Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

Abstract

SARS-CoV-2 surveillance of viral populations in wastewater samples is recognized as a useful tool for monitoring epidemic waves and boosting health preparedness. Next generation sequencing of viral RNA isolated from wastewater is a convenient and cost-effective strategy to understand the molecular epidemiology of SARS-CoV-2 and provide insights on the population dynamics of viral variants at the community level. However, in low- and middle-income countries, isolated groups have performed wastewater monitoring and data has not been extensively shared in the scientific community. Here we report the results of monitoring the co-circulation and abundance of variants of concern (VOCs) of SARS-CoV-2 in Uruguay, a small country in Latin America, between November 2020—July 2021 using wastewater surveillance. RNA isolated from wastewater was characterized by targeted sequencing of the Receptor Binding Domain region within the spike gene. Two computational approaches were used to track the viral variants. The results of the wastewater analysis showed the transition in the overall predominance of viral variants in wastewater from No-VOCs to successive VOCs, in agreement with clinical surveillance from sequencing of nasal swabs. The mutations K417T, E484K and N501Y, that characterize the Gamma VOC, were detected as early as December 2020, several weeks before the first clinical case was reported. Interestingly, a non-synonymous mutation described in the Delta VOC, L452R, was detected at a very low frequency since April 2021 when using a recently described sequence analysis tool (SAM Refiner). Wastewater NGS-based surveillance of SARS-CoV-2 is a reliable and complementary tool for monitoring the introduction and prevalence of VOCs at a community level allowing early public health decisions. This approach allows the tracking of symptomatic and asymptomatic individuals, who are generally under-reported in countries with limited clinical testing capacity. Our results suggests that wastewater-based epidemiology can contribute to improving public health responses in low- and middle-income countries.

Targeted amplicon sequencing of wastewater samples for detecting SARS-CoV-2 variants with high sensitivity and resolution

“…There are some reports that employed targeted amplicon sequencing for analyzing SARS-CoV-2 RNA in sewages with or without nested PCR ( Cancela et al, 2023 ; Iwamoto et al, 2023 ; Smyth et al, 2022 ). These researches successfully captured the transitions of major variants/lineages in wastewater of each community, but their methodologies did not cover the recent Omicron sublineages (e.g., BQ.1.1 and XBB.1) due to the limited regions of RBD analyzed.…”

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

“…Since then, the recombinant XBB (Nextstrain clade 22F) has risen to global abundance, and convergent mutations have made it increasingly challenging to disentangle lineages. As we write, SARS-CoV-2 genome sequencing has been deployed in wastewater from across the globe (e.g., USA, Canada, Uruguay, Japan, Italy, India, Spain) to augment surveillance efforts during Gamma, Delta, and Omicron (BA.1 to XBB/BQ) waves 12,13,25,26,48 . The uptake of wastewater sequencing data to bring lineage-level information to WBS highlights the importance of benchmarking and developing standards.…”

“…Designing primers to distinguish among VOCs by qPCR 9 can be laborious and is hindered by novel viral mutations 10 . A complementary approach to qPCR is to measure viral diversity by sequencing parts, or the entirety, of the viral genomes found in wastewater [11][12][13][14][15] .…”

Tackling covid-19 variants

“…Declining testing rates have made case surveillance challenging, but wastewater surveillance can help understand the circulation of SARS-CoV-2 in the population 14. Many countries used wastewater surveillance to support their public health response during the covid-19 pandemic, including the US, the Netherlands, Spain, Hong Kong, Bangladesh, and Uruguay 15161718192021. Despite the clear need for these wastewater programmes, some challenges remain.…”