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Sequencing analysis of SARS-CoV-2 cases in Slovenian long-term care facilities to support outbreak control [Elektronski vir]Kogoj, Rok ...Introduction: 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. Methods: 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. Results: 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. Discussion: 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.Source: Frontiers in public health [Elektronski vir]. - ISSN 2296-2565 (Vol. 12, iss. [article no.] 1406777, May 2024, str. 1-13)Type of material - e-article ; adult, seriousPublish date - 2024Language - englishCOBISS.SI-ID - 197563395
Author
Kogoj, Rok |
Grašek, Manja, dr. med. |
Suljič, Alen |
Zakotnik, Samo |
Vlaj, Doroteja |
Kotnik Koman, Kaja |
Fafangel, Mario |
Petrovec, Miroslav |
Avšič-Županc, Tatjana |
Korva, Miša
Topics
SARS-CoV-2 |
next-generation sequencing |
long-term care facility |
outbreak control |
pylogeny |
ustanova za dolgotrajno oskrbo |
sekvenciranje naslednje generacije |
nadzor izbruhov |
filogenija
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Database name | Field | Year |
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Links to authors' personal bibliographies | Links to information on researchers in the SICRIS system |
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Kogoj, Rok | 29937 |
Grašek, Manja, dr. med. | 55390 |
Suljič, Alen | 52539 |
Zakotnik, Samo | 51960 |
Vlaj, Doroteja | ![]() |
Kotnik Koman, Kaja | ![]() |
Fafangel, Mario | 37740 |
Petrovec, Miroslav | 15902 |
Avšič-Županc, Tatjana | 10331 |
Korva, Miša | 30696 |
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