Population-based SARS-CoV-2 whole genome sequencing and contact tracing during the COVID-19 pandemic in Switzerland.
J Infect Dis
; 2023 Mar 27.
Artículo
en Inglés
| MEDLINE | ID: covidwho-2321605
ABSTRACT
BACKGROUND:
Testing and contact tracing (CT) can interrupt transmission chains SARS-CoV-2. Whole genome sequencing (WGS) can potentially strengthen these investigations and provide insights on transmission.METHODS:
We included all laboratory-confirmed COVID-19 cases diagnosed between June 4 to July 26, 2021, in a Swiss canton. We defined CT clusters based on epidemiological links reported in the CT data and genomic clusters as sequences with no single nucleotide polymorphism (SNP) differences between any two pairs of sequences being compared. We assessed the agreement between CT clusters and genomic clusters.RESULTS:
Of 359 COVID-19 cases, 213 were sequenced. Overall, agreement between CT and genomic clusters was low (Kappa coefficient=0.13). Out of 24 CT clusters with at least two sequenced samples, 9 (37.5%) were also linked based on genomic sequencing but in four of these, WGS found additional cases in other CT clusters. Household was most often reported source of infection (101, 28.1%) and home addresses coincided well with CT clusters In 44 out of 54 CT clusters containing at least two cases (81.5%), all cases of the cluster had the same home address. However, only a quarter of household transmission was confirmed by WGS (6 out of 26 genomic clusters, 23.1%). A sensitivity analysis using ≤1 SNP differences to define genomic clusters resulted in similar results.CONCLUSIONS:
WGS data supplemented epidemiological CT data, supported the detection of potential additional clusters missed by CT, and identified misclassified transmissions and sources of infection. Household transmission was overestimated by CT.
Texto completo:
Disponible
Colección:
Bases de datos internacionales
Base de datos:
MEDLINE
Tipo de estudio:
Estudios diagnósticos
Idioma:
Inglés
Año:
2023
Tipo del documento:
Artículo
País de afiliación:
Infdis
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