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Saasa N, M’kandawire E, Ndebe J, Mwenda M, Chimpukutu F, Mukubesa AN, Njobvu F, Shempela DM, Sikalima J, Chiyesu C, Muvwanga B, Nampokolwe SM, Sulwe C, Khondiwa T, Jennings T, Kamanga A, Simulundu E, Mulube C, Mwasinga W, Mumeka J, Simwanza J, Sakubita P, Kapona O, Mulenga CSA, Chipoya M, Musonda K, Kapata N, Sinyange N, Kapina M, Siwila J, Shawa M, Kajihara M, Takada A, Sawa H, Choonga SA, Chilengi R, Muyunda E, Nalubamba KS, Hang’ombe BM. Detection of Human Adenovirus and Rotavirus in Wastewater in Lusaka, Zambia: Demonstrating the Utility of Environmental Surveillance for the Community. Pathogens 2024; 13:486. [PMID: 38921784 PMCID: PMC11206273 DOI: 10.3390/pathogens13060486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Enteric infections due to viral pathogens are a major public health concern. Detecting the risk areas requires a strong surveillance system for pathogenic viruses in sources such as wastewater. Towards building an environmental surveillance system in Zambia, we aimed to identify group A rotavirus (RVA) and human adenovirus (HAdV) in wastewater. Convenient sampling was conducted at four study sites every Tuesday for five consecutive weeks. The research team focused on three different methods of viral concentration to determine the suitability in terms of cost and applicability for a regular surveillance system: the bag-mediated filtration system (BMFS), polyethylene glycol-based (PEG) precipitation, and skimmed milk (SM) flocculation. We screened 20 wastewater samples for HAdV and RVA using quantitative polymerase chain reaction (qPCR) and conventional polymerase chain reaction (cPCR). Of the 20 samples tested using qPCR, 18/20 (90%) tested positive for HAdV and 14/20 (70%) tested positive for RVA. For the genetic sequencing, qPCR positives were subjected to cPCR, of which 12 positives were successfully amplified. The human adenovirus was identified with a nucleotide identity range of 98.48% to 99.53% compared with the reference genome from GenBank. The BMFS and SM flocculation were the most consistent viral concentration methods for HAdV and RVA, respectively. A statistical analysis of the positives showed that viral positivity differed by site (p < 0.001). SM and PEG may be the most appropriate options in resource-limited settings such as Zambia due to the lower costs associated with these concentration methods. The demonstration of HAdV and RVA detection in wastewater suggests the presence of the pathogens in the communities under study and the need to establish a routine wastewater surveillance system for the identification of pathogens.
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Affiliation(s)
- Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
| | - Ethel M’kandawire
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
| | - Joseph Ndebe
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
| | - Mulenga Mwenda
- PATH-Zambia, National Malaria Elimination Centre, Chainama Hospital Grounds, Lusaka 10101, Zambia; (M.M.); (F.N.); (C.C.); (T.J.); (A.K.); (C.M.); (E.M.)
| | - Fred Chimpukutu
- Effluents and Pollution Control, Lusaka Water Supply and Sanitation Company, Stand No. 871/2, Katemo Road, Rhodes Park, P.O. Box 50198, Lusaka 10101, Zambia; (F.C.); (J.M.)
| | - Andrew Nalishuwa Mukubesa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
| | - Fred Njobvu
- PATH-Zambia, National Malaria Elimination Centre, Chainama Hospital Grounds, Lusaka 10101, Zambia; (M.M.); (F.N.); (C.C.); (T.J.); (A.K.); (C.M.); (E.M.)
| | - Doreen Mainza Shempela
- Churches Health Association of Zambia (CHAZ), CHAZ Complex, Meanwood Drive (off Great East Road), Plot No. 2882/B/5/10, P.O. Box 34511, Lusaka 10101, Zambia; (D.M.S.); (J.S.)
| | - Jay Sikalima
- Churches Health Association of Zambia (CHAZ), CHAZ Complex, Meanwood Drive (off Great East Road), Plot No. 2882/B/5/10, P.O. Box 34511, Lusaka 10101, Zambia; (D.M.S.); (J.S.)
| | - Carol Chiyesu
- PATH-Zambia, National Malaria Elimination Centre, Chainama Hospital Grounds, Lusaka 10101, Zambia; (M.M.); (F.N.); (C.C.); (T.J.); (A.K.); (C.M.); (E.M.)
| | - Bruce Muvwanga
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
| | - Sarah M. Nampokolwe
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
| | - Clement Sulwe
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
| | - Thokozile Khondiwa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
| | - Todd Jennings
- PATH-Zambia, National Malaria Elimination Centre, Chainama Hospital Grounds, Lusaka 10101, Zambia; (M.M.); (F.N.); (C.C.); (T.J.); (A.K.); (C.M.); (E.M.)
| | - Ameck Kamanga
- PATH-Zambia, National Malaria Elimination Centre, Chainama Hospital Grounds, Lusaka 10101, Zambia; (M.M.); (F.N.); (C.C.); (T.J.); (A.K.); (C.M.); (E.M.)
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
- Macha Research Trust, Choma 10101, Zambia
| | - Conceptor Mulube
- PATH-Zambia, National Malaria Elimination Centre, Chainama Hospital Grounds, Lusaka 10101, Zambia; (M.M.); (F.N.); (C.C.); (T.J.); (A.K.); (C.M.); (E.M.)
| | - Wizaso Mwasinga
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
| | - Jalaimo Mumeka
- Effluents and Pollution Control, Lusaka Water Supply and Sanitation Company, Stand No. 871/2, Katemo Road, Rhodes Park, P.O. Box 50198, Lusaka 10101, Zambia; (F.C.); (J.M.)
| | - John Simwanza
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Patrick Sakubita
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Otridah Kapona
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Chilufya Susan Aneta Mulenga
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Musole Chipoya
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Kunda Musonda
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Nathan Kapata
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Nyambe Sinyange
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Muzala Kapina
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Joyce Siwila
- Department of Clinical Studies, School of Veterinary Medicine, The University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia; (J.S.); (K.S.N.)
| | - Misheck Shawa
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (M.S.); (M.K.); (H.S.)
| | - Masahiro Kajihara
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (M.S.); (M.K.); (H.S.)
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (E.M.); (J.N.); (A.N.M.); (B.M.); (S.M.N.); (C.S.); (T.K.); (E.S.); (W.M.); (A.T.)
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (M.S.); (M.K.); (H.S.)
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Sapporo 001-0020, Japan
- One Health Research Center, Hokkaido University, N18 W9, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (M.S.); (M.K.); (H.S.)
- One Health Research Center, Hokkaido University, N18 W9, Sapporo 001-0020, Japan
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Sapporo 001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, N21 W11, Sapporo 001-0021, Japan
| | - Simulyamana A. Choonga
- Ministry of Health, Lusaka Provincial Health Office, 3 Saise Road, P.O. Box 32573, Lusaka 10101, Zambia;
| | - Roma Chilengi
- Zambia National Public Health Institute, Stand 1186, Corner of Chaholi & Addis Ababa Road, Rhodes Park, Lusaka 10101, Zambia; (J.S.); (P.S.); (O.K.); (C.S.A.M.); (M.C.); (K.M.); (N.K.); (N.S.); (M.K.); (R.C.)
| | - Earnest Muyunda
- PATH-Zambia, National Malaria Elimination Centre, Chainama Hospital Grounds, Lusaka 10101, Zambia; (M.M.); (F.N.); (C.C.); (T.J.); (A.K.); (C.M.); (E.M.)
| | - King S. Nalubamba
- Department of Clinical Studies, School of Veterinary Medicine, The University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia; (J.S.); (K.S.N.)
| | - Bernard M. Hang’ombe
- Department of Paraclinical Studies, School of Veterinary Medicine, The University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia;
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
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Philo SE, Zhou NA, Lillis LM, Raghava V, Abraham D, Kumar V, Kumar N, Rigby J, Harrison JC, Fagnant-Sperati CS, Kossik AL, Ong AQW, Swanstrom R, Burnor E, Demeke B, Beck NK, Shirai JH, Libby SJ, Boyle DS, Feasey N, Kang G, Meschke JS. Development, confirmation, and application of a seeded Escherichia coli process control organism to validate Salmonella enterica serovar Typhi environmental surveillance methods. PLoS One 2024; 19:e0301624. [PMID: 38713678 DOI: 10.1371/journal.pone.0301624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/19/2024] [Indexed: 05/09/2024] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of Typhoid fever. Blood culture is the gold standard for clinical diagnosis, but this is often difficult to employ in resource limited settings. Environmental surveillance of waste-impacted waters is a promising supplement to clinical surveillance, however validating methods is challenging in regions where S. Typhi concentrations are low. To evaluate existing S. Typhi environmental surveillance methods, a novel process control organism (PCO) was created as a biosafe surrogate. Using a previous described qPCR assay, a modified PCR amplicon for the staG gene was cloned into E. coli. We developed a target region that was recognized by the Typhoid primers in addition to a non-coding internal probe sequence. A multiplex qPCR reaction was developed that differentiates between the typhoid and control targets, with no cross-reactivity or inhibition of the two probes. The PCO was shown to mimic S. Typhi in lab-based experiments with concentration methods using primary wastewater: filter cartridge, recirculating Moore swabs, membrane filtration, and differential centrifugation. Across all methods, the PCO seeded at 10 CFU/mL and 100 CFU/mL was detected in 100% of replicates. The PCO is detected at similar quantification cycle (Cq) values across all methods at 10 CFU/mL (Average = 32.4, STDEV = 1.62). The PCO was also seeded into wastewater at collection sites in Vellore (India) and Blantyre (Malawi) where S. Typhi is endemic. All methods tested in both countries were positive for the seeded PCO. The PCO is an effective way to validate performance of environmental surveillance methods targeting S. Typhi in surface water.
