Spatiotemporal Surveillance of SARS-CoV-2 in the Sewage of Three Major Urban Areas in Peru: Generating Valuable Data Where Clinical Testing Is Extremely Limited

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This article references 57 other publications.

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   Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset

   Karlinsky, Ariel; Kobak, Dmitry

   eLife (2021), 10 (), e69336CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)

   Comparing the impact of the COVID-19 pandemic between countries or across time is difficult because the reported nos. of cases and deaths can be strongly affected by testing capacity and reporting policy. Excess mortality, defined as the increase in all-cause mortality relative to the expected mortality, is widely considered as a more objective indicator of the COVID-19 death toll. However, there has been no global, frequently updated repository of the all-cause mortality data across countries. To fill this gap, we have collected weekly, monthly, or quarterly all-cause mortality data from 103 countries and territories, openly available as the regularly updated World Mortality Dataset. We used this dataset to compute the excess mortality in each country during the COVID-19 pandemic. We found that in several worst-affected countries (Peru, Ecuador, Bolivia, Mexico) the excess mortality was above 50% of the expected annual mortality (Peru, Ecuador, Bolivia, Mexico) or above 400 excess deaths per 100,000 population (Peru, Bulgaria, North Macedonia, Serbia). At the same time, in several other countries (e.g. Australia and New Zealand) mortality during the pandemic was below the usual level, presumably due to social distancing measures decreasing the non-COVID infectious mortality. Furthermore, we found that while many countries have been reporting the COVID-19 deaths very accurately, some countries have been substantially underreporting their COVID-19 deaths (e.g. Nicaragua, Russia, Uzbekistan), by up to two orders of magnitude (Tajikistan). Our results highlight the importance of open and rapid all-cause mortality reporting for pandemic monitoring.
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   Hernández-Vásquez, A.; Barrenechea-Pulache, A.; Azañedo, D. COVID-19 testing in Peru: low access and inequalities. Journal of Public Health (Oxford, England) 2021, 43, e504– e506,  DOI: 10.1093/pubmed/fdab125

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    Collivignarelli, M. C.; Collivignarelli, C.; Miino, M. C.; Abbà, A.; Pedrazzani, R.; Bertanza, G. SARS-CoV-2 in sewer systems and connected facilities. Process Saf. Environ. Prot. 2020, 143, 196– 203,  DOI: 10.1016/j.psep.2020.06.049

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    SARS-CoV-2 in sewer systems and connected facilities

    Collivignarelli, Maria Cristina; Collivignarelli, Carlo; Carnevale Miino, Marco; Abba, Alessandro; Pedrazzani, Roberta; Bertanza, Giorgio

    Process Safety and Environmental Protection (2020), 143 (), 196-203CODEN: PSEPEM; ISSN:0957-5820. (Elsevier B.V.)

    A review. As for the SARS coronavirus in the 2003 epidemic, the presence of SARS-CoV-2 has been demonstrated in faeces and, in some cases, urine of infected people, as well as in wastewater. This paper proposes a crit. review of the state of the art regarding studies on the presence of SARS-CoV-2 in wastewater and sewage sludge, the factors affecting its inactivation and the main proposed treatments. In-vitro tests demonstrated low resistance of SARS-CoV-2 to high temp., while even significant changes in pH would not seem to det. the disappearance of the virus. In real wastewater and in sewage sludge, to date studies on the influence of the different parameters on the inactivation of SARS-CoV-2 are not available. Therefore, studies involving other HCoVs such as SARS-CoV and HCoV-229E have been also considered, in order to formulate a hypothesis regarding its behavior in sewage and throughout the steps of biol. treatments in WWTPs. Finally, SARS-CoV-2 in wastewater might track the epidemic trends: although being extremely promising, an effective and wide application of this approach requires a deeper knowledge of the amts. of viruses excreted through the faeces and the actual detectability of viral RNA in sewage.
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    Tian, Y.; Rong, L.; Nian, W.; He, Y. Gastrointestinal features in COVID-19 and the possibility of faecal transmission. Alimentary pharmacology & therapeutics 2020, 51 (9), 843– 851,  DOI: 10.1111/apt.15731

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    Review article: gastrointestinal features in COVID-19 and the possibility of faecal transmission

    Tian, Yuan; Rong, Long; Nian, Weidong; He, Yan

    Alimentary Pharmacology and Therapeutics (2020), 51 (9), 843-851CODEN: APTHEN; ISSN:0269-2813. (Wiley-Blackwell)

    A review. Summary : Background : There is little published evidence on the gastrointestinal features of COVID-19. Aims : To report on the gastrointestinal manifestations and pathol. findings of patients with COVID-19, and to discuss the possibility of faecal transmission. Methods : We have reviewed gastrointestinal features of, and faecal test results in, COVID-19 from case reports and retrospective clin. studies relating to the digestive system published since the outbreak. Results : With an incidence of 3% (1/41)-79% (159/201), gastrointestinal symptoms of COVID-19 included anorexia 39.9% (55/138)-50.2% (101/201), diarrhoea 2% (2/99)-49.5% (146/295), vomiting 3.6% (5/138)-66.7% (4/6), nausea 1% (1/99)-29.4% (59/201), abdominal pain 2.2% (3/138)-6.0% (12/201) and gastrointestinal bleeding 4% (2/52)-13.7% (10/73). Diarrhoea was the most common gastrointestinal symptom in children and adults, with a mean duration of 4.1 ± 2.5 days, and was obsd. before and after diagnosis. Vomiting was more prominent in children. About 3.6% (5/138)-15.9% (32/201) of adult and 6.5% (2/31)-66.7% (4/6) of children patients presented vomiting. Adult and children patients can present with digestive symptoms in the absence of respiratory symptoms. The incidence of digestive manifestations was higher in the later than in the early stage of the epidemic, but no differences in digestive symptoms among different regions were found. Among the group of patients with a higher proportion of severe cases, the proportion of gastrointestinal symptoms in severe patients was higher than that in nonsevere patients (anorexia 66.7% vs 30.4%; abdominal pain 8.3% vs 0%); while in the group of patients with a lower severe rate, the proportion with gastrointestinal symptoms was similar in severe and nonsevere cases (nausea and vomiting 6.9% vs 4.6%; diarrhoea 5.8% vs 3.5%). Angiotensin converting enzyme 2 and virus nucleocapsid protein were detected in gastrointestinal epithelial cells, and infectious virus particles were isolated from faeces. Faecal PCR testing was as accurate as respiratory specimen PCR detection. In 36% (5/14)-53% (39/73) faecal PCR became pos., 2-5 days later than sputum PCR pos. Faecal excretion persisted after sputum excretion in 23% (17/73)-82% (54/66) patients for 1-11 days. Conclusions : Gastrointestinal symptoms are common in patients with COVID-19, and had an increased prevalence in the later stage of the recent epidemic in China. SARS-CoV-2 enters gastrointestinal epithelial cells, and the faeces of COVID-19 patients are potentially infectious.
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    Prolonged presence of SARS-CoV-2 viral RNA in faecal samples

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    Wang, Wenling; Xu, Yanli; Gao, Ruqin; Lu, Roujian; Han, Kai; Wu, Guizhen; Tan, Wenjie

    JAMA, the Journal of the American Medical Association (2020), 323 (18), 1843-1844CODEN: JAMAAP; ISSN:1538-3598. (American Medical Association)

    The present article describes about detection of SARS-CoV-2 in different types of clin. specimens.
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    Xiao, Fei; Sun, Jing; Xu, Yonghao; Li, Fang; Huang, Xiaofang; Li, Heying; Zhao, Jingxian; Huang, Jicheng; Zhao, Jincun

    Emerging Infectious Diseases (2020), 26 (8), 1920-1922CODEN: EIDIFA; ISSN:1080-6059. (Centers for Disease Control and Prevention)

    Severe acute respiratory syndrome coronavirus 2 was isolated from feces of a patient in China with coronavirus disease who died. Confirmation of infectious virus in feces affirms the potential for fecal-oral or fecal-respiratory transmission and warrants further study.
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    de Oliveira, L. C. Viability of SARS-CoV-2 in river water and wastewater at different temperatures and solids content. Water research 2021, 195, 117002,  DOI: 10.1016/j.watres.2021.117002

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    Viability of SARS-CoV-2 in river water and wastewater at different temperatures and solids content

    de Oliveira, Leonardo Camilo; Torres-Franco, Andres Felipe; Lopes, Bruna Coelho; Santos, Beatriz Senra Alvares da Silva; Costa, Erica Azevedo; Costa, Michelle S.; Reis, Marcus Tulius P.; Melo, Marilia C.; Polizzi, Rodrigo Bicalho; Teixeira, Mauro Martins; Mota, Cesar Rossas

    Water Research (2021), 195 (), 117002CODEN: WATRAG; ISSN:0043-1354. (Elsevier Ltd.)

