TY - JOUR
T1 - Exploring the diversity of coronavirus in sewage during COVID-19 pandemic
T2 - Don't miss the forest for the trees
AU - Martínez-Puchol, Sandra
AU - Itarte, Marta
AU - Rusiñol, Marta
AU - Forés, Eva
AU - Mejías-Molina, Cristina
AU - Andrés, Cristina
AU - Antón, Andrés
AU - Quer, Josep
AU - Abril, Josep F.
AU - Girones, Rosina
AU - Bofill-Mas, Sílvia
N1 - Publisher Copyright:
© 2021 The Authors
PY - 2021/12/15
Y1 - 2021/12/15
N2 - In the wake of the COVID-19 pandemic, the use of next generation sequencing (NGS) has proved to be an important tool for the genetic characterization of SARS-CoV-2 from clinical samples. The use of different available NGS tools applied to wastewater samples could be the key for an in-depth study of the excreted virome, not only focusing on SARS-CoV-2 circulation and typing, but also to detect other potentially pandemic viruses within the same family. With this aim, 24-hours composite wastewater samples from March and July 2020 were sequenced by applying specific viral NGS as well as target enrichment NGS. The full virome of the analyzed samples was obtained, with human Coronaviridae members (CoV) present in one of those samples after applying the enrichment. One contig was identified as HCoV-OC43 and 8 contigs as SARS-CoV-2. CoVs from other animal hosts were also detected when applying this technique. These contigs were compared with those obtained from contemporary clinical specimens by applying the same target enrichment approach. The results showed that there is a co-circulation in urban areas of human and animal coronaviruses infecting domestic animals and rodents. NGS enrichment-based protocols might be crucial to describe the occurrence and genetic characteristics of SARS-CoV-2 and other Coronaviridae family members within the excreted virome present in wastewater.
AB - In the wake of the COVID-19 pandemic, the use of next generation sequencing (NGS) has proved to be an important tool for the genetic characterization of SARS-CoV-2 from clinical samples. The use of different available NGS tools applied to wastewater samples could be the key for an in-depth study of the excreted virome, not only focusing on SARS-CoV-2 circulation and typing, but also to detect other potentially pandemic viruses within the same family. With this aim, 24-hours composite wastewater samples from March and July 2020 were sequenced by applying specific viral NGS as well as target enrichment NGS. The full virome of the analyzed samples was obtained, with human Coronaviridae members (CoV) present in one of those samples after applying the enrichment. One contig was identified as HCoV-OC43 and 8 contigs as SARS-CoV-2. CoVs from other animal hosts were also detected when applying this technique. These contigs were compared with those obtained from contemporary clinical specimens by applying the same target enrichment approach. The results showed that there is a co-circulation in urban areas of human and animal coronaviruses infecting domestic animals and rodents. NGS enrichment-based protocols might be crucial to describe the occurrence and genetic characteristics of SARS-CoV-2 and other Coronaviridae family members within the excreted virome present in wastewater.
KW - Coronavirus
KW - Next generation sequencing
KW - Sewage virome
KW - Target enrichment sequencing
KW - Viral metagenomics
UR - http://www.scopus.com/inward/record.url?scp=85112132304&partnerID=8YFLogxK
U2 - 10.1016/j.scitotenv.2021.149562
DO - 10.1016/j.scitotenv.2021.149562
M3 - Article
C2 - 34391155
AN - SCOPUS:85112132304
SN - 0048-9697
VL - 800
JO - Science of the total environment
JF - Science of the total environment
M1 - 149562
ER -