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      Viruses in wastewater: occurrence, abundance and detection methods

      research-article
      a , b , c , d , b , c , a , e , f , b , c , g ,   b , c , *
      The Science of the Total Environment
      Published by Elsevier B.V.
      ASTM, American Society for Testing Materials, CER, Cation exchange resin, cDNA, Complementary DNA, cPCR, Conventional Polymerase Chain Reaction, COVID-19, Coronavirus disease 2019, CPE, Cytopathic effects, DNA, Deoxyribonucleic Acid, EV, Enterovirus, EVE, Enzymatic virus elution, ELISA, Enzyme Linked Immunosorbent Assay, EFM, Epifluorescence Microscopy, FCM, Flow Cytometry, GUI, Graphical user interface, HAV, Hepatitis A virus, HFUFS, Hollow fibre ultrafiltration system, HAdV, Human adenovirus, HAdV2, Human adenovirus 2, HAdV 40, Human adenovirus 40, HEV, Hepatitis E virus, HSV1, Herpes Simplex Virus Type 1, HHV, Human herpesvirus, IFA, Immunofluorescence Assay, ICC-PCR, Integrated Cell Culture-Polymerase Chain Reaction, ICC-RT-qPCR, Integrated Cell Culture-real time RT-PCR, JCPyV, JC Polyomavirus, HPV, Human papillomavirus, HPyV, Human polyomavirus, HTtV, Human Torque teno virus, μPAD, Microfluidic paper analytic device, MMTV, Mouse mammary tumour virus, MHV, Murine Hepatitis Virus, NGS, Next Generation Sequencing, NoV, Norovirus, NoV GI, Norovirus GI, NoV GII, Norovirus GII, PMMV, Pepper Mild Mottle Virus, PTA, Phosphotungstic acid, PEG, Polyethylene Glycol, PCR, Polymerase Chain Reaction, PV, Poliovirus, PV1, Poliovirus 1, φ6, Pseudomonas phage, PFGE, Pulsed-Field Gel Electrophoresis, qPCR, Real-Time Polymerase Chain Reaction, RT-PCR, Reverse Transcription-Polymerase Chain Reaction, RT-qPCR, Real Time RT-PCR, RNA, Ribonucleic Acid, RoV, Rotavirus, RoV-A, Rotavirus A, SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2, TEM, Transmission Electron Microscopy, VIRADEL, Virus Adsorption-Elution, Virus detection, Virus concentration, Sequencing, SARS-CoV-2, Sludge, Emerging viruses

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          Abstract

          This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review.

          Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review.

          A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.

          Graphical abstract

          Highlights

          • An overview on virus occurrence, detection and viability in wastewater and sludge

          • Molecular methods are extensively used to detect viruses in wastewater.

          • Use of sequencing to monitor virus abundance and diversity in wastewater and sludge

          • Detection and quantification of viruses in wastewater to monitor disease outbreaks

          • Research need: studies on detection methods of emerging viruses such as SARS-CoV-2

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          Author and article information

          Contributors
          Journal
          Sci Total Environ
          Sci. Total Environ
          The Science of the Total Environment
          Published by Elsevier B.V.
          0048-9697
          1879-1026
          19 July 2020
          19 July 2020
          : 140910
          Affiliations
          [a ]Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines
          [b ]Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084 Fisciano, Italy
          [c ]Inter-University Consortium of Relevant Risks (C.U.G.RI.), Via Giovanni Paolo II, Fisciano, SA, Italy
          [d ]Laboratory of Microbiology, University of Salerno, 84084 Fisciano, Italy
          [e ]Department of Chemical Engineering, College of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines
          [f ]Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
          [g ]Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98105-2700, United States
          Author notes
          [* ]Corresponding author at: Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084 Fisciano, Italy. vnaddeo@ 123456unisa.it
          Article
          S0048-9697(20)34439-9 140910
          10.1016/j.scitotenv.2020.140910
          7368910
          32758747
          4dbc55a0-b7fa-472c-b40a-f28bce2b247b
          © 2020 Published by Elsevier B.V.

          Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

          History
          : 26 May 2020
          : 9 July 2020
          : 10 July 2020
          Categories
          Article

          General environmental science
          astm, american society for testing materials,cer, cation exchange resin,cdna, complementary dna,cpcr, conventional polymerase chain reaction,covid-19, coronavirus disease 2019,cpe, cytopathic effects,dna, deoxyribonucleic acid,ev, enterovirus,eve, enzymatic virus elution,elisa, enzyme linked immunosorbent assay,efm, epifluorescence microscopy,fcm, flow cytometry,gui, graphical user interface,hav, hepatitis a virus,hfufs, hollow fibre ultrafiltration system,hadv, human adenovirus,hadv2, human adenovirus 2,hadv 40, human adenovirus 40,hev, hepatitis e virus,hsv1, herpes simplex virus type 1,hhv, human herpesvirus,ifa, immunofluorescence assay,icc-pcr, integrated cell culture-polymerase chain reaction,icc-rt-qpcr, integrated cell culture-real time rt-pcr,jcpyv, jc polyomavirus,hpv, human papillomavirus,hpyv, human polyomavirus,httv, human torque teno virus,μpad, microfluidic paper analytic device,mmtv, mouse mammary tumour virus,mhv, murine hepatitis virus,ngs, next generation sequencing,nov, norovirus,nov gi, norovirus gi,nov gii, norovirus gii,pmmv, pepper mild mottle virus,pta, phosphotungstic acid,peg, polyethylene glycol,pcr, polymerase chain reaction,pv, poliovirus,pv1, poliovirus 1,φ6, pseudomonas phage,pfge, pulsed-field gel electrophoresis,qpcr, real-time polymerase chain reaction,rt-pcr, reverse transcription-polymerase chain reaction,rt-qpcr, real time rt-pcr,rna, ribonucleic acid,rov, rotavirus,rov-a, rotavirus a,sars-cov-2, severe acute respiratory syndrome coronavirus 2,tem, transmission electron microscopy,viradel, virus adsorption-elution,virus detection,virus concentration,sequencing,sars-cov-2,sludge,emerging viruses
          General environmental science
          astm, american society for testing materials, cer, cation exchange resin, cdna, complementary dna, cpcr, conventional polymerase chain reaction, covid-19, coronavirus disease 2019, cpe, cytopathic effects, dna, deoxyribonucleic acid, ev, enterovirus, eve, enzymatic virus elution, elisa, enzyme linked immunosorbent assay, efm, epifluorescence microscopy, fcm, flow cytometry, gui, graphical user interface, hav, hepatitis a virus, hfufs, hollow fibre ultrafiltration system, hadv, human adenovirus, hadv2, human adenovirus 2, hadv 40, human adenovirus 40, hev, hepatitis e virus, hsv1, herpes simplex virus type 1, hhv, human herpesvirus, ifa, immunofluorescence assay, icc-pcr, integrated cell culture-polymerase chain reaction, icc-rt-qpcr, integrated cell culture-real time rt-pcr, jcpyv, jc polyomavirus, hpv, human papillomavirus, hpyv, human polyomavirus, httv, human torque teno virus, μpad, microfluidic paper analytic device, mmtv, mouse mammary tumour virus, mhv, murine hepatitis virus, ngs, next generation sequencing, nov, norovirus, nov gi, norovirus gi, nov gii, norovirus gii, pmmv, pepper mild mottle virus, pta, phosphotungstic acid, peg, polyethylene glycol, pcr, polymerase chain reaction, pv, poliovirus, pv1, poliovirus 1, φ6, pseudomonas phage, pfge, pulsed-field gel electrophoresis, qpcr, real-time polymerase chain reaction, rt-pcr, reverse transcription-polymerase chain reaction, rt-qpcr, real time rt-pcr, rna, ribonucleic acid, rov, rotavirus, rov-a, rotavirus a, sars-cov-2, severe acute respiratory syndrome coronavirus 2, tem, transmission electron microscopy, viradel, virus adsorption-elution, virus detection, virus concentration, sequencing, sars-cov-2, sludge, emerging viruses

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