Wastewater surveillance of SARS-CoV-2 variants in October–November 2022 in Italy: detection of XBB.1, BA.2.75 and rapid spread of the BQ.1 lineage

Rosa, Giuseppina La; Brandtner, David; Ferraro, Giusy Bonanno; Veneri, Carolina; Mancini, Pamela; Iaconelli, Marcello; Lucentini, Luca; Giudice, Claudia Del; Orlandi, Lidia; Suffredini, Elisabetta

doi:10.1016/j.scitotenv.2023.162339

Cited by 22 publications

(24 citation statements)

References 19 publications

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“…211 As expected, the variant that was prevalent before being replaced by BQ.1/BQ.1.1 in late 2022 quickly became the dominant SARS-CoV-2 lineage in Italy. 211 By further analyzing existing sequencing data and studying the general patterns and differences of SARS-CoV-2 genomes in different regions, researchers can gain a better understanding of the virus's evolution and transmission modes. 212 One study analyzed 186,682 samples of SARS-CoV-2 isolates from different locations worldwide and classified them into 303 subgroups using PhenoGraph, an unsupervised learning classifier.…”

Section: Regional Lineage Replacementmentioning

confidence: 55%

“…211 They found that the proportion of samples containing mutations from the BQ.1 and BQ1.1 lineages increased significantly in November, reaching 43%. 211 As expected, the variant that was prevalent before being replaced by BQ.1/BQ.1.1 in late 2022 quickly became the dominant SARS-CoV-2 lineage in Italy. 211 By further analyzing existing sequencing data and studying the general patterns and differences of SARS-CoV-2 genomes in different regions, researchers can gain a better understanding of the virus's evolution and transmission modes.…”

Section: Regional Lineage Replacementmentioning

confidence: 97%

“…Nanopore sequencing can be used to monitor urban wastewater and predict the spread of VOCs across a country 211 . In Italy, researchers collected 332 wastewater samples from 20 regions and autonomous provinces between October and November 2022 and sequenced them using both Sanger and nanopore sequencing 211 . They found that the proportion of samples containing mutations from the BQ.1 and BQ1.1 lineages increased significantly in November, reaching 43% 211 .…”

Section: Application Of Nanopore Sequencing Technology During the Cov...mentioning

confidence: 99%

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Nanopore sequencing technology and its applications

Zheng

Zhou

Ding

et al. 2023

MedComm

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Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third‐generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID‐19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus‐2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID‐19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID‐19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.

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Section: Regional Lineage Replacementmentioning

confidence: 55%

Section: Regional Lineage Replacementmentioning

confidence: 97%

Section: Application Of Nanopore Sequencing Technology During the Cov...mentioning

confidence: 99%

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Nanopore sequencing technology and its applications

Zheng

Zhou

Ding

et al. 2023

MedComm

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“…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] .…”

Section: Introductionmentioning

confidence: 99%

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

Sutcliffe,

Kraemer,

Ellmen

et al. 2023

Preprint

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Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic “novel” lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances, and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1% frequency, results were more reliable above a 5% threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of noise or bias in wastewater sequencing data and to appreciate the commonalities and differences across methods.

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“…Therefore, in recognition of the immense potential of WBS, the European Commission recommended to Member States the implementation of regular SARS-CoV-2 monitoring through molecular analyses and sequencing of wastewater ( Commission Recommendation (EU) 2021/472 , 2021). Hence, a considerable number of studies with diverse aims, from establishing methodologies to finding new mutations, have reported results from WBS of European sub-populations (Agrawal et al, 2021; Amman et al, 2022; Galani et al, 2022; Izquierdo-Lara et al, 2021, 2023; Katharina et al, 2022; La Rosa et al, 2023; Medema et al, 2020; Monteiro et al, 2022; Pérez-Cataluña et al, 2022; Perez-Zabaleta et al, 2023). However, it is important to note that such studies are not limited to Europe; similar investigations have been conducted in American (Crits-Christoph et al, 2021; Fontenele et al, 2021; Gregory et al, 2022; Karthikeyan et al, 2022; Nemudryi et al, 2020; Peccia et al, 2020; Sapoval et al, 2023; Silva et al, 2022; Smyth et al, 2022; Swift et al, 2022) and Asian (Bar-Or et al, 2021) sub-populations as well.…”

Section: Introductionmentioning

confidence: 99%

Systematic SARS-CoV-2 S Gene Sequencing in Wastewater Samples Enables Early Lineage Detection and Uncovers Rare Mutations in Portugal

Reis,

Pinto,

Monteiro

et al. 2023

Preprint

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As the COVID-19 pandemic reached its peak, many countries implemented genomic surveillance systems to track the evolution and transmission of SARS-CoV-2. Transition from the pandemic to the endemic phase prioritized alternative testing strategies to maintain effective epidemic surveillance at the population level, with less intensive sequencing efforts. One such promising approach was Wastewater-Based Surveillance (WBS), which offers non-invasive, cost-effective means for analysing virus trends at the sewershed level. From 2020 onwards, wastewater has been recognized as an instrumental source of information for public health, with national and international authorities exploring options to implement national wastewater surveillance systems and increasingly relying on WBS as early warning of potential pathogen outbreaks. In Portugal, several pioneer projects joined the academia, water utilities and Public Administration around WBS.To validate WBS as an effective genomic surveillance strategy, it is crucial to collect long term performance data. In this work, we present one year of systematic SARS-CoV-2 wastewater surveillance in Portugal, representing 35% of the mainland population. We employed two complementary methods for lineage determination - allelic discrimination by RT-PCR and S gene sequencing. This combination allowed us to monitor variant evolution in near-real-time and identify low-frequency mutations.Over the course of this year-long study, spanning from May 2022 to April 2023, we successfully tracked the dominant Omicron sub-lineages, their progression and evolution, which aligned with concurrent clinical surveillance data. Our results underscore the effectiveness of WBS as a tracking system for virus variants, with the ability to unveil mutations undetected via massive sequencing of clinical samples from Portugal, demonstrating the ability of WBS to uncover new mutations and detect rare genetic variants.Our findings emphasize that knowledge of the genetic diversity of SARS-CoV-2 at the population level can be extended far beyond via the combination of routine clinical genomic surveillance with wastewater sequencing and genotyping.

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Wastewater surveillance of SARS-CoV-2 variants in October–November 2022 in Italy: detection of XBB.1, BA.2.75 and rapid spread of the BQ.1 lineage

Cited by 22 publications

References 19 publications

Nanopore sequencing technology and its applications

Nanopore sequencing technology and its applications

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

Systematic SARS-CoV-2 S Gene Sequencing in Wastewater Samples Enables Early Lineage Detection and Uncovers Rare Mutations in Portugal

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