    COVID-19 patients can excrete viable SARS-CoV-2 virus via urine and faeces, which has raised concerns over the possibility of COVID-19 transmission via aerosolized contaminated water or via the faecal-oral route. These concerns are esp. exacerbated in many low- and middle-income countries, where untreated sewage is frequently discharged to surface waters. SARS-CoV-2 RNA has been detected in river water (RW) and raw wastewater (WW) samples. However, little is known about SARS-CoV-2 viability in these environmental matrixes. Detg. the persistence of SARS-CoV-2 in water under different environmental conditions is of great importance for basic assumptions in quant. microbial risk assessment (QMRA). In this study, the persistence of SARS-CoV-2 was assessed using plaque assays following spiking of RW and WW samples with infectious SARS-CoV-2 that was previously isolated from a COVID-19 patient. These assays were carried out on autoclaved RW and WW samples, filtered (0.22μm) and unfiltered, at 4°C and 24°C. Linear and nonlinear regression models were adjusted to the data. The Weibull regression model achieved the lowest root mean square error (RMSE) and was hence chosen to est. T90 and T99 (time required for 1 log and 2 log redns., resp.). SARS-CoV-2 remained viable longer in filtered compared with unfiltered samples. RW and WW showed T90 values of 1.9 and 1.2 day and T99 values of 6.4 and 4.0 days, resp. When samples were filtered through 0.22μm pore size membranes, T90 values increased to 3.3 and 1.5 days, and T99 increased to 8.5 and 4.5 days, for RW and WW samples, resp. Remarkable increases in SARS-CoV-2 persistence were obsd. in assays at 4°C, which showed T90 values of 7.7 and 5.5 days, and T99 values of 18.7 and 17.5 days for RW and WW, resp. These results highlight the variability of SARS-CoV-2 persistence in water and wastewater matrixes and can be highly relevant to efforts aimed at quantifying water-related risks, which could be valuable for understanding and controlling the pandemic.
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    Heller, L.; Mota, C. R.; Greco, D. B. COVID-19 faecal-oral transmission: Are we asking the right questions?. Sci. Total Environ. 2020, 729, 138919,  DOI: 10.1016/j.scitotenv.2020.138919

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    COVID-19 faecal-oral transmission: Are we asking the right questions?

    Heller, Leo; Mota, Cesar R.; Greco, Dirceu B.

    Science of the Total Environment (2020), 729 (), 138919CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    A brief review with commentary. Detection of the SARS-CoV-2 virus in stools and sewage has recently been reported, raising the hypothesis of fecal-oral transmission. If confirmed, this could have far-reaching consequences for public health and for pandemic control strategies. In this paper, we argue that a comprehensive and more nuanced anal. is required to test this hypothesis, taking into consideration both environmental dynamics and the persistence of viral infectivity. First, we examine the evidence regarding the presence of the virus in stools and sewage. Then we discuss the current framework of disease transmission through water and excreta and how the transmission of a respiratory disease fits into it. Against this background, we propose a framework to test the fecal-oral hypothesis, unpacking the different environmental routes from feces to the mouth of a susceptible person. This framework should not be seen as a confirmation of the hypothesis but rather as an expanded view of its complexities, which could help shaping an agenda for research into a no. of unanswered questions. Finally, the paper briefly discusses practical implications, based on current knowledge, for containment of the pandemic.
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    Giacobbo, A.; Rodrigues, M. A. S.; Zoppas Ferreira, J.; Bernardes, A. M.; de Pinho, M. N. A critical review on SARS-CoV-2 infectivity in water and wastewater. What do we know?. Sci. Total Environ. 2021, 774, 145721,  DOI: 10.1016/j.scitotenv.2021.145721

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    A critical review on SARS-CoV-2 infectivity in water and wastewater. What do we know?

    Giacobbo, Alexandre; Rodrigues, Marco Antonio Siqueira; Zoppas Ferreira, Jane; Bernardes, Andrea Moura; de Pinho, Maria Norberta

    Science of the Total Environment (2021), 774 (), 145721CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    A review. The COVID-19 outbreak circulating the world is far from being controlled, and possible contamination routes are still being studied. There are no confirmed cases yet, but little is known about the infection possibility via contact with sewage or contaminated water as well as with aerosols generated during the pumping and treatment of these aq. matrixes. Therefore, this article presents a literature review on the detection of SARS-CoV-2 in human excreta and its pathways through the sewer system and wastewater treatment plants until it reaches the water bodies, highlighting their occurrence and infectivity in sewage and natural water. Research lines are still indicated, which we believe are important for improving the detection, quantification, and mainly the infectivity analyzes of SARS-CoV-2 and other enveloped viruses in sewage and natural water. In fact, up till now, no case of transmission via contact with sewage or contaminated water has been reported and the few studies conducted with these aq. matrixes have not detected infectious viruses. On the other hand, studies are showing that SARS-CoV-2 can remain viable, i.e., infectious, for ≤4.3 and 6 days in sewage and water, resp., and that other species of coronavirus may remain viable in these aq. matrixes for >1 yr, depending on the sample conditions. These are strong pieces of evidence that the contamination mediated by contact with sewage or contaminated water cannot be ruled out, even because other more resistant and infectious mutations of SARS-CoV-2 may appear.
18. 18

    Mohapatra, S. The novel SARS-CoV-2 pandemic: Possible environmental transmission, detection, persistence and fate during wastewater and water treatment. Science of The Total Environment 2021, 765, 142746,  DOI: 10.1016/j.scitotenv.2020.142746

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    The novel SARS-CoV-2 pandemic: Possible environmental transmission, detection, persistence and fate during wastewater and water treatment

    Mohapatra, Sanjeeb; Menon, N. Gayathri; Mohapatra, Gayatree; Pisharody, Lakshmi; Pattnaik, Aryamav; Menon, N. Gowri; Bhukya, Prudhvi Lal; Srivastava, Manjita; Singh, Meenakshi; Barman, Muneesh Kumar; Gin, Karina Yew-Hoong; Mukherji, Suparna

    Science of the Total Environment (2021), 765 (), 142746CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    A review. The contagious SARS-CoV-2 virus, responsible for COVID-19 disease, has infected >27 million people across the globe within a few months. While literature on SARS-CoV-2 indicates that its transmission may occur predominantly via aerosolization of virus-laden droplets, the possibility of alternate routes of transmission and(or) reinfection via the environment requires considerable scientific attention. This review aims to collate information on possible transmission routes of this virus to ascertain its fate in the environment. Concomitant with the presence of SARS-CoV-2 viral RNA in feces and saliva of infected patients, studies also indicated its occurrence in raw wastewater, primary sludge, and river water. Therefore sewerage system could be a possible route of virus outbreak, a possible tool to assess viral community spread and future surveillance technique. Hence, this review looked into detection, occurrence, and fate of SARS-CoV-2 during primary, secondary, and tertiary wastewater and water treatment processes based on published literature on SARS-CoV and other enveloped viruses. The review also highlights the need for focused research on occurrence and fate of SARS-CoV-2 in various environmental matrixes. Utilization of this information in environmental transmission models developed for other enveloped and enteric viruses can facilitate risk assessment studies. Preliminary research efforts with SARS-CoV-2 and established scientific reports on other coronaviruses indicate that the threat of virus transmission from the aquatic environment may be currently non-existent. However, the presence of viral RNA in wastewater provides an early warning that highlights the need for effective sewage treatment to prevent a future outbreak of SARS-CoV-2.
19. 19

    Ahmed, W. Decay of SARS-CoV-2 and surrogate murine hepatitis virus RNA in untreated wastewater to inform application in wastewater-based epidemiology. Environmental Research 2020, 191, 110092,  DOI: 10.1016/j.envres.2020.110092

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    Decay of SARS-CoV-2 and surrogate murine hepatitis virus RNA in untreated wastewater to inform application in wastewater-based epidemiology

    Ahmed, Warish; Bertsch, Paul M.; Bibby, Kyle; Haramoto, Eiji; Hewitt, Joanne; Huygens, Flavia; Gyawali, Pradip; Korajkic, Asja; Riddell, Shane; Sherchan, Samendra P.; Simpson, Stuart L.; Sirikanchana, Kwanrawee; Symonds, Erin M.; Verhagen, Rory; Vasan, Seshadri S.; Kitajima, Masaaki; Bivins, Aaron

    Environmental Research (2020), 191 (), 110092CODEN: ENVRAL; ISSN:0013-9351. (Elsevier Inc.)