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Affiliation(s)
- Sarah E Philo
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Nicolette A Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | | | | | | | - Vinoth Kumar
- Christian Medical College Vellore, Vellore, India
| | - Nirmal Kumar
- Christian Medical College Vellore, Vellore, India
| | - Jonathan Rigby
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Joanna Ciol Harrison
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Christine S Fagnant-Sperati
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Alexandra L Kossik
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Angelo Q W Ong
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rachael Swanstrom
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Elisabeth Burnor
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bethel Demeke
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Nicola K Beck
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jeffry H Shirai
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Stephen J Libby
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | | | - Nicholas Feasey
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - John Scott Meschke
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
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Nejati A, Tabatabaei SM, Mahmoudi S, Zahraei SM, Tabatabaie H, Razaghi M, Khodakhah F, Yousefi M, Mollaei-Kandelousi Y, Keyvanlou M, Soheili P, Pouyandeh S, Samimi-Rad K, Shahmahmoodi S. Environmental Surveillance of Poliovirus and Non-polio Enteroviruses in Iran, 2017-2023: First Report of Imported Wild Poliovirus Type 1 Since 2000. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09600-8. [PMID: 38658427 DOI: 10.1007/s12560-024-09600-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
In Iran, which is at high risk of the Wild Poliovirus (WPV) and Vaccine-Derived Poliovirus (VDPV) importation due to its neighborhood with two polio endemic countries, Pakistan and Afghanistan, Environmental Surveillance (ES) was established in November 2017. Sistan-Balouchestan province was chosen for the ES due to its vicinity with Pakistan and Afghanistan. Five sewage collection sites in 4 cities (Zahedan, Zabol, Chabahar and Konarak) were selected in the high-risk areas. Since the establishment of ES in November 2017 till the end of 2023, 364 sewage specimens were collected and analyzed. The ES detected polioviruses which have the highest significance for polio eradication program, that is, Wild Poliovirus type 1 (WPV1) and Poliovirus type 2 (PV2). In April and May 2019, three of 364 (0.8%) sewage specimens from Konarak were positive for imported WPV1. According to phylogenetic analysis, they were highly related to WPV1 circulating in Karachi (Sindh province) in Pakistan. PV2 was also detected in 5.7% (21/364) of the sewage specimens, most of which proved to be imported from the neighboring countries. Of 21 isolated PV2s, 7 were VDPV2, of which 5 proved to be imported from the neighboring countries as there was VDPV2 circulating in Pakistan at the time of sampling, and 2 were ambiguous VDPVs (aVDPV) with unknown source. According to the findings of this study, as long as WPV1 and VDPV2 outbreaks are detected in Iran's neighboring countries, there is a definite need for continuation and expansion of the environmental surveillance.
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Affiliation(s)
- Ahmad Nejati
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mehdi Tabatabaei
- Health Promotion Research Center, Zahedan University of Medical Sciences, Sistan Balouchestan Province, Zahedan, Iran
| | - Sussan Mahmoudi
- Vaccine Preventable Diseases Department, Center for Communicable Diseases Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Seyed Mohsen Zahraei
- Vaccine Preventable Diseases Department, Center for Communicable Diseases Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Hamideh Tabatabaie
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Razaghi
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farshad Khodakhah
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Yousefi
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaghoub Mollaei-Kandelousi
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Keyvanlou
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Parastoo Soheili
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Shayan Pouyandeh
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Katayoon Samimi-Rad
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Shohreh Shahmahmoodi
- National Polio Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Al-Qassimi MA, Al Amad M, Al-Dar A, Al Sakaf E, Al Hadad A, Raja'a YA. Circulating vaccine derived polio virus type 2 outbreak and response in Yemen, 2021-2022, a retrospective descriptive analysis. BMC Infect Dis 2024; 24:321. [PMID: 38491425 PMCID: PMC10943856 DOI: 10.1186/s12879-024-09215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/12/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The outbreaks of circulating Vaccine Derived Polio Viruses (cVDPVs) have emerged as a major challenge for the final stage of polio eradication. In Yemen, an explosive outbreak of cVDPV2 was reported from August 2021 to December 2022. This study aims to compare the patterns of cVDPV2 outbreak, response measures taken by health authorities, and impacts in southern and northern governorates. METHOD A retrospective descriptive study of confirmed cases of VDPV2 was performed. The data related to cVDPV2 as well as stool specimens and environmental samples that were shipped to WHO-accredited labs were collected by staff of surveillance. Frequencies and percentages were used to characterize and compare the confirmed cases from the southern and northern governorates. The average delayed time as a difference in days between the date of sample collection and lab confirmation was calculated. RESULTS The cVDPV2 was isolated from 227 AFP cases reported from 19/23 Yemeni governorates and from 83% (39/47) of environmental samples with an average of 7 months delayed from sample collection. However, the non-polio AFP (NPAFP) and adequate stool specimen rates in the north were 6.7 and 87% compared to 6.4 and 87% in the south, 86% (195) and 14%(32) out of the total 227 confirmed cases were detected from northern and southern governorates, respectively. The first and second cases of genetically linked isolates experienced paralysis onset on 30 August and 1st September 2021. They respectively were from Taiz and Marib governorates ruled by southern authorities that started vaccination campaigns as a response in February 2022. Thus, in contrast to 2021, the detected cases in 2022 from the total cases detected in the south were lower accounting for 22% (7 of 32) of compared to 79% (155 of 195) of the total cases the north. CONCLUSION A new emerging cVDPV2 was confirmed in Yemen. The result of this study highlighted the impact of vaccination campaigns in containing the cVDPV2 outbreak. Maintaining a high level of immunization coverage and switching to nOPV2 instead of tOPV and mOPV2 in campaigns are recommended and environmental surveillance should be expanded in such a risky country.
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Affiliation(s)
- Mutahar Ahmed Al-Qassimi
- National Polio surveillance coordinator, Yemen Ministry of Public Health and Population, Sana'a, Yemen.
| | - Mohammed Al Amad
- Department of Community Medicine, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen
| | - Ahmed Al-Dar
- Department of Community Medicine, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen
| | - Ehab Al Sakaf
- General Director for Diseases Control and Surveillance, Yemen Ministry of Public Health and Population, Sana'a, Yemen
| | - Ahmed Al Hadad
- Faculty of Medicine and Health Sciences, Sana'a university, Sana'a, Yemen
- Yemen National Certification of polio eradication Committee chairperson, Sana'a, Yemen
| | - Yahia Ahmed Raja'a
- Faculty of Medicine and Health Sciences, Sana'a university, Sana'a, Yemen
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Ansari N, Kabir F, Khan W, Khalid F, Malik AA, Warren JL, Mehmood U, Kazi AM, Yildirim I, Tanner W, Kalimuddin H, Kanwar S, Aziz F, Memon A, Alam MM, Ikram A, Meschke JS, Jehan F, Omer SB, Nisar MI. Environmental surveillance for COVID-19 using SARS-CoV-2 RNA concentration in wastewater - a study in District East, Karachi, Pakistan. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2024; 20:100299. [PMID: 38234701 PMCID: PMC10794106 DOI: 10.1016/j.lansea.2023.100299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/18/2023] [Accepted: 09/28/2023] [Indexed: 01/19/2024]
Abstract
Background Wastewater-based surveillance is used to track the temporal patterns of the SARS-CoV-2 virus in communities. Viral RNA particle detection in wastewater samples can indicate an outbreak within a catchment area. We describe the feasibility of using a sewage network to monitor SARS-CoV-2 trend and use of genomic sequencing to describe the viral variant abundance in an urban district in Karachi, Pakistan. This was among the first studies from Pakistan to demonstrate the surveillance for SARS-CoV-2 from a semi-formal sewage system. Methods Four sites draining into the Lyari River in District East, Karachi, were identified and included in the current study. Raw sewage samples were collected early morning twice weekly from each site between June 10, 2021 and January 17, 2022, using Bag Mediated Filtration System (BMFS). Secondary concentration of filtered samples was achieved by ultracentrifugation and skim milk flocculation. SARS-CoV-2 RNA concentrations in the samples were estimated using PCR (Qiagen ProMega kits for N1 & N2 genes). A distributed-lag negative binomial regression model within a hierarchical Bayesian framework was used to describe the relationship between wastewater RNA concentration and COVID-19 cases from the catchment area. Genomic sequencing was performed using Illumina iSeq100. Findings Among the 151 raw sewage samples included in the study, 123 samples (81.5%) tested positive for N1 or N2 genes. The average SARS-CoV-2 RNA concentrations in the sewage samples at each lag (1-14 days prior) were associated with the cases reported for the respective days, with a peak association observed on lag day 10 (RR: 1.15; 95% Credible Interval: 1.10-1.21). Genomic sequencing showed that the delta variant dominated till September 2022, while the omicron variant was identified in November 2022. Interpretation Wastewater-based surveillance, together with genomic sequencing provides valuable information for monitoring the community temporal trend of SARS-CoV-2. Funding PATH, Bill & Melinda Gates Foundation, and Global Innovation Fund.
