PDF(Pubmed)
Abstract：
UNASSIGNED: Residents of long-term care facilities (LTCFs) are at high risk of morbidity and mortality due to COVID-19, especially when new variants of concern (VOC) emerge. To provide intradisciplinary data in order to tailor public health interventions during future epidemics, available epidemiologic and genomic data from Slovenian LTCFs during the initial phases of the COVID-19 pandemic was analyzed.
UNASSIGNED: The first part of the study included SARS-CoV-2 reverse-transcription Real-Time PCR (rtRT-PCR) positive LTCF residents, from 21 facilities with COVID-19 outbreaks occurring in October 2020. The second part of the study included SARS-CoV-2 rtRT-PCR positive LTCF residents and staff between January and April 2021, when VOC Alpha emerged in Slovenia. Next-generation sequencing (NGS) was used to acquire SARS-CoV-2 genomes, and lineage determination. In-depth phylogenetic and mutational profile analysis were performed and coupled with available field epidemiological data to assess the dynamics of SARS-CoV-2 introduction and transmission.
UNASSIGNED: 370/498 SARS-CoV-2 positive residents as well as 558/699 SARS-CoV-2 positive residents and 301/358 staff were successfully sequenced in the first and second part of the study, respectively. In October 2020, COVID-19 outbreaks in the 21 LTCFs were caused by intra-facility transmission as well as multiple independent SARS-CoV-2 introductions. The Alpha variant was confirmed in the first LTCF resident approximately 1.5 months after the first Alpha case was identified in Slovenia. The data also showed a slower replacement of existing variants by Alpha in residents compared to staff and the general population.
UNASSIGNED: Multiple SARS CoV-2 introductions as well as intra-facility spreading impacted disease transmission in Slovenian LTCFs. Timely implementation of control measures aimed at limiting new introductions while controlling in-facility transmission are of paramount importance, especially as new VOCs emerge. Sequencing, in conjunction with epidemiological data, can facilitate the determination of the need for future improvements in control measures to protect LTCF residents from COVID-19 or other respiratory infections.
UNASSIGNED: The first part of the study included SARS-CoV-2 reverse-transcription Real-Time PCR (rtRT-PCR) positive LTCF residents, from 21 facilities with COVID-19 outbreaks occurring in October 2020. The second part of the study included SARS-CoV-2 rtRT-PCR positive LTCF residents and staff between January and April 2021, when VOC Alpha emerged in Slovenia. Next-generation sequencing (NGS) was used to acquire SARS-CoV-2 genomes, and lineage determination. In-depth phylogenetic and mutational profile analysis were performed and coupled with available field epidemiological data to assess the dynamics of SARS-CoV-2 introduction and transmission.
UNASSIGNED: 370/498 SARS-CoV-2 positive residents as well as 558/699 SARS-CoV-2 positive residents and 301/358 staff were successfully sequenced in the first and second part of the study, respectively. In October 2020, COVID-19 outbreaks in the 21 LTCFs were caused by intra-facility transmission as well as multiple independent SARS-CoV-2 introductions. The Alpha variant was confirmed in the first LTCF resident approximately 1.5 months after the first Alpha case was identified in Slovenia. The data also showed a slower replacement of existing variants by Alpha in residents compared to staff and the general population.
UNASSIGNED: Multiple SARS CoV-2 introductions as well as intra-facility spreading impacted disease transmission in Slovenian LTCFs. Timely implementation of control measures aimed at limiting new introductions while controlling in-facility transmission are of paramount importance, especially as new VOCs emerge. Sequencing, in conjunction with epidemiological data, can facilitate the determination of the need for future improvements in control measures to protect LTCF residents from COVID-19 or other respiratory infections.
摘要：
■长期护理机构（LTCF）的居民由于COVID-19而面临很高的发病和死亡风险，特别是当出现新的关注变种（VOC）时。提供学科内数据，以便在未来的流行病期间调整公共卫生干预措施，分析了在COVID-19大流行的初始阶段来自斯洛文尼亚LTCF的可用流行病学和基因组数据.
■研究的第一部分包括SARS-CoV-2逆转录实时PCR（rtRT-PCR）阳性LTCF居民，来自2020年10月发生COVID-19疫情的21家设施。研究的第二部分包括2021年1月至4月的SARS-CoV-2rtRT-PCR阳性LTCF居民和工作人员，当时VOCAlpha在斯洛文尼亚出现。下一代测序（NGS）用于获取SARS-CoV-2基因组，和血统确定。进行了深入的系统发育和突变谱分析，并结合可用的现场流行病学数据，以评估SARS-CoV-2引入和传播的动态。
■370/498名SARS-CoV-2阳性居民以及558/699名SARS-CoV-2阳性居民和301/358名工作人员在研究的第一和第二部分中成功测序，分别。2020年10月，21个LTCF中的COVID-19疫情是由设施内传播以及多个独立的SARS-CoV-2引入引起的。在斯洛文尼亚发现第一个Alpha病例后约1.5个月，第一个LTCF居民中确认了Alpha变异。数据还显示，与工作人员和普通人群相比，居民中Alpha对现有变体的替换速度较慢。
■多次引入SARSCoV-2以及设施内传播影响了斯洛文尼亚LTCF的疾病传播。及时实施旨在限制新引进同时控制设施内传输的控制措施至关重要，尤其是随着新的VOCs的出现。测序,结合流行病学数据，可以帮助确定未来需要改进控制措施，以保护LTCF居民免受COVID-19或其他呼吸道感染。
■研究的第一部分包括SARS-CoV-2逆转录实时PCR（rtRT-PCR）阳性LTCF居民，来自2020年10月发生COVID-19疫情的21家设施。研究的第二部分包括2021年1月至4月的SARS-CoV-2rtRT-PCR阳性LTCF居民和工作人员，当时VOCAlpha在斯洛文尼亚出现。下一代测序（NGS）用于获取SARS-CoV-2基因组，和血统确定。进行了深入的系统发育和突变谱分析，并结合可用的现场流行病学数据，以评估SARS-CoV-2引入和传播的动态。
■370/498名SARS-CoV-2阳性居民以及558/699名SARS-CoV-2阳性居民和301/358名工作人员在研究的第一和第二部分中成功测序，分别。2020年10月，21个LTCF中的COVID-19疫情是由设施内传播以及多个独立的SARS-CoV-2引入引起的。在斯洛文尼亚发现第一个Alpha病例后约1.5个月，第一个LTCF居民中确认了Alpha变异。数据还显示，与工作人员和普通人群相比，居民中Alpha对现有变体的替换速度较慢。
■多次引入SARSCoV-2以及设施内传播影响了斯洛文尼亚LTCF的疾病传播。及时实施旨在限制新引进同时控制设施内传输的控制措施至关重要，尤其是随着新的VOCs的出现。测序,结合流行病学数据，可以帮助确定未来需要改进控制措施，以保护LTCF居民免受COVID-19或其他呼吸道感染。