    Wastewater-based epidemiol. (WBE) demonstrates potential for COVID-19 community transmission monitoring; however, data on the stability of SARS-CoV-2 RNA in wastewater are needed to interpret WBE results. The decay rates of RNA from SARS-CoV-2 and a potential surrogate, murine hepatitis virus (MHV), were investigated by reverse transcription-quant. polymerase chain reaction (RT-qPCR) in untreated wastewater, autoclaved wastewater, and dechlorinated tap water stored at 4, 15, 25, and 37°C. Temp., followed by matrix type, most greatly influenced SARS-CoV-2 RNA first-order decay rates (k). The av. T90 (time required for 1-log10 redn.) of SARS-CoV-2 RNA ranged from 8.04 to 27.8 days in untreated wastewater, 5.71 to 43.2 days in autoclaved wastewater, and 9.40 to 58.6 days in tap water. The av. T90 for RNA of MHV at 4 to 37°C ranged from 7.44 to 56.6 days in untreated wastewater, 5.58-43.1 days in autoclaved wastewater, and 10.9 to 43.9 days in tap water. There was no statistically significant difference between RNA decay of SARS-CoV-2 and MHV; thus, MHV is suggested as a suitable persistence surrogate. Decay rate consts. for all temps. were comparable across all matrixes for both viral RNAs, except in untreated wastewater for SARS-CoV-2, which showed less sensitivity to elevated temps. Therefore, SARS-CoV-2 RNA is likely to persist long enough in untreated wastewater to permit reliable detection for WBE application.
20. 20

    Gonzalez, R. COVID-19 surveillance in Southeastern Virginia using wastewater-based epidemiology. Water research 2020, 186, 116296,  DOI: 10.1016/j.watres.2020.116296

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    COVID-19 surveillance in Southeastern Virginia using wastewater-based epidemiology

    Gonzalez, Raul; Curtis, Kyle; Bivins, Aaron; Bibby, Kyle; Weir, Mark H.; Yetka, Kathleen; Thompson, Hannah; Keeling, David; Mitchell, Jamie; Gonzalez, Dana

    Water Research (2020), 186 (), 116296CODEN: WATRAG; ISSN:0043-1354. (Elsevier Ltd.)

    Wastewater-based epidemiol. (WBE) has been used to analyze markers in wastewater treatment plant (WWTP) influent to characterize emerging chems., drug use patterns, or disease spread within communities. This approach can be particularly helpful in understanding outbreaks of disease like the novel Coronavirus disease-19 (COVID-19) when combined with clin. datasets. In this study, three RT-ddPCR assays (N1, N2, N3) were used to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in weekly samples from nine WWTPs in southeastern Virginia. In the first several weeks of sampling, SARS-CoV-2 detections were sporadic. Frequency of detections and overall concns. of RNA within samples increased from mid March into late July. During the twenty-one week study, SARS-CoV-2 concns. ranged from 101 to 104 copies 100 mL-1 in samples where viral RNA was detected. Fluctuations in population normalized loading rates in several of the WWTP service areas agreed with known outbreaks during the study. Here we propose several ways that data can be presented spatially and temporally to be of greatest use to public health officials. As the COVID-19 pandemic wanes, it is likely that communities will see increased incidence of small, localized outbreaks. In these instances, WBE could be used as a pre-screening tool to better target clin. testing needs in communities with limited resources.
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    Sherchan, S. P. First detection of SARS-CoV-2 RNA in wastewater in North America: a study in Louisiana, USA. Science of The Total Environment 2020, 743, 140621,  DOI: 10.1016/j.scitotenv.2020.140621

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    First detection of SARS-CoV-2 RNA in wastewater in North America: A study in Louisiana, USA

    Sherchan, Samendra P.; Shahin, Shalina; Ward, Lauren M.; Tandukar, Sarmila; Aw, Tiong G.; Schmitz, Bradley; Ahmed, Warish; Kitajima, Masaaki

    Science of the Total Environment (2020), 743 (), 140621CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    The authors investigated the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater samples in southern Louisiana, USA. Untreated and treated wastewater samples were collected on five occasions over a four-month period from Jan. to Apr. 2020. The wastewater samples were concd. via ultrafiltration (Method A), and an adsorption-elution method using electroneg. membranes (Method B). SARS-CoV-2 RNA was detected in 2 out of 15 wastewater samples using two reverse transcription-quant. polymerase chain reaction (RT-qPCR) assays (CDC N1 and N2). None of the secondary treated and final effluent samples tested pos. for SARS-CoV-2 RNA. To the authors' knowledge, this is the first study reporting the detection of SARS-CoV-2 RNA in wastewater in North America, including the USA. However, concn. methods and RT-qPCR assays need to be refined and validated to increase the sensitivity of SARS-CoV-2 RNA detection in wastewater.
22. 22

    Mota, C. R. Assessing spatial distribution of COVID-19 prevalence in Brazil using decentralised sewage monitoring. Water Res. 2021, 202, 117388,  DOI: 10.1016/j.watres.2021.117388

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    22

    Assessing spatial distribution of COVID-19 prevalence in Brazil using decentralized sewage monitoring

    Mota, Cesar R.; Bressani-Ribeiro, Thiago; Araujo, Juliana C.; Leal, Cintia D.; Leroy-Freitas, Deborah; Machado, Elayne C.; Espinosa, Maria Fernanda; Fernandes, Luyara; Leao, Thiago L.; Chamhum-Silva, Lucas; Azevedo, Lariza; Morandi, Thiago; Freitas, Gabriel Tadeu O.; Costa, Michelle S.; Carvalho, Beatriz O.; Reis, Marcus Tulius P.; Melo, Marilia C.; Ayrimoraes, Sergio R.; Chernicharo, Carlos A. L.

    Water Research (2021), 202 (), 117388CODEN: WATRAG; ISSN:0043-1354. (Elsevier Ltd.)

    Brazil has become one of the epicentres of the COVID-19 pandemic, with cases heavily concd. in large cities. Testing data is extremely limited and unreliable, which restricts health authorities' ability to deal with the pandemic. Given the stark demog., social and economic heterogeneities within Brazilian cities, it is important to identify hotspots so that the limited resources available can have the greatest impact. This study shows that decentralised monitoring of SARS-CoV-2 RNA in sewage can be used to assess the distribution of COVID-19 prevalence in the city. The methodol. developed in this study allowed the identification of hotspots by comprehensively monitoring sewers distributed through Belo Horizonte, Brazil's third largest city. Our results show that the most vulnerable neighborhoods in the city were the hardest hit by the pandemic, indicating that, for many Brazilians, the situation is much worse than reported by official figures.
23. 23

    Medema, G.; Heijnen, L.; Elsinga, G.; Italiaander, R.; Brouwer, A. Presence of SARS-Coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in the Netherlands. Environ. Sci. Technol. Lett. 2020, 7 (7), 511– 516,  DOI: 10.1021/acs.estlett.0c00357

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    23

    Presence of SARS-Coronavirus-2 RNA in Sewage and Correlation with Reported COVID-19 Prevalence in the Early Stage of the Epidemic in The Netherlands

    Medema, Gertjan; Heijnen, Leo; Elsinga, Goffe; Italiaander, Ronald; Brouwer, Anke

    Environmental Science & Technology Letters (2020), 7 (7), 511-516CODEN: ESTLCU; ISSN:2328-8930. (American Chemical Society)

    In the current COVID-19 pandemic, a significant proportion of cases shed SARS-Coronavirus-2 (SARS-CoV-2) with their faeces. To det. if SARS-CoV-2 RNA was present in sewage during the emergence of COVID-19 in The Netherlands, sewage samples of six cities and the airport were tested using four qRT-PCR assays, three targeting the nucleocapsid gene (N1-N3) and one the envelope gene (E). No SARS-CoV-2 RNA was detected on Feb. 6, 3 wk before the first Dutch case was reported. On March 4/5, one or more gene fragments were detected in sewage of three sites, in concns. of 2.6-30 gene copies per mL. In Amersfoort, N3 was detected in sewage 6 days before the first cases were reported. As the prevalence of COVID-19 in these cities increased in March, the RNA signal detected by each qRT-PCR assay increased, for N1-N3 up to 790-2200 gene copies per mL. This increase correlated significantly with the increase in reported COVID-19 prevalence. The detection of the virus RNA in sewage, even when the COVID-19 prevalence is low, and the correlation between concn. in sewage and reported prevalence of COVID-19, indicate that sewage surveillance could be a sensitive tool to monitor the circulation of the virus in the population.
24. 24

    Nemudryi, A. Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater. Cell Reports Medicine 2020, 1 (6), 100098,  DOI: 10.1016/j.xcrm.2020.100098

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    24

    Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater

    Nemudryi, Artem; Nemudraia, Anna; Wiegand, Tanner; Surya, Kevin; Buyukyoruk, Murat; Cicha, Calvin; Vanderwood, Karl K.; Wilkinson, Royce; Wiedenheft, Blake

    Cell Reports Medicine (2020), 1 (6), 100098CODEN: CRMEDE; ISSN:2666-3791. (Elsevier Inc.)