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Affiliation(s)
- Nadia Ansari
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Furqan Kabir
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Waqasuddin Khan
- CITRIC Centre for Bioinformatics and Computational Biology, Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Farah Khalid
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Amyn Abdul Malik
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Section of Infectious Diseases and Global Health, Department of Paediatrics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Joshua L. Warren
- Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Usma Mehmood
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Abdul Momin Kazi
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Inci Yildirim
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Section of Infectious Diseases and Global Health, Department of Paediatrics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Windy Tanner
- Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Hussain Kalimuddin
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Samiah Kanwar
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
- CITRIC Centre for Bioinformatics and Computational Biology, Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Fatima Aziz
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Arslan Memon
- District Health Office (East), Karachi, Pakistan
| | | | - Aamer Ikram
- National Institutes of Health, Chak Shahzad, Islamabad, Pakistan
| | | | - Fyezah Jehan
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
- CITRIC Centre for Bioinformatics and Computational Biology, Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
| | - Saad B. Omer
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Section of Infectious Diseases and Global Health, Department of Paediatrics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Yale School of Public Health, Yale University, New Haven, CT, USA
- Yale School of Nursing, Orange, CT, USA
| | - Muhammad Imran Nisar
- Faculty of Health Sciences, Department of Paediatrics and Child Health, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
- CITRIC Centre for Bioinformatics and Computational Biology, Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan
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Barnes KG, Levy JI, Gauld J, Rigby J, Kanjerwa O, Uzzell CB, Chilupsya C, Anscombe C, Tomkins-Tinch C, Mbeti O, Cairns E, Thole H, McSweeney S, Chibwana MG, Ashton PM, Jere KC, Meschke JS, Diggle P, Cornick J, Chilima B, Jambo K, Andersen KG, Kawalazira G, Paterson S, Nyirenda TS, Feasey N. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems. Nat Commun 2023; 14:7883. [PMID: 38036496 PMCID: PMC10689440 DOI: 10.1038/s41467-023-43047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
The COVID-19 pandemic has profoundly impacted health systems globally and robust surveillance has been critical for pandemic control, however not all countries can currently sustain community pathogen surveillance programs. Wastewater surveillance has proven valuable in high-income settings, but less is known about the utility of water surveillance of pathogens in low-income countries. Here we show how wastewater surveillance of SAR-CoV-2 can be used to identify temporal changes and help determine circulating variants quickly. In Malawi, a country with limited community-based COVID-19 testing capacity, we explore the utility of rivers and wastewater for SARS-CoV-2 surveillance. From May 2020-May 2022, we collect water from up to 112 river or defunct wastewater treatment plant sites, detecting SARS-CoV-2 in 8.3% of samples. Peak SARS-CoV-2 detection in water samples predate peaks in clinical cases. Sequencing of water samples identified the Beta, Delta, and Omicron variants, with Delta and Omicron detected well in advance of detection in patients. Our work highlights how wastewater can be used to detect emerging waves, identify variants of concern, and provide an early warning system in settings with no formal sewage systems.
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Affiliation(s)
- Kayla G Barnes
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Joshua I Levy
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jillian Gauld
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan Rigby
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Oscar Kanjerwa
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Christopher B Uzzell
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Chisomo Chilupsya
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Catherine Anscombe
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Christopher Tomkins-Tinch
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Omar Mbeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Herbert Thole
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Shannon McSweeney
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Marah G Chibwana
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Philip M Ashton
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
| | - Khuzwayo C Jere
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - John Scott Meschke
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Peter Diggle
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
| | - Benjamin Chilima
- CHICAS, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Kondwani Jambo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Public Health Institute of Malawi, Lilongwe, Malawi
| | - Kristian G Andersen
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Scripps Research Translational Institute, La Jolla, CA, USA
| | - Gift Kawalazira
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Tonney S Nyirenda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
- School of Medicine, University of St Andrews, St Andrews, UK
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7
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Barnes K, Levy J, Andersen K, Gauld J, Rigby J, Kanjerwa O, Uzzell C, Chilupsya C, Anscombe C, Tomkins-Tinch C, Mbeti O, Cairns E, Thole H, McSweeney S, Chibwana M, Ashton P, Jere K, Meschke J, Diggle P, Cornick J, Jambo K, Kawalazira G, Paterson S, Nyirenda T, Feasey N, Chilima B. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems. RESEARCH SQUARE 2023:rs.3.rs-2801767. [PMID: 37090541 PMCID: PMC10120776 DOI: 10.21203/rs.3.rs-2801767/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The COVID-19 pandemic continues to impact health systems globally and robust surveillance is critical for pandemic control, however not all countries can sustain community surveillance programs. Wastewater surveillance has proven valuable in high-income settings, but little is known about how river and informal sewage in low-income countries can be used for environmental surveillance of SARS-CoV-2. In Malawi, a country with limited community-based COVID-19 testing capacity, we explored the utility of rivers and wastewater for SARS-CoV-2 surveillance. From May 2020 - January 2022, we collected water from up to 112 river or informal sewage sites/month, detecting SARS-CoV-2 in 8.3% of samples. Peak SARS-CoV-2 detection in water samples predated peaks in clinical cases. Sequencing of water samples identified the Beta, Delta, and Omicron variants, with Delta and Omicron detected well in advance of detection in patients. Our work highlights wastewater can be used for detecting emerging waves, identifying variants of concern and function as an early warning system in settings with no formal sewage systems.
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Affiliation(s)
| | | | - Kristian Andersen
- Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA
| | - Jillian Gauld
- Institute for Disease Modeling, Bill & Melinda Gates Foundation
| | - Jonathan Rigby
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | - Oscar Kanjerwa
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Chisomo Chilupsya
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | | | | | - Edward Cairns
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
| | - Herbert Thole
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences
| | - Shannon McSweeney
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | - Marah Chibwana
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences
| | | | | | | | | | - Jennifer Cornick
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
| | | | | | | | - Tonney Nyirenda
- Department of Pathology, Kamuzu University of Health Sciences
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8
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Belgasmi H, Miles SJ, Sayyad L, Wong K, Harrington C, Gerloff N, Coulliette-Salmond AD, Guntapong R, Tacharoenmuang R, Ayutthaya AIN, Apostol LNG, Valencia MLD, Burns CC, Benito GR, Vega E. CaFÉ: A Sensitive, Low-Cost Filtration Method for Detecting Polioviruses and Other Enteroviruses in Residual Waters. FRONTIERS IN ENVIRONMENTAL SCIENCE 2022; 10:10.3389/fenvs.2022.914387. [PMID: 35928599 PMCID: PMC9344547 DOI: 10.3389/fenvs.2022.914387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Acute flaccid paralysis (AFP) surveillance has been used to identify polio cases and target vaccination campaigns since the inception of the Global Poliovirus Eradication Initiative (GPEI) in 1988. To date, only Afghanistan and Pakistan have failed to interrupt wild poliovirus transmission. Circulation of vaccine-derived polioviruses (VDPV) continues to be a problem in high-risk areas of the Eastern Mediterranean, African, and Southeast Asian regions. Environmental surveillance (ES) is an important adjunct to AFP surveillance, helping to identify circulating polioviruses in problematic areas. Stools from AFP cases and contacts (>200,000 specimens/year) and ES samples (>642 sites) are referred to 146 laboratories in the Global Polio Laboratory Network (GPLN) for testing. Although most World Health Organization supported laboratories use the two-phase separation method due to its simplicity and effectiveness, alternative simple, widely available, and cost-effective methods are needed. The CAFÉ (Concentration and Filtration Elution) method was developed from existing filtration methods to handle any type of sewage or residual waters. At $10-20 US per sample for consumable materials, CAFÉ is cost effective, and all equipment and reagents are readily available from markets and suppliers globally. The report describes the results from a parallel study of CAFÉ method with the standard two-phase separation method. The study was performed with samples collected from five countries (Guatemala, Haïti, Thailand, Papua New Guinea, and the Philippines), run in three laboratories-(United States, Thailand and in the Philippines) to account for regional and sample-to-sample variability. Samples from each site were divided into two 500 ml aliquots and processed by both methods, with no other additional concentration or manipulation. The results of 338 parallel-tested samples show that the CAFÉ method is more sensitive than the two-phase separation method for detection of non-polio enteroviruses (p-value < 0.0001) and performed as well as the two-phase separation method for polioviruses detection with no significant difference (p-value > 0.05). The CAFÉ method is a robust, sensitive, and cost-effective method for isolating enteroviruses from residual waters.
