Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.
Nature
; 609(7925): 101-108, 2022 09.
Article
em En
| MEDLINE
| ID: mdl-35798029
ABSTRACT
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1-3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
Texto completo:
1
Coleções:
01-internacional
Contexto em Saúde:
4_TD
Base de dados:
MEDLINE
Assunto principal:
Águas Residuárias
/
Vigilância Epidemiológica Baseada em Águas Residuárias
/
SARS-CoV-2
/
COVID-19
Tipo de estudo:
Guideline
/
Prognostic_studies
/
Risk_factors_studies
/
Screening_studies
Limite:
Humans
Idioma:
En
Revista:
Nature
Ano de publicação:
2022
Tipo de documento:
Article