    SARS-CoV-2 has recently been detected in feces, which indicates that wastewater may be used to monitor viral prevalence in the community. Here, we use RT-qPCR to monitor wastewater for SARS-CoV-2 RNA over a 74-day time course. We show that changes in SARS-CoV-2 RNA concns. follow symptom onset gathered by retrospective interview of patients but precedes clin. test results. In addn., we det. a nearly complete (98.5%) SARS-CoV-2 genome sequence from wastewater and use phylogenetic anal. to infer viral ancestry. Collectively, this work demonstrates how wastewater can be used as a proxy to monitor viral prevalence in the community and how genome sequencing can be used for genotyping viral strains circulating in a community.
25. 25

    Peccia, J. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nat. Biotechnol. 2020, 38 (10), 1164– 1167,  DOI: 10.1038/s41587-020-0684-z

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    Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics

    Peccia, Jordan; Zulli, Alessandro; Brackney, Doug E.; Grubaugh, Nathan D.; Kaplan, Edward H.; Casanovas-Massana, Arnau; Ko, Albert I.; Malik, Amyn A.; Wang, Dennis; Wang, Mike; Warren, Joshua L.; Weinberger, Daniel M.; Arnold, Wyatt; Omer, Saad B.

    Nature Biotechnology (2020), 38 (10), 1164-1167CODEN: NABIF9; ISSN:1087-0156. (Nature Research)

    Abstr.: We measured severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concns. in primary sewage sludge in the New Haven, Connecticut, USA, metropolitan area during the Coronavirus Disease 2019 (COVID-19) outbreak in Spring 2020. SARS-CoV-2 RNA was detected throughout the more than 10-wk study and, when adjusted for time lags, tracked the rise and fall of cases seen in SARS-CoV-2 clin. test results and local COVID-19 hospital admissions. Relative to these indicators, SARS-CoV-2 RNA concns. in sludge were 0-2 d ahead of SARS-CoV-2 pos. test results by date of specimen collection, 0-2 d ahead of the percentage of pos. tests by date of specimen collection, 1-4 d ahead of local hospital admissions and 6-8 d ahead of SARS-CoV-2 pos. test results by reporting date. Our data show the utility of viral RNA monitoring in municipal wastewater for SARS-CoV-2 infection surveillance at a population-wide level. In communities facing a delay between specimen collection and the reporting of test results, immediate wastewater results can provide considerable advance notice of infection dynamics.
26. 26

    Ahmed, W. First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community. Science of The Total Environment 2020, 728, 138764,  DOI: 10.1016/j.scitotenv.2020.138764

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    26

    First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

    Ahmed, Warish; Angel, Nicola; Edson, Janette; Bibby, Kyle; Bivins, Aaron; O'Brien, Jake W.; Choi, Phil M.; Kitajima, Masaaki; Simpson, Stuart L.; Li, Jiaying; Tscharke, Ben; Verhagen, Rory; Smith, Wendy J. M.; Zaugg, Julian; Dierens, Leanne; Hugenholtz, Philip; Thomas, Kevin V.; Mueller, Jochen F.

    Science of the Total Environment (2020), 728 (), 138764CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    Infection with SARS-CoV-2, the etiol. agent of the ongoing COVID-19 pandemic, is accompanied by the shedding of the virus in stool. Therefore, the quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiol. (WBE). In the current work, SARS-CoV-2 RNA was concd. from wastewater in a catchment in Australia and viral RNA copies were enumerated using reverse transcriptase quant. polymerase chain reaction (RT-qPCR) resulting in two pos. detections within a six day period from the same wastewater treatment plant (WWTP). The estd. viral RNA copy nos. obsd. in the wastewater were then used to est. the no. of infected individuals in the catchment via Monte Carlo simulation. Given the uncertainty and variation in the input parameters, the model estd. a median range of 171 to 1,090 infected persons in the catchment, which is in reasonable agreement with clin. observations. This work highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities. The work also draws attention to the need for further methodol. and mol. assay validation for enveloped viruses in wastewater.
27. 27

    La Rosa, G. First detection of SARS-CoV-2 in untreated wastewaters in Italy. Science of The Total Environment 2020, 736, 139652,  DOI: 10.1016/j.scitotenv.2020.139652

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    27

    First detection of SARS-CoV-2 in untreated wastewaters in Italy

    La Rosa, Giuseppina; Iaconelli, Marcello; Mancini, Pamela; Bonanno Ferraro, Giusy; Veneri, Carolina; Bonadonna, Lucia; Lucentini, Luca; Suffredini, Elisabetta

    Science of the Total Environment (2020), 736 (), 139652CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    Several studies have demonstrated the advantages of environmental surveillance through the monitoring of sewage for the assessment of viruses circulating in a given community (wastewater-based epidemiol., WBE). During the COVID-19 public health emergency, many reports have described the presence of SARS-CoV-2 RNA in stools from COVID-19 patients, and a few studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide. Italy is among the world's worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, 12 influent sewage samples, collected between Feb. and Apr. 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concn., the std. WHO procedure for Poliovirus surveillance. Mol. anal. was undertaken with 3 nested protocols, including a newly designed SARS-CoV-2 specific primer set. SARS-CoV-2 RNA detection was accomplished in vols. of 250 mL of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clin. data. Overall, 6 out of 12 samples were pos. One of the pos. results was obtained in a Milan wastewater sample collected a few days after the 1st notified Italian case of autochthonous SARS-CoV-2. The study confirms that WBE has the potential to be applied to SARS-CoV-2 as a sensitive tool to study spatial and temporal trends of virus circulation in the population.
28. 28

    Barril, P. A. Evaluation of viral concentration methods for SARS-CoV-2 recovery from wastewaters. Science of The Total Environment 2021, 756, 144105,  DOI: 10.1016/j.scitotenv.2020.144105

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    28

    Evaluation of viral concentration methods for SARS-CoV-2 recovery from wastewaters

    Barril, Patricia Angelica; Pianciola, Luis Alfredo; Mazzeo, Melina; Ousset, Maria Julia; Jaureguiberry, Maria Virginia; Alessandrello, Mauricio; Sanchez, Gloria; Oteiza, Juan Martin

    Science of the Total Environment (2021), 756 (), 144105CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    Wastewater-based epidemiol. (WBE) is a useful tool that has the potential to act as a complementary approach to monitor the presence of SARS-CoV-2 in the community and as an early alarm system for COVID-19 outbreak. Many studies reported low concns. of SARS-CoV-2 in sewage and also revealed the need for methodol. validation for enveloped viruses concn. in wastewater. The aim of this study was to evaluate different methodologies for the concn. of viruses in wastewaters and to select and improve an option that maximizes the recovery of SARS-CoV-2. A total of 11 concn. techniques based on different principles were evaluated: adsorption-elution protocols with neg. charged membranes followed by polyethylene glycol (PEG) pptn. (Methods 1-2), PEG pptn. (Methods 3-7), aluminum polychloride (PAC) flocculation (Method 8), ultrafiltration (Method 9), skim milk flocculation (Method 10) and adsorption-elution with neg. charged membrane followed by ultrafiltration (Method 11). To evaluate the performance of these concn. techniques, feline calicivirus (FCV) was used as a process control in order to avoid the risk assocd. with handling SARS-CoV-2. Two protocols, one based on PEG pptn. and the other on PAC flocculation, showed high efficiency for FCV recovery from wastewater (62.2% and 45.0%, resp.). These two methods were then tested for the specific recovery of SARS-CoV-2. Both techniques could recover SARS-CoV-2 from wastewater, PAC flocculation showed a lower limit of detection (4.3 x 102 GC/mL) than PEG pptn. (4.3 x 103 GC/mL). This work provides a crit. overview of current methods used for virus concn. in wastewaters and the anal. of sensitivity for the specific recovery of SARS-CoV-2 in sewage. The data obtained here highlights the viability of WBE for the surveillance of COVID-19 infections in the community.
29. 29

    Hillary, L. S. Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK. Water Res. 2021, 200, 117214,  DOI: 10.1016/j.watres.2021.117214

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    29

    Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK

    Hillary, Luke S.; Farkas, Kata; Maher, Kathryn H.; Lucaci, Anita; Thorpe, Jamie; Distaso, Marco A.; Gaze, William H.; Paterson, Steve; Burke, Terry; Connor, Thomas R.; McDonald, James E.; Malham, Shelagh K.; Jones, David L.