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Affiliation(s)
- Hanen Belgasmi
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Stacey Jeffries Miles
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | - Chelsea Harrington
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Nancy Gerloff
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Angela D Coulliette-Salmond
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
- U.S Public Health Service, Rockville, MD, United States
| | - Ratigorn Guntapong
- Department of Medical Science, Enteric Viruses Section, National Institute of Health, Nonthaburi, Thailand
| | - Ratana Tacharoenmuang
- Department of Medical Science, Enteric Viruses Section, National Institute of Health, Nonthaburi, Thailand
| | | | | | | | - Cara C. Burns
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gloria-Rey Benito
- Pan American Health Organization, World Health Organization, Washington, DC, United States
| | - Everardo Vega
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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9
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Zhu Y, Wu X, Gu A, Dobelle L, Cid C, Li J, Hoffmann MR. Membrane-Based In-Gel Loop-Mediated Isothermal Amplification (mgLAMP) System for SARS-CoV-2 Quantification in Environmental Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:862-873. [PMID: 34967203 PMCID: PMC8751019 DOI: 10.1021/acs.est.1c04623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 05/06/2023]
Abstract
Since the COVID-19 pandemic is expected to become endemic, quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambient waters is critical for environmental surveillance and for early detection of outbreaks. Herein, we report the development of a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system that is designed for the rapid point-of-use quantification of SARS-CoV-2 particles in environmental waters. The mgLAMP system integrates the viral concentration, in-assay viral lysis, and on-membrane hydrogel-based RT-LAMP quantification using enhanced fluorescence detection with a target-specific probe. With a sample-to-result time of less than 1 h, mgLAMP successfully detected SARS-CoV-2 below 0.96 copies/mL in Milli-Q water. In surface water, the lowest detected SARS-CoV-2 concentration was 93 copies/mL for mgLAMP, while the reverse transcription quantitative polymerase chain reaction (RT-qPCR) with optimal pretreatment was inhibited at 930 copies/mL. A 3D-printed portable device is designed to integrate heated incubation and fluorescence illumination for the simultaneous analysis of nine mgLAMP assays. Smartphone-based imaging and machine learning-based image processing are used for the interpretation of results. In this report, we demonstrate that mgLAMP is a promising method for large-scale environmental surveillance of SARS-CoV-2 without the need for specialized equipment, highly trained personnel, and labor-intensive procedures.
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Affiliation(s)
- Yanzhe Zhu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Xunyi Wu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Alan Gu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Leopold Dobelle
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Clément
A. Cid
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Jing Li
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Michael R. Hoffmann
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
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Giri S, Mohan VR, Srinivasan M, Kumar N, Kumar V, Dhanapal P, Venkatesan J, Gunasekaran A, Abraham D, John J, Kang G. Case-Control Study of Household and Environmental Transmission of Typhoid Fever in India. J Infect Dis 2021; 224:S584-S592. [PMID: 35238355 PMCID: PMC8892545 DOI: 10.1093/infdis/jiab378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background Typhoid fever causes substantial morbidity and mortality in low- and middle-income countries. We conducted a case-control study in Vellore, southern India, to understand risk factors for transmission of typhoid. Methods From April 2018 to October 2019, households of blood culture-confirmed typhoid cases that occurred within a fever surveillance cohort aged 6 months–15 years, and controls matched for age, sex, geographic location, and socioeconomic status, were recruited. Information on risk factors was obtained using standard questionnaires. Household and environmental samples were collected for detection of Salmonella Typhi using real-time polymerase chain reaction. Multivariable analysis was used to evaluate associations between risk factors and typhoid. Results One hundred pairs of cases and controls were recruited. On multivariable regression analysis, mothers eating food from street vendors during the previous week (odds ratio [OR] = 2.04; 95% confidence interval [CI], 1.03–4.12; P = .04) was independently associated with typhoid, whereas treatment of household drinking water (OR = 0.45; 95% CI, 0.25–0.80; P = .007) was protective. There was no significant difference in S Typhi detection between the environmental samples from case and control households. Conclusions Street-vended food is a risk factor for typhoid in densely populated urban communities of Vellore. Improved sanitation facilities and awareness about point-of-use water treatment are likely to contribute to typhoid control.
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Affiliation(s)
- Sidhartha Giri
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | | | - Nirmal Kumar
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Vinoth Kumar
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Pavithra Dhanapal
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | - Annai Gunasekaran
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Dilip Abraham
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Jacob John
- Department of Community Health, Christian Medical College, Vellore, India
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
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Zohra T, Ikram A, Salman M, Amir A, Saeed A, Ashraf Z, Ahad A. Wastewater based environmental surveillance of toxigenic Vibrio cholerae in Pakistan. PLoS One 2021; 16:e0257414. [PMID: 34591885 PMCID: PMC8483414 DOI: 10.1371/journal.pone.0257414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/01/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Pakistan has been experiencing intervals of sporadic cases and localized outbreaks in the last two decades. No proper study has been carried out in order to find out the environmental burden of toxigenic V. cholerae as well as how temporal and environmental factors associated in driving cholera across the country. METHODS We tested waste water samples from designated national environment surveillance sites in Pakistan with RT-PCR assay. Multistage sampling technique were utilized for samples collection and for effective sample processing Bag-Mediated Filtration system, were employed. Results were analysed by district and month wise to understand the geographic distribution and identify the seasonal pattern of V. cholera detection in Pakistan. RESULTS Between May 2019, and February 2020, we obtained and screened 160 samples in 12 districts across Pakistan. Out of 16 sentinel environmental surveillance sites, 15 sites showed positive results against cholera toxigenic gene with mostly lower CT value (mean, 34±2) and have significant difference (p < 0.05). The highest number of positive samples were collected from Sindh in month of November, then in June it is circulating in different districts of Pakistan including four Provinces respectively. CONCLUSION V. cholera detection do not follow a clear seasonal pattern. However, the poor sanitation problems or temperature and rainfall may potentially influence the frequency and duration of cholera across the country. Occurrence of toxigenic V. cholerae in the environment samples showed that cholera is endemic, which is an alarming for a potential future cholera outbreaks in the country.
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Affiliation(s)
- Tanzeel Zohra
- Public Health Laboratories Division, Department of Microbiology, National Institute of Health, Islamabad, Pakistan
| | - Aamer Ikram
- Public Health Laboratories Division, Department of Microbiology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Public Health Laboratories Division, Department of Microbiology, National Institute of Health, Islamabad, Pakistan
| | - Afreenish Amir
- Public Health Laboratories Division, Department of Microbiology, National Institute of Health, Islamabad, Pakistan
| | - Asim Saeed
- Public Health Laboratories Division, Department of Microbiology, National Institute of Health, Islamabad, Pakistan
| | - Zurva Ashraf
- Public Health Laboratories Division, Department of Microbiology, National Institute of Health, Islamabad, Pakistan
| | - Abdul Ahad
- Public Health Laboratories Division, Department of Microbiology, National Institute of Health, Islamabad, Pakistan
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Kiulia NM, Gonzalez R, Thompson H, Aw TG, Rose JB. Quantification and Trends of Rotavirus and Enterovirus in Untreated Sewage Using Reverse Transcription Droplet Digital PCR. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:154-169. [PMID: 33591485 DOI: 10.1007/s12560-020-09455-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
The quantification and trends in concentrations for naturally occurring rotaviruses (RV) and enteroviruses (EV) in untreated sewage in various wastewater systems have not often been compared. There is now greater interest in monitoring the infections in the community including live vaccine efficacy by evaluating untreated sewage. The goals of this study were to 1) survey the concentrations of naturally occurring RV and EV in untreated sewage using a reverse transcription-droplet digital polymerase chain reaction (RT-ddPCR) and 2) investigate the use of a new adsorption elution (bag-mediated filtration system (BMFS) using ViroCap filters) against more traditional polyethylene glycol (PEG) precipitation for virus concentration. Sewage samples were collected from lagoons in Kenya and Michigan (MI), the United States (USA) and from wastewater treatment plants (WWTPs) in the USA. RVs were detected at geometric mean concentrations in various locations, California (CA) 1.31 × 105 genome copies/L (gc/L), Kenya (KE) 2.71 × 104 gc/L and Virginia (VA) 1.48 × 105 gc/L, and EVs geometric means were 3.72 × 106 gc/L (CA), 1.18 × 104 gc/L (Kenya), and 6.18 × 103 gc/L (VA). The mean RV concentrations using BMFS-ViroCap in split samples compared to PEG precipitation methods demonstrated that the levels were only 9% (#s BMFS/PEG) in the Michigan lagoons which was significantly different (p < 0.01). This suggests that RV concentrations in Kenya are around 1.69 × 106 gc/L. Overall, there was no difference in concentrations for the other sampling locations across the methods of virus recovery (i.e., PEG precipitation and HA filters) using one-way ANOVA (F = 1.7, p = 0.2739) or Tukey-Kramer pairwise comparisons (p > 0.05). This study provides useful data on RV and EV concentrations in untreated sewage in Kenya and the USA. It also highlights on the usefulness of the RT-ddPCR for absolute quantification of RV and EV in sewage samples. The BMFS using ViroCap filters while less efficient compared to the more traditional PEG precipitation method was able to recover RVs and EVs in untreated sewage and may be useful in poor resource settings while underestimating viruses by 1 to 1.5 logs.
