital. Whole viral genome sequencing distinguished the two clusters according to the viral haplotype. However, the source of infection was unclear in 14 patients with COVID-19 who were clinically unlinked to clusters 1 or 2. These patients, who had no clear history of infectious contact within the hospital (‘undetermined source of infection’), had haplotypes similar to those in cluster 2 but did not have two of the mutations used to characterize cluster 2, suggesting that these 14 cases of ‘undetermined source of infection’ were not derived from cluster 2. Whole viral genome sequencing can be useful for confirming that sporadic COVID-19 cases with an undetermined source of infection are indeed not part of clusters at the institutional level.
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影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
64.5
作者：
Korber, Bette;Fischer, Will M.;Montefiori, David C.
通讯作者：
Montefiori, David C.
QualiMap 2：高通量测序数据的高级多样本质量控制。
DOI：
10.1093/bioinformatics/btv566
发表时间：
2016-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Okonechnikov K;Conesa A;García-Alcalde F
通讯作者：
García-Alcalde F
DOI：
10.1093/bioinformatics/btp352
发表时间：
2009-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Handsaker B;Wysoker A;Fennell T;Ruan J;Homer N;Marth G;Abecasis G;Durbin R;1000 Genome Project Data Processing Subgroup
通讯作者：
1000 Genome Project Data Processing Subgroup
影响因子：
8.4
作者：
Penarrubia, Luis;Ruiz, Maria;Pareja, Josep
通讯作者：
Pareja, Josep