    Water Research (2021), 200 (), 117214CODEN: WATRAG; ISSN:0043-1354. (Elsevier Ltd.)

    SARS-CoV-2 and the resulting COVID-19 pandemic represents one of the greatest recent threats to human health, wellbeing and economic growth. Wastewater-based epidemiol. (WBE) of human viruses can be a useful tool for population-scale monitoring of SARS-CoV-2 prevalence and epidemiol. to help prevent further spread of the disease, particularly within urban centers. Here, we present a longitudinal anal. (March-July 2020) of SARS-CoV-2 RNA prevalence in sewage across six major urban centers in the UK (total population equiv. 3 million) by q(RT-)PCR and viral genome sequencing. Our results demonstrate that levels of SARS-CoV-2 RNA generally correlated with the abundance of clin. cases recorded within the community in large urban centers, with a marked decline in SARS-CoV-2 RNA abundance following the implementation of lockdown measures. The strength of this assocn. was weaker in areas with lower confirmed COVID-19 case nos. Further, sequence anal. of SARS-CoV-2 from wastewater suggested that multiple genetically distinct clusters were co-circulating in the local populations covered by our sample sites, and that the genetic variants obsd. in wastewater reflected similar SNPs obsd. in contemporaneous samples from cases tested in clin. diagnostic labs. We demonstrate how WBE can be used for both community-level detection and tracking of SARS-CoV-2 and other virus' prevalence, and can inform public health policy decisions. Although greater understanding of the factors that affect SARS-CoV-2 RNA concn. in wastewater are needed for the full integration of WBE data into outbreak surveillance. In conclusion, our results lend support to the use of routine WBE for monitoring of SARS-CoV-2 and other human pathogenic viruses circulating in the population and assessment of the effectiveness of disease control measures.
30. 30

    Randazzo, W.; Truchado, P.; Cuevas-Ferrando, E.; Simón, P.; Allende, A.; Sánchez, G. SARS-CoV-2 RNA in wastewater anticipated COVID-19 occurrence in a low prevalence area. Water Res. 2020, 181, 115942,  DOI: 10.1016/j.watres.2020.115942

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    SARS-CoV-2 RNA in wastewater anticipated COVID-19 occurrence in a low prevalence area

    Randazzo, Walter; Truchado, Pilar; Cuevas-Ferrando, Enric; Simon, Pedro; Allende, Ana; Sanchez, Gloria

    Water Research (2020), 181 (), 115942CODEN: WATRAG; ISSN:0043-1354. (Elsevier Ltd.)

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 200,000 reported COVID-19 cases in Spain resulting in more than 20,800 deaths as of Apr. 21, 2020. Faecal shedding of SARS-CoV-2 RNA from COVID-19 patients has extensively been reported. Therefore, we investigated the occurrence of SARS-CoV-2 RNA in six wastewater treatments plants (WWTPs) serving the major municipalities within the Region of Murcia (Spain), the area with the lowest COVID-19 prevalence within Iberian Peninsula. Firstly, an aluminum hydroxide adsorption-pptn. concn. method was validated using a porcine coronavirus (Porcine Epidemic Diarrhea Virus, PEDV) and mengovirus (MgV). The procedure resulted in av. recoveries of 10 ± 3.5% and 10 ± 2.1% in influent water (n = 2) and 3.3 ± 1.6% and 6.2 ± 1.0% in effluent water (n = 2) samples for PEDV and MgV, resp. Then, the method was used to monitor the occurrence of SARS-CoV-2 from March 12 to Apr. 14, 2020 in influent, secondary and tertiary effluent water samples. The detection of SARS-CoV-2 in wastewater in early stages of the spread of COVID-19 highlights the relevance of this strategy as an early indicator of the infection within a specific population. At this point, this environmental surveillance could be implemented by municipalities right away as a tool, designed to help authorities to coordinate the exit strategy to gradually lift its coronavirus lockdown.
31. 31

    Shah, S.; Gwee, S. X. W.; Ng, J. Q. X.; Lau, N.; Koh, J.; Pang, J. Wastewater surveillance to infer COVID-19 transmission: A systematic review. Science of The Total Environment 2022, 804, 150060,  DOI: 10.1016/j.scitotenv.2021.150060

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    Wastewater surveillance to infer COVID-19 transmission: A systematic review

    Shah, Shimoni; Gwee, Sylvia Xiao Wei; Ng, Jamie Qiao Xin; Lau, Nicholas; Koh, Jiayun; Pang, Junxiong

    Science of the Total Environment (2022), 804 (), 150060CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    A review. Successful detection of SARS-COV-2 in wastewater suggests the potential utility of wastewater-based epidemiol. (WBE) for COVID-19 community surveillance. This systematic review aims to assess the performance of wastewater surveillance as early warning system of COVID-19 community transmission. A systematic search was conducted in PubMed, Medline, Embase and the WBE Consortium Registry according to PRISMA guidelines for relevant articles published until 31st July 2021. Relevant data were extd. and summarized. Quality of each paper was assessed using an assessment tool adapted from Bilotta et al.'s tool for environmental science. Of 763 studies identified, 92 studies distributed across 34 countries were shortlisted for qual. synthesis. A total of 26,197 samples were collected between Jan. 2020 and May 2021 from various locations serving population ranging from 321 to 11,400,000 inhabitants. Overall sample positivity was moderate at 29.2% in all examd. settings with the spike (S) gene having max. rate of pos. detections and nucleocapsid (N) gene being the most targeted. Wastewater signals preceded confirmed cases by up to 63 days, with 13 studies reporting sample positivity before the first cases were detected in the community. At least 50 studies reported an assocn. of viral load with community cases. While wastewater surveillance cannot replace large-scale diagnostic testing, it can complement clin. surveillance by providing early signs of potential transmission for more active public health responses. However, more studies using standardized and validated methods are required along with risk anal. and modeling to understand the dynamics of viral outbreaks.
32. 32

    La Rosa, G. SARS-CoV-2 has been circulating in northern Italy since December 2019: Evidence from environmental monitoring. Science of the total environment 2021, 750, 141711,  DOI: 10.1016/j.scitotenv.2020.141711

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    SARS-CoV-2 has been circulating in northern Italy since December 2019: Evidence from environmental monitoring

    La Rosa, Giuseppina; Mancini, Pamela; Bonanno Ferraro, Giusy; Veneri, Carolina; Iaconelli, Marcello; Bonadonna, Lucia; Lucentini, Luca; Suffredini, Elisabetta

    Science of the Total Environment (2021), 750 (), 141711CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease COVID-19, a public health emergency worldwide, and Italy is among the most severely affected countries. The first autochthonous Italian case of COVID-19 was documented on Feb. 21, 2020. We investigated the possibility that SARS-CoV-2 emerged in Italy earlier than that date, by analyzing 40 composite influent wastewater samples collected - in the framework of other wastewater-based epidemiol. projects - between Oct. 2019 and Feb. 2020 from five wastewater treatment plants (WWTPs) in three cities and regions in northern Italy (Milan/Lombardy, Turin/Piedmont and Bologna/Emilia Romagna). Twenty-four addnl. samples collected in the same WWTPs between Sept. 2018 and June 2019 (i.e. long before the onset of the epidemic) were included as 'blank' samples. Viral concn. was performed according to the std. World Health Organization procedure for poliovirus sewage surveillance, with modifications. Mol. anal. was undertaken with both nested RT-PCR and real-rime RT-PCR assays. A total of 15 pos. samples were confirmed by both methods. The earliest dates back to 18 Dec. 2019 in Milan and Turin and 29 Jan. 2020 in Bologna. Virus concn. in the samples ranged from below the limit of detection (LOD) to 5.6 x 104 genome copies (g.c.)/L, and most of the samples (23 out of 26) were below the limit of quantification of PCR. Our results demonstrate that SARS-CoV-2 was already circulating in northern Italy at the end of 2019. Moreover, it was circulating in different geog. regions simultaneously, which changes our previous understanding of the geog. circulation of the virus in Italy. Our study highlights the importance of environmental surveillance as an early warning system, to monitor the levels of virus circulating in the population and identify outbreaks even before cases are notified to the healthcare system.
33. 33

    Farkas, K.; Hillary, L. S.; Malham, S. K.; McDonald, J. E.; Jones, D. L. Wastewater and public health: the potential of wastewater surveillance for monitoring COVID-19. Curr. Opin. Environ. Sci. Health 2020, 17, 14– 20,  DOI: 10.1016/j.coesh.2020.06.001

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    Wastewater and public health: the potential of wastewater surveillance for monitoring COVID-19

    Farkas Kata; Malham Shelagh K; Hillary Luke S; McDonald James E; Jones David L; Jones David L

    Current opinion in environmental science & health (2020), 17 (), 14-20 ISSN:.

