The wastewater microbiome: A novel insight for COVID-19 surveillance

Wastewater-Based Epidemiology is a tool to face and mitigate COVID-19 outbreaks by evaluating conditions in a specific community. This study aimed to analyze the microbiome profiles using nanopore technology for full-length 16S rRNA sequencing in wastewater samples collected from a penitentiary (P), a residential care home (RCH), and a quarantine or health care facilities (HCF). During the study, the wastewater samples from the RCH and the P were negative for SARS-CoV-2 based on qPCRs, except during the fourth week when was detected. Unexpectedly, the wastewater microbiome from RCH and P prior to week four was correlated with the samples collected from the HCF, suggesting a core bacterial community is expelled from the digest tract of individuals infected with SARS-CoV-2. The microbiota of wastewater sample positives for SARS-CoV-2 was strongly associated with enteric bacteria previously reported in patients with risk factors for COVID-19. We provide novel evidence that the wastewater microbiome associated with gastrointestinal manifestations appears to precede the SARSCoV-2 detection in sewage. This finding suggests that the wastewaters microbiome can be applied as an indicator of community-wide SARS-CoV-2 surveillance. (C) 2020 Elsevier B.V. All rights reserved.

Automated summary

Wastewater-Based Epidemiology is a useful tool for assessing and mitigating COVID-19 outbreaks in specific communities. This study utilized nanopore technology to analyze microbiome profiles in wastewater samples collected from different facilities. The research found that the wastewater microbiome can serve as an indicator for community-wide SARS-CoV-2 surveillance and highlighted a correlation between the enteric bacteria of infected individuals and the presence of the virus in wastewater samples.