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Affiliation(s)
- Nicholas M Kiulia
- The Water Quality, Environmental and Molecular Microbiology Laboratory, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA.
- Enteric Pathogens and Water Research Laboratory, Institute of Primate Research, P.O. Box 24481-00502, Karen, Nairobi, Kenya.
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA, 23455, USA
| | - Hannah Thompson
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA, 23455, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA, 70112, USA
| | - Joan B Rose
- The Water Quality, Environmental and Molecular Microbiology Laboratory, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
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13
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Zhou NA, Tharpe C, Meschke JS, Ferguson CM. Survey of rapid development of environmental surveillance methods for SARS-CoV-2 detection in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144852. [PMID: 33486187 PMCID: PMC7808727 DOI: 10.1016/j.scitotenv.2020.144852] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 05/18/2023]
Abstract
Environmental surveillance as a part of wastewater-based epidemiology (WBE) of SARS-CoV-2 can provide an early, cost-effective, unbiased community-level indicator of circulating COVID-19 in a population. The objective of this study was to determine how widely SARS-CoV-2 detection in wastewater is being investigated and what methods are used. A survey was developed and distributed, with results showing that methods were rapidly applied to conduct SARS-CoV-2 WBE, primarily to test wastewater influent from large urban wastewater treatment plants. Additionally, most methods utilized small wastewater volumes and the primary concentration methods used were polyethylene glycol precipitation, membrane filtration and centrifugal ultrafiltration followed by nucleic acid extraction and assay for primarily nucleocapsid gene targets (N1, N2, and/or N3). Since this survey was performed, many laboratories have continued to optimize and implement a variety of methods for SARS-CoV-2 WBE. Method comparison studies completed since this survey was conducted will assist in developing WBE as a supplemental tool to support public health and policy decision making responses.
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Affiliation(s)
- Nicolette A Zhou
- Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, United States of America
| | - Courtney Tharpe
- Water Research Foundation, 1199 N Fairfax St., Suite 900, Alexandria, VA 22314, United States of America
| | - John Scott Meschke
- Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, United States of America
| | - Christobel M Ferguson
- Water Research Foundation, 1199 N Fairfax St., Suite 900, Alexandria, VA 22314, United States of America.
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14
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Philo SE, Keim EK, Swanstrom R, Ong AQW, Burnor EA, Kossik AL, Harrison JC, Demeke BA, Zhou NA, Beck NK, Shirai JH, Meschke JS. A comparison of SARS-CoV-2 wastewater concentration methods for environmental surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:144215. [PMID: 33340739 PMCID: PMC7832770 DOI: 10.1016/j.scitotenv.2020.144215] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 05/08/2023]
Abstract
Wastewater1 surveillance of SARS-CoV-2 may be a useful supplement to clinical surveillance as it is shed in feces, there are many asymptomatic cases, and diagnostic testing can have capacity limitations and extended time to results. Although numerous studies have utilized wastewater surveillance for SARS-CoV-2, the methods used were developed and/or standardized for other pathogens. This study evaluates multiple methods for concentration and recovery of SARS-CoV-2 and seeded human coronavirus OC43 from municipal primary wastewater and/or sludge from the Greater Seattle Area (March-July 2020). Methods evaluated include the bag-mediated filtration system (BMFS), with and without Vertrel™ extraction, skimmed milk flocculation, with and without Vertrel™ extraction, polyethylene glycol (PEG) precipitation, ultrafiltration, and sludge extraction. Total RNA was extracted from wastewater concentrates and analyzed for SARS-CoV-2 and OC43 with RT-qPCR. Skimmed milk flocculation without Vertrel™ extraction performed consistently over time and between treatment plants in Seattle-area wastewater with the lowest average OC43 Cq value and smallest variability (24.3; 95% CI: 23.8-24.9), most frequent SARS-CoV-2 detection (48.8% of sampling events), and highest average OC43 percent recovery (9.1%; 95% CI: 6.2-11.9%). Skimmed milk flocculation is also beneficial because it is feasible in low-resource settings. While the BMFS had the highest average volume assayed of 11.9 mL (95% CI: 10.7-13.1 mL), the average OC43 percent recovery was low (0.7%; 95% CI: 0.4-1.0%). Ultrafiltration and PEG precipitation had low average OC43 percent recoveries of 1.0% (95% CI: 0.5-1.6%) and 3.2% (95% CI: 1.3-5.1%), respectively. The slopes and efficiency for the SARS-CoV-2 standard curves were not consistent over time, confirming the need to include a standard curve each run rather than using a single curve for multiple plates. Results suggest that the concentration and detection methods used must be validated for the specific water matrix using a recovery control to assess performance over time.
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Affiliation(s)
- Sarah E Philo
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Erika K Keim
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Rachael Swanstrom
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Angelo Q W Ong
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Elisabeth A Burnor
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Alexandra L Kossik
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Joanna C Harrison
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Bethel A Demeke
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Nicolette A Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Nicola K Beck
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Jeffry H Shirai
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - J Scott Meschke
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA.
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15
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Linden YS, Fagnant-Sperati CS, Kossik AL, Harrison JC, Beck NK, Boyle DS, Meschke JS. Method Development for Enteric Virus Recovery from Primary Sludge. Viruses 2021; 13:v13030440. [PMID: 33803454 PMCID: PMC8000433 DOI: 10.3390/v13030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/19/2021] [Accepted: 03/05/2021] [Indexed: 11/16/2022] Open
Abstract
Enteric viruses, such as poliovirus, are a leading cause of gastroenteritis, which causes 2–3 million deaths annually. Environmental surveillance of wastewater supplements clinical surveillance for monitoring enteric virus circulation. However, while many environmental surveillance methods require liquid samples, some at-risk locations utilize pit latrines with waste characterized by high solids content. This study’s objective was to develop and evaluate enteric virus concentration protocols for high solids content samples. Two existing protocols were modified and tested using poliovirus type 1 (PV1) seeded into primary sludge. Method 1 (M1) utilized acid adsorption, followed by 2 or 3 elutions (glycine/sodium chloride and/or threonine/sodium chloride), and skimmed milk flocculation. Method 2 (M2) began with centrifugation. The liquid fraction was filtered through a ViroCap filter and eluted (beef extract/glycine). The solid fraction was eluted (beef extract/disodium hydrogen phosphate/citric acid) and concentrated by skimmed milk flocculation. Recovery was enumerated by plaque assay. M1 yielded higher PV1 recovery than M2, though this result was not statistically significant (26.1% and 15.9%, respectively). M1 was further optimized, resulting in significantly greater PV1 recovery when compared to the original protocol (p < 0.05). This method can be used to improve understanding of enteric virus presence in communities without liquid waste streams.
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Affiliation(s)
- Yarrow S. Linden
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98195, USA; (Y.S.L.); (C.S.F.-S.); (A.L.K.); (J.C.H.); (N.K.B.)
| | - Christine S. Fagnant-Sperati
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98195, USA; (Y.S.L.); (C.S.F.-S.); (A.L.K.); (J.C.H.); (N.K.B.)
| | - Alexandra L. Kossik
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98195, USA; (Y.S.L.); (C.S.F.-S.); (A.L.K.); (J.C.H.); (N.K.B.)
| | - Joanna Ciol Harrison
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98195, USA; (Y.S.L.); (C.S.F.-S.); (A.L.K.); (J.C.H.); (N.K.B.)
| | - Nicola K. Beck
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98195, USA; (Y.S.L.); (C.S.F.-S.); (A.L.K.); (J.C.H.); (N.K.B.)
| | - David S. Boyle
- PATH, 2201 Westlake Ave, Suite 200, Seattle, WA 98121, USA;
| | - John Scott Meschke
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98195, USA; (Y.S.L.); (C.S.F.-S.); (A.L.K.); (J.C.H.); (N.K.B.)
