COPMAN: A novel high-throughput and highly sensitive method to detect viral nucleic acids including SARS-CoV-2 RNA in wastewater

Katayama, Yuka Adachi; Hayase, Shin; Ando, Yuichi; Kuroita, Tomohiro; Okada, Kazuya; Iwamoto, Ryo; Yanagimoto, Toru; Kitajima, Masaaki; Masago, Yusaku

doi:10.1016/j.scitotenv.2022.158966

Cited by 11 publications

(8 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Since our chief objective was to determine non-enveloped diarrheal viruses from the SW, we used non-enveloped MNV as the process control and the PEG precipitation (ppt) method for the concentration of the virus, which remained the most popular and widely used method for the concentration of non-enveloped diarrheal viruses from wastewater. Nonetheless, in agreement with recent evidence (Adachi Katayama et al, 2023 ), the weakness of the PEG ppt method for the detection of nCoV from SW has been found in the present study.…”

Section: Discussionsupporting

confidence: 93%

“…Recent evidence suggests that, unlike non-enveloped viruses, the detection of enveloped nCoV from the sewage is much more difficult, particularly from the effluent (Hata et al, 2021 ; Kitamura et al, 2021 ). Very recently, Adachi Katayama et al ( 2023 ) demonstrated a novel highly sensitive COPMAN (Coagulation and Proteolysis method using Magnetic beads for detection of Nucleic acids) method to detect nCoV from wastewater. Since our chief objective was to determine non-enveloped diarrheal viruses from the SW, we used non-enveloped MNV as the process control and the PEG precipitation (ppt) method for the concentration of the virus, which remained the most popular and widely used method for the concentration of non-enveloped diarrheal viruses from wastewater.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Genotype Diversity of Enteric Viruses in Wastewater Amid the COVID-19 Pandemic

et al. 2023

View full text Add to dashboard Cite

Viruses remain the leading cause of acute gastroenteritis (AGE) worldwide. Recently, we reported the abundance of AGE viruses in raw sewage water (SW) during the COVID-19 pandemic, when viral AGE patients decreased dramatically in clinics. Since clinical samples were not reflecting the actual state, it remained important to determine the circulating strains in the SW for preparedness against impending outbreaks. Raw SW was collected from a sewage treatment plant in Japan from August 2018 to March 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major gastroenteritis viruses by RT-PCR. Genotypes and evolutionary relationships were evaluated through sequence-based analyses. Major AGE viruses like rotavirus A (RVA), norovirus (NoV) GI and GII, and astrovirus (AstV) increased sharply (10–20%) in SW during the COVID-19 pandemic, though some AGE viruses like sapovirus (SV), adenovirus (AdV), and enterovirus (EV) decreased slightly (3–10%). The prevalence remained top in the winter. Importantly, several strains, including G1 and G3 of RVA, GI.1 and GII.2 of NoV, GI.1 of SV, MLB1 of AstV, and F41 of AdV, either emerged or increased amid the pandemic, suggesting that the normal phenomenon of genotype changing remained active over this time. This study crucially presents the molecular characteristics of circulating AGE viruses, explaining the importance of SW investigation during the pandemic when a clinical investigation may not produce the complete scenario.

show abstract

Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Genotype Diversity of Enteric Viruses in Wastewater Amid the COVID-19 Pandemic

et al. 2023

View full text Add to dashboard Cite

show abstract

“…We are aware of the existence of multiple variants of PEG precipitation protocols including different combinations of usage of PEG-6000 ( 33 , 34 ) or PEG-8000 ( 35 , 36 ), different PEG concentrations ranging from 8%, 10% up to 50% ( 29 , 34 ), different NaCl concentrations ( 37 – 39 ), and different times of incubation varying from 15 min to overnight (18 h) ( 11 , 40 ). Not having the capacity to test all of them, we decided to use the protocol utilizing 10% PEG-8000 with 0.3 M NaCl overnight incubation.…”

Section: Discussionmentioning

confidence: 99%

Comparison of the methods for isolation and detection of SARS-CoV-2 RNA in municipal wastewater

Lucansky

Samec

Burjanivova

et al. 2023

Front. Public Health

View full text Add to dashboard Cite

IntroductionCoronavirus SARS-CoV-2 is a causative agent responsible for the current global pandemic situation known as COVID-19. Clinical manifestations of COVID-19 include a wide range of symptoms from mild (i.e., cough, fever, dyspnea) to severe pneumonia-like respiratory symptoms. SARS-CoV-2 has been demonstrated to be detectable in the stool of COVID-19 patients. Waste-based epidemiology (WBE) has been shown as a promising approach for early detection and monitoring of SARS-CoV-2 in the local population performed via collection, isolation, and detection of viral pathogens from environmental sources.MethodsIn order to select the optimal protocol for monitoring the COVID-19 epidemiological situation in region Turiec, Slovakia, we (1) compared methods for SARS-CoV-2 separation and isolation, including virus precipitation by polyethylene glycol (PEG), virus purification via ultrafiltration (Vivaspin®) and subsequent isolation by NucleoSpin RNA Virus kit (Macherey-Nagel), and direct isolation from wastewater (Zymo Environ Water RNA Kit); (2) evaluated the impact of water freezing on SARS- CoV-2 separation, isolation, and detection; (3) evaluated the role of wastewater filtration on virus stability; and (4) determined appropriate methods including reverse transcription-droplet digital PCR (RT-ddPCR) and real-time quantitative polymerase chain reaction (RT-qPCR) (targeting the same genes, i.e., RdRp and gene E) for quantitative detection of SARS-CoV-2 in wastewater samples.Results(1) Usage of Zymo Environ Water RNA Kit provided superior quality of isolated RNA in comparison with both ultracentrifugation and PEG precipitation. (2) Freezing of wastewater samples significantly reduces the RNA yield. (3) Filtering is counterproductive when Zymo Environ Water RNA Kit is used. (4) According to the specificity and sensitivity, the RT-ddPCR outperforms RT-qPCR.DiscussionThe results of our study suggest that WBE is a valuable early warning alert and represents a non-invasive approach to monitor viral pathogens, thus protects public health on a regional and national level. In addition, we have shown that the sensitivity of testing the samples with a nearer detection limit can be improved by selecting the appropriate combination of enrichment, isolation, and detection methods.

show abstract

“…Also, different organizations, institutions, and government departments have been providing various guidelines, standards, and protocols for wastewater surveillance. Although polymerase chain reaction (PCR)-based detection is the mostly used method and a de facto gold standard, researchers are continuously developing more sensitive and higher throughput analytical methods such as COPMAN and EPISENS-S [ 24 , 25 , 26 , 27 ]. This leads to the generation of inconsistent data from different testing facilities such that results may not be comparable within or among different programs or jurisdictions.…”

Section: Future Research To Improve the Wbe Methodologiesmentioning

confidence: 99%