Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias.
Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias.
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DOI：
10.1093/infdis/jiac348
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发表时间：
2022-11-11
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影响因子：
--
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在严重急性呼吸综合征冠状病毒2(SARS-CoV-2)大流行期间，医护人员面临着从工作场所内通过患者和工作人员以及来自外部社区感染的风险，使我们解决传播链以告知医院感染控制政策的能力变得更加复杂。在这里，我们展示了在大流行早期，当流通中的病毒多样性有限时，纳入公共基因组数据库的序列如何有助于基因组监测。我们对2020年3月至5月期间从波士顿医疗中心卫生工作者那里丢弃的诊断SARS-CoV-2分离株的子集进行了测序，并将该数据集与GISAID中保存的周围社区的公开可用序列相结合，目的是推断特定的传播途径。将我们的数据与公开可用序列联系起来，发现在卫生工作者中，2019年冠状病毒病病例中有73%(95%可信区间，63%-84%)可能是新的引入方式，而不是医院传播。我们认为，将SARS-CoV-2引入医院环境是频繁的，扩大公共基因组监测可以在确定传播途径时更好地帮助控制感染。当外部社区中基因组相似的病原体感染队列成员时，使用基因组序列的暴发分析虚假地确定了传播。我们通过例子说明如何避免这种情况--利用2020年初波士顿医疗中心爆发的SARS-CoV-2疫情中的社区序列。
Throughout the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, healthcare workers (HCWs) have faced risk of infection from within the workplace via patients and staff as well as from the outside community, complicating our ability to resolve transmission chains in order to inform hospital infection control policy. Here we show how the incorporation of sequences from public genomic databases aided genomic surveillance early in the pandemic when circulating viral diversity was limited. We sequenced a subset of discarded, diagnostic SARS-CoV-2 isolates between March and May 2020 from Boston Medical Center HCWs and combined this data set with publicly available sequences from the surrounding community deposited in GISAID with the goal of inferring specific transmission routes. Contextualizing our data with publicly available sequences reveals that 73% (95% confidence interval, 63%–84%) of coronavirus disease 2019 cases in HCWs are likely novel introductions rather than nosocomial spread. We argue that introductions of SARS-CoV-2 into the hospital environment are frequent and that expanding public genomic surveillance can better aid infection control when determining routes of transmission. Outbreak analyses using genomic sequences spuriously identify transmission when genomically similar pathogens in the outside community infect cohort members. We show how to avoid this by example--leveraging community sequences within a SARS-CoV-2 outbreak at Boston Medical Center during early 2020.
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DOI：
10.1093/cid/ciab281
发表时间：
2021-09-15
期刊：
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
影响因子：
--
作者：
Braun KM;Moreno GK;Buys A;Somsen ED;Bobholz M;Accola MA;Anderson L;Rehrauer WM;Baker DA;Safdar N;Lepak AJ;O'Connor DH;Friedrich TC
通讯作者：
Friedrich TC
影响因子：
14.9
作者：
Wilm A;Aw PP;Bertrand D;Yeo GH;Ong SH;Wong CH;Khor CC;Petric R;Hibberd ML;Nagarajan N
通讯作者：
Nagarajan N
影响因子：
5.3
作者：
Sagulenko P;Puller V;Neher RA
通讯作者：
Neher RA
影响因子：
5.4
作者：
Leonard, Ashley Sobel;Weissman, Daniel B.;Koelle, Katia
通讯作者：
Koelle, Katia
影响因子：
6.6
作者：
Yu, Guangchuang;Smith, David K.;Lam, Tommy Tsan-Yuk
通讯作者：
Lam, Tommy Tsan-Yuk