    Pathogenic viruses represent one of the greatest threats to human well-being. As evidenced by the COVID-19 global pandemic, however, halting the spread of highly contagious diseases is notoriously difficult. Successful control strategies therefore have to rely on effective surveillance. Here, we describe how monitoring wastewater from urban areas can be used to detect the arrival and subsequent decline of pathogens, such as SARS-CoV-2. As the amount of virus shed in faeces and urine varies largely from person to person, it is very difficult to quantitatively determine the number of people who are infected in the population. More research on the surveillance of viruses in wastewater using accurate and validated methods, as well as subsequent risk analysis and modelling is paramount in understanding the dynamics of viral outbreaks.
34. 34

    Mallapaty, S. How sewage could reveal true scale of coronavirus outbreak. Nature 2020, 580 (7802), 176– 177,  DOI: 10.1038/d41586-020-00973-x

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    How sewage could reveal true scale of coronavirus outbreak

    Mallapaty, Smriti

    Nature (London, United Kingdom) (2020), 580 (7802), 176-177CODEN: NATUAS; ISSN:0028-0836. (Nature Research)

    Wastewater testing could also be used as an early-warning sign if the SARS-CoV-2 virus returns.
35. 35

    Colosi, L. M. Development of wastewater pooled surveillance of SARS-CoV-2 from congregate living settings. Appl. Environ. Microbiol. 2021, 87, e0043321,  DOI: 10.1128/AEM.00433-21

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    Haak, L. Spatial and temporal variability and data bias in wastewater surveillance of SARS-CoV-2 in a sewer system. Science of The Total Environment 2022, 805, 150390,  DOI: 10.1016/j.scitotenv.2021.150390

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    Spatial and temporal variability and data bias in wastewater surveillance of SARS-CoV-2 in a sewer system

    Haak, Laura; Delic, Blaga; Li, Lin; Guarin, Tatiana; Mazurowski, Lauren; Dastjerdi, Niloufar Gharoon; Dewan, Aimee; Pagilla, Krishna

    Science of the Total Environment (2022), 805 (), 150390CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    The response to disease outbreaks, such as SARS-CoV-2, can be constrained by a limited ability to measure disease prevalence early at a localized level. Wastewater based epidemiol. is a powerful tool identifying disease spread from pooled community sewer networks or at influent to wastewater treatment plants. However, this approach is often not applied at a granular level that permits detection of local hot spots. This study examines the spatial patterns of SARS-CoV-2 in sewage through a spatial sampling strategy across neighborhood-scale sewershed catchments. Sampling was conducted across the Reno-Sparks metropolitan area from Nov. to mid-Dec. of 2020. This research utilized local spatial autocorrelation tests to identify the evolution of statistically significant neighborhood hot spots in sewershed sub-catchments that were identified to lead waves of infection, with adjacent neighborhoods obsd. to lag with increasing viral RNA concns. over subsequent dates. The correlations between the sub-catchments over the sampling period were also characterized using principal component anal. Results identified distinct time series patterns, with sewersheds in the urban center, outlying suburban areas, and outlying urbanized districts generally following unique trends over the sampling period. Several demog. parameters were identified as having important gradients across these areas, namely population d., poverty levels, household income, and age. These results provide a more strategic approach to identify disease outbreaks at the neighborhood level and characterized how sampling site selection could be designed based on the spatial and demog. characteristics of neighborhoods.
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    Gutierrez-Espino, C.; Peru: Estado de la población en el año del bicentenario, 2021; Instituto Nacional de Estadística e Informática (INEI): Lima, 2021.

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    There is no corresponding record for this reference.
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    Katayama, H.; Shimasaki, A.; Ohgaki, S. Development of a virus concentration method and its application to detection of enterovirus and Norwalk virus from coastal seawater. Appl. Environ. Microbiol. 2002, 68 (3), 1033– 1039,  DOI: 10.1128/AEM.68.3.1033-1039.2002

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    Development of a virus concentration method and its application to detection of enterovirus and norwalk virus from coastal seawater

    Katayama, Hiroyuki; Shimasaki, Akihiro; Ohgaki, Shinichiro

    Applied and Environmental Microbiology (2002), 68 (3), 1033-1039CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    We developed a new procedure for concn. of enteric viruses from water using a neg. charged membrane. Rinsing the membrane with 0.5 mM H2SO4 (pH 3.0) in order to elute cations prior to viral elution with 1 mM NaOH (pH 10.5) promoted poliovirus recovery yields from 33 to 95% when applied to pure water and 38 to 89% when applied to natural seawater from Tokyo Bay, Japan, resp. This method showed av. recovery yields of spiked poliovirus of 62% (n = 8) from 1 L of artificial seawater. This method showed higher recovery yields (>61%) than that of the conventional method using pos. charged membrane (6%) when applied to seawater. This method is also free from beef ext. elution, which has an inhibitory effect in the subsequent viral genome detection by reverse transcription-PCR. Naturally occurring Norwalk viruses from 2 L of Tokyo Bay water in winter and infectious enteroviruses from 2 L of recreational coastal seawater in summer were detected by using this viral concn. method.
39. 39

    Boxus, M.; Letellier, C.; Kerkhofs, P. Real Time RT-PCR for the detection and quantitation of bovine respiratory syncytial virus. Journal of virological methods 2005, 125 (2), 125– 130,  DOI: 10.1016/j.jviromet.2005.01.008

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    Real Time RT-PCR for the detection and quantitation of bovine respiratory syncytial virus

    Boxus, M.; Letellier, C.; Kerkhofs, P.

    Journal of Virological Methods (2005), 125 (2), 125-130CODEN: JVMEDH; ISSN:0166-0934. (Elsevier B.V.)

    A quant. Real Time RT-PCR assay was developed to detect and quantify bovine respiratory syncytial virus (BRSV) in the respiratory tract of infected animals. A pair of primers and a TaqMan probe targeting conserved regions of the nucleoprotein gene of BRSV were designed. The detection limit of the assay was shown to be 103 RNA copies and std. curve demonstrated a linear range from 103 to 108 copies as well as an excellent reproducibility. The efficiency of the BRSV Real Time RT-PCR was then assessed by detecting BRSV in lungs, tracheas and bronchoalveaolar fluids (BAL) samples of exptl. infected calves. The assay was shown to be 100 times more sensitive than conventional RT-PCR and was more efficient for BRSV diagnosis. Finally, the Real Time RT-PCR was used to quantify BRSV load in BAL fluids of four exptl. infected calves for 14 days. The high sensitivity, rapidity and reproducibility of the BRSV Real Time RT-PCR make this method suitable for diagnostic and for the evaluation of the efficiency of new vaccines.
40. 40

    Ahmed, W. Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater. Science of The Total Environment 2020, 739, 139960,  DOI: 10.1016/j.scitotenv.2020.139960

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    40

    Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater

    Ahmed, Warish; Bertsch, Paul M.; Bivins, Aaron; Bibby, Kyle; Farkas, Kata; Gathercole, Amy; Haramoto, Eiji; Gyawali, Pradip; Korajkic, Asja; McMinn, Brian R.; Mueller, Jochen F.; Simpson, Stuart L.; Smith, Wendy J. M.; Symonds, Erin M.; Thomas, Kevin V.; Verhagen, Rory; Kitajima, Masaaki

    Science of the Total Environment (2020), 739 (), 139960CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    There is currently a clear benefit for many countries to utilize wastewater-based epidemiol. (WBE) as part of ongoing measures to manage the coronavirus disease 2019 (COVID-19) global pandemic. Since most wastewater virus concn. methods were developed and validated for nonenveloped viruses, it is imperative to det. the efficiency of the most commonly used methods for the enveloped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Municipal wastewater seeded with a human coronavirus (CoV) surrogate, murine hepatitis virus (MHV), was used to test the efficiency of 7 wastewater virus concn. methods: (A-C) adsorption-extn. with 3 different pre-treatment options, (D-E) centrifugal filter device methods with 2 different devices, (F) polyethylene glycol (PEG 8000) pptn., and (G) ultracentrifugation. MHV was quantified by reverse-transcription quant. polymerase chain reaction and the recovery efficiency was calcd. for each method. The mean MHV recoveries ranged 26.7-65.7%. The most efficient methods were adsorption-extn. methods with MgCl2 pre-treatment (Method C), and without pre-treatment (Method B). The 3rd most efficient method used the Amicon Ultra-15 centrifugal filter device (Method D) and its recovery efficiency was not different from the most efficient methods. The methods with the worst recovery efficiency included the adsorption-extn. method with acidification (A), followed by PEG pptn. (F). Our results suggest that absorption-extn. methods with minimal or without pre-treatment can provide suitably rapid, cost-effective and relatively straightforward recovery of enveloped viruses in wastewater. The MHV is a promising process control for SARS-CoV-2 surveillance and can be used as a quality control measure to support community-level epidemic mitigation and risk assessment.
41. 41

    Kantor, R. S.; Nelson, K. L.; Greenwald, H. D.; Kennedy, L. C. Challenges in measuring the recovery of SARS-CoV-2 from wastewater. Environ. Sci. Technol. 2021, 55 (6), 3514– 3519,  DOI: 10.1021/acs.est.0c08210

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    Challenges in Measuring the Recovery of SARS-CoV-2 from Wastewater

    Kantor, Rose S.; Nelson, Kara L.; Greenwald, Hannah D.; Kennedy, Lauren C.

