Detection and quantification of SARS-CoV-2 RNA in wastewater influent in relation to reported COVID-19 incidence in Finland

Tiwari, Ananda; Lipponen, Anssi; Hokajärvi, Anna-Maria; Luomala, Oskari; Sarekoski, Anniina; Rytkönen, Annastiina; Österlund, Pamela; Al-Hello, Haider; Juutinen, Aapo; Miettinen, Ilkka T.; Savolainen-Kopra, Carita; Pitkänen, Tarja

doi:10.1016/j.watres.2022.118220

Cited by 69 publications

(36 citation statements)

References 42 publications

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“…To accomplish the social implementation of WBE, sensitive methods for the detection of SARS-CoV-2 RNA from wastewater have been developed in previous studies, but they require special and expensive equipment (e.g., Precellys, ddPCR, InnovaPrep) ( Ahmed et al, 2020b ; Kim et al, 2022 ; McMinn et al, 2021 ). In addition, many of the previous studies focused on liquids in wastewater for the detection of SARS-CoV-2 RNA, rather than solids ( Reynolds et al, 2022 ; Tiwari et al, 2022 ; Zdenkova et al, 2022 ). There has been an urgent need for a practical method for the detection of SARS-CoV-2 RNA in wastewater to monitor COVID-19 in low-prevalence communities ( Kitajima et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

The Efficient and Practical virus Identification System with ENhanced Sensitivity for Solids (EPISENS-S): A rapid and cost-effective SARS-CoV-2 RNA detection method for routine wastewater surveillance

Ando

Iwamoto

Kobayashi

et al. 2022

Science of The Total Environment

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Section: Discussionmentioning

confidence: 99%

The Efficient and Practical virus Identification System with ENhanced Sensitivity for Solids (EPISENS-S): A rapid and cost-effective SARS-CoV-2 RNA detection method for routine wastewater surveillance

Ando

Iwamoto

Kobayashi

et al. 2022

Science of The Total Environment

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“…The idea of wastewater-based epidemiology has been effective for monitoring SARS-CoV-2 ( Hokajärvi et al, 2021 ; Tiwari et al, 2022a ), as viruses are highly host-specific and do not multiply outside a host. But in the case of AMR, the interpretation is not so straightforward.…”

Section: Discussionmentioning

confidence: 99%

“…A total of seven 24-h composite wastewater (WW) influent samples (untreated municipal sewage) were collected in seven different months between October 2011 and August 2012 ( Figure 1 ), from Viikinmäki WWTP in Helsinki, Finland. On average, the daily influent volume at the Vikinmäki WWTP is about 296,000 m 3 ( Tiwari et al, 2022a ). The WWTP collects sewage from about 800,000 inhabitants (14.5% of the total population of Finland), including domestic households, nursing homes, primary health care centers, and hospitals in Helsinki and neighboring municipalities, namely Kerava, Tuusula, Järvenpää, Sipoo, and the eastern half of Vantaa.…”

Section: Methodsmentioning

confidence: 99%

Wastewater Surveillance Detected Carbapenemase Enzymes in Clinically Relevant Gram-Negative Bacteria in Helsinki, Finland; 2011–2012

et al. 2022

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Antimicrobial resistance profiling of pathogens helps to identify the emergence of rare or new resistance threats and prioritize possible actions to be taken against them. The analysis of wastewater (WW) can reveal the circulation of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARG) among the catchment communities. Here, we analyzed WW influent samples to determine the prevalence of carbapenemase genes-carrying Gram-negative bacteria (Carba-GNB) in Helsinki, Finland. This study set important historical reference points from the very early stage of the carbapenemase era, during the period 2011–2012. A total of 405 bacterial isolates grown on CHROMagarKPC (n = 195) and CHROMagarESBL (n = 210) from WW influent samples were collected between October 2011 and August 2012 and were analyzed. The bacterial DNA from the isolates was extracted, and the prevalence of carbapenemases genes blaKPC, blaNDM, blaGES, blaOXA-48, blaIMP, blaIMI, and blaVIM were screened with multiplexed PCR. All carbapenemase-positive isolates were identified taxonomically to species or genus level with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The nucleic acid extraction was successful for 399 isolates, of which 59 (14.8%) were found to carry carbapenemase genes. A total of 89.8% of the carbapenemase positive isolates (53 out of 59) were obtained from CHROMagarKPC plates and only 10.2% (six out of 59) were obtained from CHROMagar ESBL plates. Among the Carba-GNB isolates, 86.4% were blaGES (51 out of 59), 10.2% were blaKPC (six out of 59), and 3.4% were blaVIM (two out of 59). The most common carba-gene, blaGES, was carried by 10 different bacterial species, including Aeromonas spp., Enterobacter spp., and Kluyvera spp.; the blaKPC gene was carried by Escherichia coli, Klebsiella pneumoniae, and Kluyvera cryocescens; and the blaVIM gene was carried by Aeromonas hydrophila/caviae and Citrobacter amalonaticus. This study emphasizes that wastewater surveillance (WWS) can be an additional tool for monitoring antimicrobial resistance (AMR) at the population level.

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“…A previous study reported a probability of 0.75 to quantify SARS-CoV-2 gene in wastewater by RT-qPCR when the 14-day COVID-19 case rate was 152/100 000 persons. 40 In that study, viruses were concentrated from solids-removed influent samples by 10-kDa Centricon ultra-filters. 40 We are not aware of other wastewater sequencing studies that have calculated SARS-CoV-2 WGS success rates with regard to the incidence rate, but our results suggest that SARS-CoV-2 WGS with the viruses recovered by tangential-flow filtration method can be successfully applied at low COVID-19 incidence rates.…”

Section: Resultsmentioning

confidence: 99%

Improved Robustness of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method

Segelhurst

Bard

Pillsbury

et al. 2022

Preprint

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The sequencing of human virus genomes from wastewater samples is an efficient method for tracking viral transmission and evolution at the community level. However, this requires the recovery of viral nucleic acids of high quality. We developed a reusable tangential-flow filtration system to concentrate and purify viruses from wastewater for whole-genome sequencing. A pilot study was conducted with 94 wastewater samples from four local sewersheds, from which viral nucleic acids were extracted, and the whole genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was sequenced using the ARTIC V4.0 primers. Our method yielded a high probability (0.9) of recovering complete or near-complete SARS-CoV-2 genomes (>90% coverage at 10× depth) from wastewater when the COVID-19 incidence rate exceeded 33 cases per 100 000 people. The relative abundances of sequenced SARS-CoV-2 variants followed the trends observed from patient-derived samples. We also identified SARS-CoV-2 lineages in wastewater that were underrepresented or not present in the clinical whole-genome sequencing data. The developed tangential-flow filtration system can be easily adopted for the sequencing of other viruses in wastewater, particularly those at low concentrations.

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Detection and quantification of SARS-CoV-2 RNA in wastewater influent in relation to reported COVID-19 incidence in Finland

Cited by 69 publications

References 42 publications

The Efficient and Practical virus Identification System with ENhanced Sensitivity for Solids (EPISENS-S): A rapid and cost-effective SARS-CoV-2 RNA detection method for routine wastewater surveillance

The Efficient and Practical virus Identification System with ENhanced Sensitivity for Solids (EPISENS-S): A rapid and cost-effective SARS-CoV-2 RNA detection method for routine wastewater surveillance

Wastewater Surveillance Detected Carbapenemase Enzymes in Clinically Relevant Gram-Negative Bacteria in Helsinki, Finland; 2011–2012

Improved Robustness of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method

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