RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance
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Date
2023
Journal Title
Journal ISSN
Volume Title
Publisher
Elsevier Ltd
Abstract
Background The COVID-19 pandemic showcased the power of genomic sequencing to tackle the emergence and
spread of infectious diseases. However, metagenomic sequencing of total microbial RNAs in wastewater has the
potential to assess multiple infectious diseases simultaneously and has yet to be explored.
Methods A retrospective RNA-Seq epidemiological survey of 140 untreated composite wastewater samples was
performed across urban (n = 112) and rural (n = 28) areas of Nagpur, Central India. Composite wastewater
samples were prepared by pooling 422 individual grab samples collected prospectively from sewer lines of urban
municipality zones and open drains of rural areas from 3rd February to 3rd April 2021, during the second
COVID-19 wave in India. Samples were pre-processed and total RNA was extracted prior to genomic sequencing.
Findings This is the first study that has utilised culture and/or probe-independent unbiased RNA-Seq to examine
Indian wastewater samples. Our findings reveal the detection of zoonotic viruses including chikungunya, Jingmen
tick and rabies viruses, which have not previously been reported in wastewater. SARS-CoV-2 was detectable in 83
locations (59%), with stark abundance variations observed between sampling sites. Hepatitis C virus was the most
frequently detected infectious virus, identified in 113 locations and co-occurring 77 times with SARS-CoV-2; and
both were more abundantly detected in rural areas than urban zones. Concurrent identification of segmented
virus genomic fragments of influenza A virus, norovirus, and rotavirus was observed. Geographical differences
were also observed for astrovirus, saffold virus, husavirus, and aichi virus that were more prevalent in urban
samples, while the zoonotic viruses chikungunya and rabies, were more abundant in rural environments.
Interpretation RNA-Seq can effectively detect multiple infectious diseases simultaneously, facilitating geographical
and epidemiological surveys of endemic viruses that could help direct healthcare interventions against emergent and pre-existent infectious diseases as well as cost-effectively and qualitatively characterising the health status of the
population over time.
Description
Research Article
Keywords
COVID-19, Endemic viruses, RNA-Seq