    Environmental Science & Technology (2021), 55 (6), 3514-3519CODEN: ESTHAG; ISSN:0013-936X. (American Chemical Society)

    A review. Wastewater-based epidemiol. is an emerging tool for tracking the spread of SARS-CoV-2 through populations. However, many factors influence recovery and quantification of SARS-CoV-2 from wastewater, complicating data interpretation. Specifically, these factors may differentially affect the measured virus concn., depending on the lab. methods used to perform the test. Many labs. add a proxy virus to wastewater samples to det. losses assocd. with concn. and extn. of viral RNA. While measuring recovery of a proxy virus is an important process control, in this piece, we describe the caveats and limitations to the interpretation of this control, including that it typically does not account for losses during RNA extn. We recommend reporting the directly measured concn. data alongside the measured recovery efficiency, rather than attempting to correct the concn. for recovery efficiency. Even though the ability to directly compare SARS-CoV-2 concns. from different sampling locations detd. using different methods is limited, concn. data (uncorrected for recovery) can be useful for public health response.
42. 42

    2019-novel coronavirus (2019-nCoV) real-time rRT-PCR panel primers and probes. U.S. Centers for Disease Control and Prevention, 2020; Vol. 24.

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    Verbyla, M. E. Managing microbial risks from indirect wastewater reuse for irrigation in urbanizing watersheds. Environ. Sci. Technol. 2016, 50 (13), 6803– 6813,  DOI: 10.1021/acs.est.5b05398

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    Managing Microbial Risks from Indirect Wastewater Reuse for Irrigation in Urbanizing Watersheds

    Verbyla, Matthew E.; Symonds, Erin M.; Kafle, Ram C.; Cairns, Maryann R.; Iriarte, Mercedes; Mercado Guzman, Alvaro; Coronado, Olver; Breitbart, Mya; Ledo, Carmen; Mihelcic, James R.

    Environmental Science & Technology (2016), 50 (13), 6803-6813CODEN: ESTHAG; ISSN:0013-936X. (American Chemical Society)

    Limited supply of clean water in urbanizing watersheds creates challenges for safely sustaining irrigated agriculture and global food security. On-farm interventions, such as riverbank filtration (RBF), are used in developing countries to treat irrigation water from rivers with extensive fecal contamination. Using a Bayesian approach incorporating ethnog. data and pathogen measurements, quant. microbial risk assessment (QMRA) methods were employed to assess the impact of RBF on consumer health burdens for Giardia, Cryptosporidium, rotavirus, norovirus, and adenovirus infections resulting from indirect wastewater reuse, with lettuce irrigation in Bolivia as a model system. Concns. of the microbial source tracking markers pepper mild mottle virus and HF183 Bacteroides were resp. 2.9 and 5.5 log10 units lower in RBF-treated water than in the river water. Consumption of lettuce irrigated with river water caused an estd. median health burden that represents 37% of Bolivia's overall diarrheal disease burden, but RBF resulted in an estd. health burden that is only 1.1% of this overall diarrheal disease burden. Variability and uncertainty assocd. with environmental and cultural factors affecting exposure correlated more with QMRA-predicted health outcomes than factors related to disease vulnerability. Policies governing simple on-farm interventions like RBF can be intermediary solns. for communities in urbanizing watersheds that currently lack wastewater treatment.
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    Haugland, R. A.; Siefring, S. C.; Wymer, L. J.; Brenner, K. P.; Dufour, A. P. Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water research 2005, 39 (4), 559– 568,  DOI: 10.1016/j.watres.2004.11.011

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    Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis

    Haugland, Richard A.; Siefring, Shawn C.; Wymer, Larry J.; Brenner, Kristen P.; Dufour, Alfred P.

    Water Research (2005), 39 (4), 559-568CODEN: WATRAG; ISSN:0043-1354. (Elsevier B.V.)

    Cell densities of the fecal pollution indicator genus, Enterococcus, were detd. by a rapid (≤3 h) quant. polymerase chain reaction (QPCR) anal. method in 100 mL water samples collected from recreational beaches on Lake Michigan and Lake Erie during the summer of 2003. Measurements by this method were compared with counts of Enterococcus colony-forming units (CFU) detd. by Method 1600 membrane filter (MF) anal. using mEI agar. The QPCR method had an estd. 95% confidence, min. detection limit of 27 Enterococcus cells per sample in analyses of undiluted DNA exts. and quant. analyses of multiple lake water samples, spiked with known nos. of these organisms, gave geometric mean results that were highly consistent with the spike levels. At both beaches, the geometric means of ambient Enterococcus concns. in water samples, detd. from multiple collection points during each sampling visit, showed approx. lognormal distributions over the study period using both QPCR and MF analyses. These geometric means were 10-8548 cells by QPCR anal. and 1-2499 CFU by MF culture anal. in Lake Michigan (n =56) and 8-8695 cells by QPCR and 3-1941 CFU by MF culture in Lake Erie (n =47). Regression anal. of these results showed a significant pos. correlation between the 2 methods with an overall correlation coeff. of 0.68.
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    Ahmed, W. Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimization and quality control are crucial for generating reliable public health information. Current opinion in environmental science & health 2020, 17, 82– 93,  DOI: 10.1016/j.coesh.2020.09.003

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    Marusteri, M.; Bacarea, V. Comparing groups for statistical differences: how to choose the right statistical test?. Biochemia medica 2010, 20 (1), 15– 32,  DOI: 10.11613/BM.2010.004

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    Munayco, C. V. Early transmission dynamics of COVID-19 in a southern hemisphere setting: Lima-Peru: February 29th–March 30th, 2020. Infectious Disease Modelling 2020, 5, 338– 345,  DOI: 10.1016/j.idm.2020.05.001

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    Early transmission dynamics of COVID-19 in a southern hemisphere setting: Lima-Peru: February 29(th)-March 30(th), 2020

    Munayco Cesar V; Soto-Cabezas Gabriela G; Reyes Mary F; Valle Andree; Loayza Manuel; Tariq Amna; Rothenberg Richard; Chowell Gerardo; Rojas-Mezarina Leonardo; Cabezas Cesar

    Infectious Disease Modelling (2020), 5 (), 338-345 ISSN:.

    The COVID-19 pandemic that emerged in Wuhan China has generated substantial morbidity and mortality impact around the world during the last four months. The daily trend in reported cases has been rapidly rising in Latin America since March 2020 with the great majority of the cases reported in Brazil followed by Peru as of April 15th, 2020. Although Peru implemented a range of social distancing measures soon after the confirmation of its first case on March 6th, 2020, the daily number of new COVID-19 cases continues to accumulate in this country. We assessed the early COVID-19 transmission dynamics and the effect of social distancing interventions in Lima, Peru. We estimated the reproduction number, R, during the early transmission phase in Lima from the daily series of imported and autochthonous cases by the date of symptoms onset as of March 30th, 2020. We also assessed the effect of social distancing interventions in Lima by generating short-term forecasts grounded on the early transmission dynamics before interventions were put in place. Prior to the implementation of the social distancing measures in Lima, the local incidence curve by the date of symptoms onset displays near exponential growth dynamics with the mean scaling of growth parameter, p, estimated at 0.96 (95% CI: 0.87, 1.0) and the reproduction number at 2.3 (95% CI: 2.0, 2.5). Our analysis indicates that school closures and other social distancing interventions have helped slow down the spread of the novel coronavirus, with the nearly exponential growth trend shifting to an approximately linear growth trend soon after the broad scale social distancing interventions were put in place by the government. While the interventions appear to have slowed the transmission rate in Lima, the number of new COVID-19 cases continue to accumulate, highlighting the need to strengthen social distancing and active case finding efforts to mitigate disease transmission in the region.
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    Vargas-Herrera, N.; Araujo-Castillo, R. V.; Mestanza, O.; Galarza, M.; Rojas-Serrano, N.; Solari-Zerpa, L. SARS-CoV-2 Lambda and Gamma variants competition in Peru, a country with high seroprevalence. Lancet Regional Health–Americas 2021,  DOI: 10.1016/j.lana.2021.100112

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    Adhikari, S.; Pantaleo, N. P.; Feldman, J. M.; Ogedegbe, O.; Thorpe, L.; Troxel, A. B. Assessment of community-level disparities in coronavirus disease 2019 (COVID-19) infections and deaths in large US metropolitan areas. JAMA network open 2020, 3 (7), e2016938  DOI: 10.1001/jamanetworkopen.2020.16938

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    MINSA confirma tercera ola ante incremento de casos de contagio por la COVID-19; Plataforma digital única del estado Peruano, Ministerio de Salud, 2021.