- Correspondence:
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16
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Fagnant‐Sperati C, Ren Y, Zhou N, Komen E, Mwangi B, Hassan J, Chepkurui A, Nzunza R, Nyangao J, van Zyl W, Wolfaardt M, Matsapola P, Ngwana F, Jeffries‐Miles S, Coulliette‐Salmond A, Peñaranda S, Vega E, Shirai J, Kossik A, Beck N, Boyle D, Burns C, Taylor M, Borus P, Meschke J. Validation of the bag-mediated filtration system for environmental surveillance of poliovirus in Nairobi, Kenya. J Appl Microbiol 2021; 130:971-981. [PMID: 32743931 PMCID: PMC7854911 DOI: 10.1111/jam.14807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 01/15/2023]
Abstract
AIMS This study compared the bag-mediated filtration system (BMFS) and standard WHO two-phase separation methods for poliovirus (PV) environmental surveillance, examined factors impacting PV detection and monitored Sabin-like (SL) PV type 2 presence with withdrawal of oral polio vaccine type 2 (OPV2) in April 2016. METHODS AND RESULTS Environmental samples were collected in Nairobi, Kenya (Sept 2015-Feb 2017), concentrated via BMFS and two-phase separation methods, then assayed using the WHO PV isolation algorithm and intratypic differentiation diagnostic screening kit. SL1, SL2 and SL3 were detected at higher rates in BMFS than two-phase samples (P < 0·05). In BMFS samples, SL PV detection did not significantly differ with volume filtered, filtration time or filter shipment time (P > 0·05), while SL3 was detected less frequently with higher shipment temperatures (P = 0·027). SL2 was detected more frequently before OPV2 withdrawal in BMFS and two-phase samples (P < 1 × 10-5 ). CONCLUSIONS Poliovirus was detected at higher rates with the BMFS, a method that includes a secondary concentration step, than using the standard WHO two-phase method. SL2 disappearance from the environment was commensurate with OPV2 withdrawal. SIGNIFICANCE AND IMPACT OF THE STUDY The BMFS offers comparable or improved PV detection under the conditions in this study, relative to the two-phase method.
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Affiliation(s)
- C.S. Fagnant‐Sperati
- Department of Environmental and Occupational Health SciencesUniversity of WashingtonSeattleWAUSA
| | - Y. Ren
- Department of BiostatisticsUniversity of WashingtonSeattleWAUSA
| | - N.A. Zhou
- Department of Environmental and Occupational Health SciencesUniversity of WashingtonSeattleWAUSA
| | - E. Komen
- Centre for Viral ResearchKenya Medical Research InstituteNairobiKenya
| | - B. Mwangi
- Centre for Viral ResearchKenya Medical Research InstituteNairobiKenya
| | - J. Hassan
- Centre for Viral ResearchKenya Medical Research InstituteNairobiKenya
| | - A. Chepkurui
- Centre for Viral ResearchKenya Medical Research InstituteNairobiKenya
| | - R. Nzunza
- Centre for Viral ResearchKenya Medical Research InstituteNairobiKenya
| | - J. Nyangao
- Centre for Viral ResearchKenya Medical Research InstituteNairobiKenya
| | - W.B. van Zyl
- Department of Medical VirologyUniversity of PretoriaPretoriaSouth Africa
| | - M. Wolfaardt
- Department of Medical VirologyUniversity of PretoriaPretoriaSouth Africa
| | - P.N. Matsapola
- Department of Medical VirologyUniversity of PretoriaPretoriaSouth Africa
| | - F.B. Ngwana
- Department of Medical VirologyUniversity of PretoriaPretoriaSouth Africa
| | - S. Jeffries‐Miles
- Cherokee Nation Assurance a contracting agency to the Division of Viral DiseasesCenters for Disease Control and PreventionAtlantaGAUSA
| | | | - S. Peñaranda
- Division of Viral DiseasesCenters for Disease Control and PreventionAtlantaGAUSA
| | - E. Vega
- Division of Viral DiseasesCenters for Disease Control and PreventionAtlantaGAUSA
| | - J.H. Shirai
- Department of Environmental and Occupational Health SciencesUniversity of WashingtonSeattleWAUSA
| | - A.L. Kossik
- Department of Environmental and Occupational Health SciencesUniversity of WashingtonSeattleWAUSA
| | - N.K. Beck
- Department of Environmental and Occupational Health SciencesUniversity of WashingtonSeattleWAUSA
| | | | - C.C. Burns
- Division of Viral DiseasesCenters for Disease Control and PreventionAtlantaGAUSA
| | - M.B. Taylor
- Department of Medical VirologyUniversity of PretoriaPretoriaSouth Africa
| | - P. Borus
- Centre for Viral ResearchKenya Medical Research InstituteNairobiKenya
| | - J.S. Meschke
- Department of Environmental and Occupational Health SciencesUniversity of WashingtonSeattleWAUSA
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17
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Wu X, Huang X, Zhu Y, Li J, Hoffmann MR. Synthesis and application of superabsorbent polymer microspheres for rapid concentration and quantification of microbial pathogens in ambient water. Sep Purif Technol 2020; 239:116540. [PMID: 32421015 PMCID: PMC7045201 DOI: 10.1016/j.seppur.2020.116540] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A portable, hand-pressed 3D-printed system with SAP microspheres was developed. This system could achieve efficient concentration of environmental microorganisms. Superior performance was achieved with varying ionic strengths in a short time. Optimized SAP microspheres could be reused 20 times with simple procedures.
Even though numerous methods have been developed for the detection and quantification of waterborne pathogens, the application of these methods is often hindered by the very low pathogen concentrations in natural waters. Therefore, rapid and efficient sample concentration methods are urgently needed. Here we present a novel method to pre-concentrate microbial pathogens in water using a portable 3D-printed system with super-absorbent polymer (SAP) microspheres, which can effectively reduce the actual volume of water in a collected sample. The SAP microspheres absorb water while excluding bacteria and viruses by size exclusion and charge repulsion. To improve the water absorption capacity of SAP in varying ionic strength waters (0–100 mM), we optimized the formulation of SAP to 180 g⋅L−1 Acrylamide, 75 g⋅L−1 Itaconic Acid and 4.0 g⋅L−1 Bis-Acrylamide for the highest ionic strength water as a function of the extent of cross-linking and the concentration of counter ions. Fluorescence microscopy and double-layer agar plating respectively showed that the 3D-printed system with optimally-designed SAP microspheres could rapidly achieve a 10-fold increase in the concentration of Escherichia coli (E. coli) and bacteriophage MS2 within 20 min with concentration efficiencies of 87% and 96%, respectively. Fold changes between concentrated and original samples from qPCR and RT-qPCR results were found to be respectively 11.34–22.27 for E. coli with original concentrations from 104 to 106 cell·mL−1, and 8.20–13.81 for MS2 with original concentrations from 104 to 106 PFU·mL−1. Furthermore, SAP microspheres can be reused for 20 times without performance loss, significantly decreasing the cost of our concentration system.
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Affiliation(s)
- Xunyi Wu
- Linde+ Robinson Laboratories, California Institute of Technology, Pasadena, CA 91125, United States
| | - Xiao Huang
- Linde+ Robinson Laboratories, California Institute of Technology, Pasadena, CA 91125, United States
| | - Yanzhe Zhu
- Linde+ Robinson Laboratories, California Institute of Technology, Pasadena, CA 91125, United States
| | - Jing Li
- Linde+ Robinson Laboratories, California Institute of Technology, Pasadena, CA 91125, United States
| | - Michael R Hoffmann
- Linde+ Robinson Laboratories, California Institute of Technology, Pasadena, CA 91125, United States
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18
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Coulliette-Salmond AD, Alleman MM, Wilnique P, Rey-Benito G, Wright HB, Hecker JW, Miles S, Peñaranda S, Lafontant D, Corvil S, Francois J, Rossignol E, Stanislas M, Gue E, Faye PC, Castro CJ, Schmidt A, Ng TFF, Burns CC, Vega E. Haiti Poliovirus Environmental Surveillance. Am J Trop Med Hyg 2020; 101:1240-1248. [PMID: 31701857 DOI: 10.4269/ajtmh.19-0469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Poliovirus (PV) environmental surveillance was established in Haiti in three sites each in Port-au-Prince and Gonaïves, where sewage and fecal-influenced environmental open water channel samples were collected monthly from March 2016 to February 2017. The primary objective was to monitor for the emergence of vaccine-derived polioviruses (VDPVs) and the importation and transmission of wild polioviruses (WPVs). A secondary objective was to compare two environmental sample processing methods, the gold standard two-phase separation method and a filter method (bag-mediated filtration system [BMFS]). In addition, non-polio enteroviruses (NPEVs) were characterized by next-generation sequencing using Illumina MiSeq to provide insight on surrogates for PVs. No WPVs or VDPVs were detected at any site with either concentration method. Sabin (vaccine) strain PV type 2 and Sabin strain PV type 1 were found in Port-au-Prince, in March and April samples, respectively. Non-polio enteroviruses were isolated in 75-100% and 0-58% of samples, by either processing method during the reporting period in Port-au-Prince and Gonaïves, respectively. Further analysis of 24 paired Port-au-Prince samples confirmed the detection of a human NPEV and echovirus types E-3, E-6, E-7, E-11, E-19, E-20, and E-29. The comparison of the BMFS filtration method to the two-phase separation method found no significant difference in sensitivity between the two methods (mid-P-value = 0.55). The experience of one calendar year of sampling has informed the appropriateness of the initially chosen sampling sites, importance of an adequate PV surrogate, and robustness of two processing methods.
