SARS-CoV-2 transmission routes from genetic data: A Danish case study

Bluhm, Andreas; Christandl, Matthias; Gesmundo, Fulvio; Klausen, Frederik Ravn; Mančinska, Laura; Vincent, Steffan,; França, Daniel Stilck; Werner, Albert H.

doi:10.1371/journal.pone.0241405

Cited by 18 publications

(16 citation statements)

References 21 publications

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“…Previous reports have identified viruses in lineage B.1 carrying SNP C1059T (amino acid change ORF1a-T265I) in travel returners from ski holidays in Ischgl, Austria [ 9 , 21 ]. We detected 21 (4.5%) viral samples within our cohort with this feature ( Fig 4C ), divergent by up to two SNPs from the common ancestor.…”

Section: Resultsmentioning

confidence: 99%

“…During this time, many residents also travelled to ski resorts. Viral introductions from ski resorts are known from contract tracing data to have affected Germany [ 25 ], Denmark [ 21 ], Iceland [ 9 ], France, Spain, and UK [ 26 ], with Ischgl, Austria described as a source of many cases. Our data supports the finding that ski resorts in Austria and Switzerland served as dissemination hotspots.…”

Section: Discussionmentioning

confidence: 99%

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SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event

et al. 2021

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The first case of SARS-CoV-2 in Basel, Switzerland was detected on February 26th 2020. We present a phylogenetic study to explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26th until March 23rd. We sequenced SARS-CoV-2 naso-oropharyngeal swabs from 746 positive tests that were performed at the University Hospital Basel during the study period. We successfully generated 468 high quality genomes from unique patients and called variants with our COVID-19 Pipeline (COVGAP), and analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny. Epidemiological data from patient questionnaires was used to facilitate the interpretation of phylogenetic observations. The early outbreak in Basel was dominated by lineage B.1 (83·6%), detected first on March 2nd, although the first sample identified belonged to B.1.1. Within B.1, 68·2% of our samples fall within a clade defined by the SNP C15324T (‘Basel cluster’), including 157 identical sequences at the root of the ‘Basel cluster’, some of which we can specifically trace to regional spreading events. We infer the origin of B.1-C15324T to mid-February in our tri-national region. The other genomes map broadly over the global phylogenetic tree, showing several introduction events from and/or dissemination to other regions of the world via travellers. Family transmissions can also be traced in our data. A single lineage variant dominated the outbreak in the Basel area while other lineages, such as the first (B.1.1), did not propagate. A mass gathering event was the predominant initial source of cases, with travel returners and family transmissions to a lesser extent. We highlight the importance of adding specific questions to epidemiological questionnaires, to obtain data on attendance of large gatherings and their locations, as well as travel history, to effectively identify routes of transmissions in up-coming outbreaks. This phylogenetic analysis in concert with epidemiological and contact tracing data, allows connection and interpretation of events, and can inform public health interventions. Trial Registration: ClinicalTrials.gov NCT04351503.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event

et al. 2021

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“…This followed the Christmas holidays with thousands of ski tourists from endemic areas sojourning in Swiss ski resorts. During the first wave of the pandemic in 2020, skiing and associated activities resulted in a European wide spread of specific mutants linked to the alpine village Ischgl in Austria [ 42 , 43 ]. Similar, we have detected cases linked to a potential super spreading event in the ski resort of Wengen in December 2020, as reported in public news articles.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing

et al. 2021

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The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.

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“…This followed the Christmas holidays with thousands of ski tourists from endemic areas sojourning in Swiss ski resorts. During the first wave of the pandemic in 2020, skiing and associated activities resulted in an European wide spread of specific mutants linked to the alpine village Ischgl in Austria 46,47 . Similar, we have detected cases linked to a potential super spreading event in the ski resort Wengen in December 2020, as reported in public news articles.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 – implementation of Swiss-wide diagnostic screening and whole genome sequencing

Cabecinhas

Roloff

Stange

et al. 2021

Preprint

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The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations by the European Center for Disease Prevention and Control (ECDC) and World Health Organization (WHO) for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological definitions based on travel history and the S gene dropout in certain diagnostic systems. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 3492 VoCs have been identified since the detection of the first Swiss case in October 2020, with 1370 being B1.1.7, 61 B.1.351, and none P.1. The remaining 2061 cases of VoCs have been described without further lineage specification. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.

show abstract

SARS-CoV-2 transmission routes from genetic data: A Danish case study

Cited by 18 publications

References 21 publications

SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event

SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event

SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing

SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 – implementation of Swiss-wide diagnostic screening and whole genome sequencing

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