Co-occurrence of SARS-CoV-2 variants in rivers and sewage in India and Brazil

Cristiane Thompson; Camille V Leal; Renan da Silva Faustino; Luciana Leomil; Uppada Jagadeeshwari; Richa Sharma; Marcelo de Oliveira; Diogo Tschoeke; Thais Felix; Larissa Macedo; Ricardo Khouri; Hector Koolen; Felipe Landuci; Carlos de Rezende; Ícaro Strobel; Laíse de Moraes; Pablo Ivan P Ramos; Heitor de Souza; Fernando Motta; Manoel Barral-Netto; Maria de Lourdes Aguiar-Oliveira; Marilda de Siqueira; Chintalapati Sasikala; Fabiano Thompson

doi:10.1016/j.scitotenv.2024.178089

Co-occurrence of SARS-CoV-2 variants in rivers and sewage in India and Brazil

Sci Total Environ. 2024 Dec 19:958:178089. doi: 10.1016/j.scitotenv.2024.178089. Online ahead of print.

Authors

Cristiane Thompson¹, Camille V Leal², Renan da Silva Faustino³, Luciana Leomil², Uppada Jagadeeshwari⁴, Richa Sharma⁴, Marcelo de Oliveira², Diogo Tschoeke², Thais Felix², Larissa Macedo², Ricardo Khouri⁵, Hector Koolen⁶, Felipe Landuci², Carlos de Rezende⁷, Ícaro Strobel⁵, Laíse de Moraes⁵, Pablo Ivan P Ramos⁸, Heitor de Souza⁹, Fernando Motta³, Manoel Barral-Netto⁵, Maria de Lourdes Aguiar-Oliveira³, Marilda de Siqueira³, Chintalapati Sasikala¹⁰, Fabiano Thompson¹¹

Affiliations

¹ Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. Electronic address: [email protected].
² Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
³ Laboratory of Respiratory Viruses, Instituto Oswaldo Cruz -FIOCRUZ, Rio de Janeiro, Brazil.
⁴ Bacterial Discovery Laboratory, Centre for Environment, JNTUH University College Of Engineering, Science & Technology Hyderabad (UCESTH), India.
⁵ Medicine and Precision Health Laboratory (MeSP2), Instituto Gonçalo Moniz, FIOCRUZ, Bahia, Brazil.
⁶ State University of Amazonas, Manaus, Brazil.
⁷ Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), State University of Northern of Rio de Janeiro Darcy Ribeiro (UENF), Campos dos Goytacazes, Brazil.
⁸ Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, FIOCRUZ, Bahia, Brazil.
⁹ Department of Clinical Medicine, Hospital Universitário Clementino Fraga Filho (HUCFF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
¹⁰ Bacterial Discovery Laboratory, Centre for Environment, JNTUH University College Of Engineering, Science & Technology Hyderabad (UCESTH), India; Smart Microbiological Services, 5-3-357, Rashtrapathi Road, Secunderabad 500003, India. Electronic address: [email protected].
¹¹ Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. Electronic address: [email protected].

PMID: 39705959
DOI: 10.1016/j.scitotenv.2024.178089

Abstract

The genomic monitoring of SARS-CoV-2 variants of concern (VOCs) in riverine and sewage water has been widely used as an epidemiological tool worldwide. But its utility for epidemiological assessments still needs to be evaluated in some areas. Our study encompassed thirteen Brazilian rivers spanning a vast urban expanse across the states of Rio de Janeiro, São Paulo, and Paraná. The sampled rivers in Rio de Janeiro are heavily contaminated with sewage. Meanwhile, the Indian samples were all wastewater before joining the water bodies from urban regions (Andhra Pradesh and Telangana). The viral copies were quantified using quantitative polymerase chain reaction (qPCR) in all examined samples (N = 91). The abundance of viral particles varied from 567 to 85,700,000 copies/ml. Subsequently, Illumina CovidSeq was applied to identify the major variants. In Brazil, while a single SARS-CoV-2 VOC was identified for just a few samples (6/50, 12 %), most samples harbored multiple VOCs (44/50, 88 %). In India only one probed sample had a single variant identified. Gamma (2021) and Omicron (2021 and 2022) were the most abundant variants. Delta and Omicron genetic material were detected in Rio de Janeiro city rivers before Brazil's first cases of these variants. Several negative samples in the Real-Time RT-PCR (qPCR) turned out to have SARS-CoV-2 sequences suggesting CovidSeq was more sensitive than RT-PCR for virus detection in environmental samples. Sewage surveillance holds promise for early detection of emerging variants driving pandemic waves, exemplified by the Delta and Omicron variants, potentially offering a preemptive advantage over clinical sample reports.

Keywords: COVID-19; Epidemiological tool; Omicron; Sewage surveillance.