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Affiliation(s)
- Angela D Coulliette-Salmond
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mary M Alleman
- Polio Eradication Branch, Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Pierre Wilnique
- Division of Epidemiology, Laboratory and Research, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Gloria Rey-Benito
- Pan American Health Organization, World Health Organization, Washington, District of Columbia
| | | | | | | | - Silvia Peñaranda
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Donald Lafontant
- Division of Epidemiology, Laboratory and Research, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Salomon Corvil
- Division of Epidemiology, Laboratory and Research, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Jeannot Francois
- Expanded Programme on Immunization, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Emmanuel Rossignol
- National Public Health Laboratory, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Magalie Stanislas
- National Public Health Laboratory, Ministry of Public Health and Population, Port-au-Prince, Haiti
| | - Edmond Gue
- Pan American Health Organization, World Health Organization Region of the Americas, Port-au-Prince, Haiti
| | - Papa C Faye
- Pan American Health Organization, World Health Organization Region of the Americas, Port-au-Prince, Haiti
| | - Christina J Castro
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee.,Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Terry Fei Fan Ng
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Cara C Burns
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Everardo Vega
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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19
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Zhou NA, Fagnant-Sperati CS, Komen E, Mwangi B, Mukubi J, Nyangao J, Hassan J, Chepkurui A, Maina C, van Zyl WB, Matsapola PN, Wolfaardt M, Ngwana FB, Jeffries-Miles S, Coulliette-Salmond A, Peñaranda S, Shirai JH, Kossik AL, Beck NK, Wilmouth R, Boyle DS, Burns CC, Taylor MB, Borus P, Meschke JS. Feasibility of the Bag-Mediated Filtration System for Environmental Surveillance of Poliovirus in Kenya. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:35-47. [PMID: 31679104 PMCID: PMC7052051 DOI: 10.1007/s12560-019-09412-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/15/2019] [Indexed: 05/24/2023]
Abstract
The bag-mediated filtration system (BMFS) was developed to facilitate poliovirus (PV) environmental surveillance, a supplement to acute flaccid paralysis surveillance in PV eradication efforts. From April to September 2015, environmental samples were collected from four sites in Nairobi, Kenya, and processed using two collection/concentration methodologies: BMFS (> 3 L filtered) and grab sample (1 L collected; 0.5 L concentrated) with two-phase separation. BMFS and two-phase samples were analyzed for PV by the standard World Health Organization poliovirus isolation algorithm followed by intratypic differentiation. BMFS samples were also analyzed by a cell culture independent real-time reverse transcription polymerase chain reaction (rRT-PCR) and an alternative cell culture method (integrated cell culture-rRT-PCR with PLC/PRF/5, L20B, and BGM cell lines). Sabin polioviruses were detected in a majority of samples using BMFS (37/42) and two-phase separation (32/42). There was statistically more frequent detection of Sabin-like PV type 3 in samples concentrated with BMFS (22/42) than by two-phase separation (14/42, p = 0.035), possibly due to greater effective volume assayed (870 mL vs. 150 mL). Despite this effective volume assayed, there was no statistical difference in Sabin-like PV type 1 and Sabin-like PV type 2 detection between these methods (9/42 vs. 8/42, p = 0.80 and 27/42 vs. 32/42, p = 0.18, respectively). This study demonstrated that BMFS can be used for PV environmental surveillance and established a feasible study design for future research.
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Affiliation(s)
- Nicolette A Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98105, USA
| | - Christine S Fagnant-Sperati
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98105, USA
| | - Evans Komen
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi, 00200, Kenya
| | - Benlick Mwangi
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi, 00200, Kenya
| | - Johnstone Mukubi
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi, 00200, Kenya
| | - James Nyangao
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi, 00200, Kenya
| | - Joanne Hassan
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi, 00200, Kenya
| | - Agnes Chepkurui
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi, 00200, Kenya
| | - Caroline Maina
- Kenya Ministry of Health, Afya House, Cathedral Road, P.O. Box 30016, Nairobi, 00100, Kenya
| | - Walda B van Zyl
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007, South Africa
| | - Peter N Matsapola
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007, South Africa
| | - Marianne Wolfaardt
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007, South Africa
| | - Fhatuwani B Ngwana
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007, South Africa
| | - Stacey Jeffries-Miles
- IHRC, Inc. (contracting agency to the Division of Viral Diseases, Centers for Diseases Control and Prevention, Atlanta, GA 30329, USA), 2 Ravinia Drive, Suite 1200, Atlanta, GA, 30329, USA
| | - Angela Coulliette-Salmond
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop H17-6, Atlanta, GA, 30329, USA
| | - Silvia Peñaranda
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop H17-6, Atlanta, GA, 30329, USA
| | - Jeffry H Shirai
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98105, USA
| | - Alexandra L Kossik
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98105, USA
| | - Nicola K Beck
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98105, USA
| | - Robyn Wilmouth
- PATH, 2201 Westlake Ave, Suite 200, Seattle, WA, 98121, USA
| | - David S Boyle
- PATH, 2201 Westlake Ave, Suite 200, Seattle, WA, 98121, USA
| | - Cara C Burns
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop H17-6, Atlanta, GA, 30329, USA
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007, South Africa
| | - Peter Borus
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi, 00200, Kenya
| | - John Scott Meschke
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98105, USA.
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20
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Estívariz CF, Pérez-Sánchez EE, Bahena A, Burns CC, Gary HE, García-Lozano H, Rey-Benito G, Peñaranda S, Castillo-Montufar KV, Nava-Acosta RS, Meschke JS, Oberste MS, Lopez-Martínez I, Díaz-Quiñonez JA. Field Performance of Two Methods for Detection of Poliovirus in Wastewater Samples, Mexico 2016-2017. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:364-373. [PMID: 31571037 PMCID: PMC10389298 DOI: 10.1007/s12560-019-09399-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
To enhance our ability to monitor poliovirus circulation and certify eradication, we evaluated the performance of the bag-mediated filtration system (BMFS) against the two-phase separation (TPS) method for concentrating wastewater samples for poliovirus detection. Sequential samples were collected at two sites in Mexico; one L was collected by grab and ~ 5 L were collected and filtered in situ with the BMFS. In the laboratory, 500 mL collected by grab were concentrated using TPS and the sample contained in the filter of the BMFS was eluted without secondary concentration. Concentrates were tested for the presence of poliovirus and non-poliovirus enterovirus (NPEV) using Global Poliovirus Laboratory Network standard procedures. Between February 16, 2016, and April 18, 2017, 125 pairs of samples were obtained. Collectors spent an average (± standard deviation) of 4.3 ± 2.2 min collecting the TPS sample versus 73.5 ± 30.5 min collecting and filtering the BMFS sample. Laboratory processing required an estimated 5 h for concentration by TPS and 3.5 h for elution. Sabin 1 poliovirus was detected in 37 [30%] samples with the TPS versus 24 [19%] samples with the BMFS (McNemar's mid p value = 0.004). Sabin 3 poliovirus was detected in 59 [47%] versus 49 (39%) samples (p = 0.043), and NPEV was detected in 67 [54%] versus 40 [32%] samples (p < 0.001). The BMFS method without secondary concentration did not perform as well as the TPS method for detecting Sabin poliovirus and NPEV. Further studies are needed to guide the selection of cost-effective environmental surveillance methods for the polio endgame.