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    Guerrero-Latorre, L.; Ballesteros, I.; Villacrés-Granda, I.; Granda, M. G.; Freire-Paspuel, B.; Ríos-Touma, B. SARS-CoV-2 in river water: Implications in low sanitation countries. Science of the Total environment 2020, 743, 140832,  DOI: 10.1016/j.scitotenv.2020.140832

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    SARS-CoV-2 in river water: Implications in low sanitation countries

    Guerrero-Latorre, Laura; Ballesteros, Isabel; Villacres-Granda, Irina; Granda, M. Genoveva; Freire-Paspuel, Byron; Rios-Touma, Blanca

    Science of the Total Environment (2020), 743 (), 140832CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    Since the beginning of COVID-19 pandemic studies on viral shedding have reported that this virus is excreted in feces in most patients. High viral loads are found at the sewage pipeline or at the entrance of wastewater treatment plants from cities where the no. of COVID-19 cases are significant. In Quito (Ecuador) as in many other cities worldwide, wastewater is directly discharged into natural waters. The aim of this study was to evaluate SARS-CoV-2 presence in urban streams from a low sanitation context. Three river locations along the urban rivers of Quito were sampled on the 5th of June during a peak of COVID-19 cases. River samples were evaluated for water quality parameters and afterwards, concd. for viral anal. using skimmed milk flocculation method. The viral concs. were quantified for SARS-CoV-2 (N1 and N2 target regions) and Human Adenovirus as a human viral indicator. The results showed that SARS-CoV-2 was detected for both target regions in all samples analyzed in a range of 2,91E+05 to 3,19E+06 GC/L for N1 and from 2,07E+05 to 2,22E+06 GC/L for N2. The high values detected in natural waters from a low sanitation region have several implications in health and ecol. that should be further assessed.
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    Sims, N.; Kasprzyk-Hordern, B. Future perspectives of wastewater-based epidemiology: monitoring infectious disease spread and resistance to the community level. Environ. Int. 2020, 139, 105689,  DOI: 10.1016/j.envint.2020.105689

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    Future perspectives of wastewater-based epidemiology: Monitoring infectious disease spread and resistance to the community level

    Sims Natalie; Kasprzyk-Hordern Barbara

    Environment international (2020), 139 (), 105689 ISSN:.

    Infectious diseases are acknowledged as one of the most critical threats to global public health today. Climate change, unprecedented population growth with accelerated rates of antimicrobial resistance, have resulted in both the emergence of novel pathogenic organisms and the re-emergence of infections that were once controlled. The consequences have led to an increased vulnerability to infectious diseases globally. The ability to rapidly monitor the spread of diseases is key for prevention, intervention and control, however several limitations exist for current surveillance systems and the capacity to cope with the rapid population growth and environmental changes. Wastewater-Based Epidemiology (WBE) is a new epidemiology tool that has potential to act as a complementary approach for current infectious disease surveillance systems and an early warning system for disease outbreaks. WBE postulates that through the analysis of population pooled wastewater, infectious disease and resistance spread, the emergence of new disease outbreak to the community level can be monitored comprehensively and in real-time. This manuscript provides critical overview of current infectious disease surveillance status, as well as it introduces WBE and its recent advancements. It also provides recommendations for further development required for WBE application as an effective tool for infectious disease surveillance.
56. 56

    Weidhaas, J. Correlation of SARS-CoV-2 RNA in wastewater with COVID-19 disease burden in sewersheds. Science of The Total Environment 2021, 775, 145790,  DOI: 10.1016/j.scitotenv.2021.145790

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    Correlation of SARS-CoV-2 RNA in wastewater with COVID-19 disease burden in sewersheds

    Weidhaas, Jennifer; Aanderud, Zachary T.; Roper, D. Keith; VanDerslice, James; Gaddis, Erica Brown; Ostermiller, Jeff; Hoffman, Ken; Jamal, Rubayat; Heck, Phillip; Zhang, Yue; Torgersen, Kevin; Laan, Jacob Vander; LaCross, Nathan

    Science of the Total Environment (2021), 775 (), 145790CODEN: STENDL; ISSN:0048-9697. (Elsevier B.V.)

    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease (COVID-19), is shed in feces and the viral RNA (RNA) is detectable in wastewater. A nine-week wastewater epidemiol. study of ten wastewater facilities, serving 39% of the state of Utah or 1.26 M individuals, was conducted in Apr. and May of 2020. COVID-19 cases were tabulated from within each sewershed boundary. RNA from SARS-CoV-2 was detectable in 61% of 126 wastewater samples. Urban sewersheds serving >100,000 individuals and tourist communities had higher detection frequencies. An outbreak of COVID-19 across two communities pos. correlated with an increase in wastewater SARS-CoV-2 RNA, while a decline in COVID-19 cases preceded a decline in RNA. SARS-CoV-2 RNA followed a first order decay rate in wastewater, while 90% of the RNA was present in the liq. phase of the influent. Infiltration and inflow, virus decay and sewershed characteristics should be considered during correlation anal. of SAR-CoV-2 with COVID-19 cases. These results provide evidence of the utility of wastewater epidemiol. to assist in public health responses to COVID-19.
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    Suo, T. ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens. Emerging microbes & infections 2020, 9 (1), 1259– 1268,  DOI: 10.1080/22221751.2020.1772678

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    ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens

    Suo, Tao; Liu, Xinjin; Feng, Jiangpeng; Guo, Ming; Hu, Wenjia; Guo, Dong; Ullah, Hafiz; Yang, Yang; Zhang, Qiuhan; Wang, Xin; Sajid, Muhanmmad; Huang, Zhixiang; Deng, Liping; Chen, Tielong; Liu, Fang; Xu, Ke; Liu, Yuan; Zhang, Qi; Liu, Yingle; Xiong, Yong; Chen, Guozhong; Lan, Ke; Chen, Yu

    Emerging Microbes & Infections (2020), 9 (1), 1259-1268CODEN: EMIMC4; ISSN:2222-1751. (Taylor & Francis Ltd.)

    Quant. real time PCR (RT-PCR) is widely used as the gold std. for clin. detection of SARS-CoV-2. However, due to the low viral load specimens and the limitations of RT-PCR, significant nos. of false neg. reports are inevitable, which results in failure to timely diagnose, cut off transmission, and assess discharge criteria. To improve this situation, an optimized droplet digital PCR (ddPCR) was used for detection of SARS-CoV-2, which showed that the limit of detection of ddPCR is significantly lower than that of RT-PCR. We further explored the feasibility of ddPCR to detect SARS-CoV-2 RNA from 77 patients, and compared with RT-PCR in terms of the diagnostic accuracy based on the results of follow-up survey. 26 Patients of COVID-19 with neg. RT-PCR reports were reported as pos. by ddPCR. The sensitivity, specificity, PPV, NPV, neg. likelihood ratio (NLR) and accuracy were improved from 40% (95% CI: 27-55%), 100% (95% CI: 54-100%), 100%, 16% (95% CI: 13-19%), 0.6 (95% CI: 0.48-0.75) and 47% (95% CI: 33-60%) for RT-PCR to 94% (95% CI: 83-99%), 100% (95% CI: 48-100%), 100%, 63% (95% CI: 36-83%), 0.06 (95% CI: 0.02-0.18), and 95% (95% CI: 84-99%) for ddPCR, resp. Moreover, 6/14 (42.9%) convalescents were detected as pos. by ddPCR at 5-12 days post discharge. Overall, ddPCR shows superiority for clin. diagnosis of SARS-CoV-2 to reduce the false neg. reports, which could be a powerful complement to the RT-PCR.