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Affiliation(s)
- Concepción F Estívariz
- Global Immunization Division, Global Health Center, Centers for Control Disease and Prevention, 1600 Clifton Rd NE, Atlanta, GA, 30329, USA.
| | - Elda E Pérez-Sánchez
- Instituto de Diagnóstico y Referencia Epidemiológico, Francisco de P. Miranda 177, Lomas de Plateros-Alvaro Obregon, Ciudad De México, 01480, Mexico
| | - Anita Bahena
- Organización Panamericana de la Salud, Ciudad de México, Montes Urales 440, 2nd floor, Col. Lomas de Chapultepec, 11000, Ciudad De Mexico, Mexico
| | - Cara C Burns
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Howard E Gary
- Global Immunization Division, Global Health Center, Centers for Control Disease and Prevention, 1600 Clifton Rd NE, Atlanta, GA, 30329, USA
| | - Herlinda García-Lozano
- Instituto de Diagnóstico y Referencia Epidemiológico, Francisco de P. Miranda 177, Lomas de Plateros-Alvaro Obregon, Ciudad De México, 01480, Mexico
| | - Gloria Rey-Benito
- Immunization Unit, Pan American Health Organization, 525 23rd Street NW, Washington, DC, 20037, USA
| | - Silvia Peñaranda
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Katy V Castillo-Montufar
- Organización Panamericana de la Salud, Ciudad de México, Montes Urales 440, 2nd floor, Col. Lomas de Chapultepec, 11000, Ciudad De Mexico, Mexico
| | - Raúl S Nava-Acosta
- Organización Panamericana de la Salud, Ciudad de México, Montes Urales 440, 2nd floor, Col. Lomas de Chapultepec, 11000, Ciudad De Mexico, Mexico
| | - John Scott Meschke
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Seattle, WA, 98195, USA
| | - M Steven Oberste
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Irma Lopez-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológico, Francisco de P. Miranda 177, Lomas de Plateros-Alvaro Obregon, Ciudad De México, 01480, Mexico
| | - José A Díaz-Quiñonez
- Instituto de Diagnóstico y Referencia Epidemiológico, Francisco de P. Miranda 177, Lomas de Plateros-Alvaro Obregon, Ciudad De México, 01480, Mexico
- División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad De México, Mexico
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21
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van Zyl WB, A Zhou N, Wolfaardt M, Matsapola PN, Ngwana FB, Symonds EM, Fagnant-Sperati CS, Shirai JH, Kossik AL, Beck NK, Komen E, Mwangi B, Nyangao J, Boyle DS, Borus P, Taylor MB, Meschke JS. Detection of potentially pathogenic enteric viruses in environmental samples from Kenya using the bag-mediated filtration system. WATER SCIENCE & TECHNOLOGY, WATER SUPPLY 2019; 19:1668-1676. [PMID: 33584163 PMCID: PMC7797634 DOI: 10.2166/ws.2019.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/14/2019] [Indexed: 05/18/2023]
Abstract
Enteric virus environmental surveillance via a highly sensitive method is critical, as many enteric viruses have low infectious doses and can persist in the environment for extended periods. This study determined the potential of the novel bag-mediated filtration system (BMFS) to recover human enteric viruses and pepper mild mottle virus (PMMoV) from wastewater and wastewater-impacted surface waters, examined PMMoV use as a fecal contamination indicator in Kenya, and identified potential BMFS process controls. From April 2015 to April 2016, BMFS samples were collected from seven sites in Kenya (n = 59). Enteroviruses and PMMoV were detected in 100% of samples, and human adenovirus, human astrovirus, hepatitis A virus, norovirus GI, norovirus GII, sapovirus, and human rotavirus were detected in the majority of samples. The consistent detection of enteroviruses and PMMoV suggests that these viruses could be used as indicators in similarly fecally contaminated sites and BMFS process controls. As contamination of surface water sources remains a global issue, enteric virus environmental surveillance is necessary. This study demonstrates an effective way to sample large volumes of wastewater and wastewater-impacted surface waters for the detection of multiple enteric viruses simultaneously.
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Affiliation(s)
- Walda B van Zyl
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
| | - Nicolette A Zhou
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Marianne Wolfaardt
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
| | - Peter N Matsapola
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
| | - Fhatuwani B Ngwana
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
| | - Erin M Symonds
- College of Marine Science, University of South Florida, 830 1st St S, St Petersburg, FL 33701, USA
| | - Christine S Fagnant-Sperati
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Jeffry H Shirai
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Alexandra L Kossik
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Nicola K Beck
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Evans Komen
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
| | - Benlick Mwangi
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
| | - James Nyangao
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
| | - David S Boyle
- PATH, 2201 Westlake Ave, Suite 200, Seattle, WA 98121, USA
| | - Peter Borus
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
| | - Maureen B Taylor
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
- College of Marine Science, University of South Florida, 830 1st St S, St Petersburg, FL 33701, USA
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
- PATH, 2201 Westlake Ave, Suite 200, Seattle, WA 98121, USA
| | - J Scott Meschke
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
- College of Marine Science, University of South Florida, 830 1st St S, St Petersburg, FL 33701, USA
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
- PATH, 2201 Westlake Ave, Suite 200, Seattle, WA 98121, USA
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22
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Falman JC, Fagnant-Sperati CS, Kossik AL, Boyle DS, Meschke JS. Evaluation of Secondary Concentration Methods for Poliovirus Detection in Wastewater. FOOD AND ENVIRONMENTAL VIROLOGY 2019. [PMID: 30612304 DOI: 10.1007/s12560-018-09364-ypmid-30612304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Effective surveillance of human enteric viruses is critical to estimate disease prevalence within a community and can be a vital supplement to clinical surveillance. This study sought to evaluate simple, effective, and inexpensive secondary concentration methods for use with ViroCap™ filter eluate for environmental surveillance of poliovirus. Wastewater was primary concentrated using cartridge ViroCap filters, seeded with poliovirus type 1 (PV1), and then concentrated using five secondary concentration methods (beef extract-Celite, ViroCap flat disc filter, InnovaPrep® Concentrating Pipette, polyethylene glycol [PEG]/sodium chloride [NaCl] precipitation, and skimmed-milk flocculation). PV1 was enumerated in secondary concentrates by plaque assay on BGMK cells. Of the five tested methods, PEG/NaCl precipitation and skimmed-milk flocculation resulted in the highest PV1 recoveries. Optimization of the skimmed-milk flocculation method resulted in a greater PV1 recovery (106 ± 24.8%) when compared to PEG/NaCl precipitation (59.5 ± 19.4%) (p = 0.004, t-test). The high PV1 recovery, short processing time, low reagent cost, no required refrigeration, and requirement for only standard laboratory equipment suggest that the skimmed-milk flocculation method would be a good candidate to be field-validated for secondary concentration of environmental ViroCap filter samples containing poliovirus.
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Affiliation(s)
- Jill C Falman
- Department of Environmental & Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA
| | - Christine S Fagnant-Sperati
- Department of Environmental & Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA
| | - Alexandra L Kossik
- Department of Environmental & Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA
| | - David S Boyle
- PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA, 98121, USA
| | - John Scott Meschke
- Department of Environmental & Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA.
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23
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Falman JC, Fagnant-Sperati CS, Kossik AL, Boyle DS, Meschke JS. Evaluation of Secondary Concentration Methods for Poliovirus Detection in Wastewater. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:20-31. [PMID: 30612304 PMCID: PMC6394643 DOI: 10.1007/s12560-018-09364-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/31/2018] [Indexed: 05/18/2023]
Abstract
Effective surveillance of human enteric viruses is critical to estimate disease prevalence within a community and can be a vital supplement to clinical surveillance. This study sought to evaluate simple, effective, and inexpensive secondary concentration methods for use with ViroCap™ filter eluate for environmental surveillance of poliovirus. Wastewater was primary concentrated using cartridge ViroCap filters, seeded with poliovirus type 1 (PV1), and then concentrated using five secondary concentration methods (beef extract-Celite, ViroCap flat disc filter, InnovaPrep® Concentrating Pipette, polyethylene glycol [PEG]/sodium chloride [NaCl] precipitation, and skimmed-milk flocculation). PV1 was enumerated in secondary concentrates by plaque assay on BGMK cells. Of the five tested methods, PEG/NaCl precipitation and skimmed-milk flocculation resulted in the highest PV1 recoveries. Optimization of the skimmed-milk flocculation method resulted in a greater PV1 recovery (106 ± 24.8%) when compared to PEG/NaCl precipitation (59.5 ± 19.4%) (p = 0.004, t-test). The high PV1 recovery, short processing time, low reagent cost, no required refrigeration, and requirement for only standard laboratory equipment suggest that the skimmed-milk flocculation method would be a good candidate to be field-validated for secondary concentration of environmental ViroCap filter samples containing poliovirus.
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Affiliation(s)
- Jill C Falman
- Department of Environmental & Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA
| | - Christine S Fagnant-Sperati
- Department of Environmental & Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA
| | - Alexandra L Kossik
- Department of Environmental & Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA
| | - David S Boyle
- PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA, 98121, USA
| | - John Scott Meschke
- Department of Environmental & Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA.
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24
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Matrajt G, Naughton B, Bandyopadhyay AS, Meschke JS. A Review of the Most Commonly Used Methods for Sample Collection in Environmental Surveillance of Poliovirus. Clin Infect Dis 2018; 67:S90-S97. [PMID: 30376094 PMCID: PMC6206110 DOI: 10.1093/cid/ciy638] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We performed a review of the environmental surveillance methods commonly used to collect and concentrate poliovirus (PV) from water samples. We compared the sampling approaches (trap vs grab), the process methods (precipitation vs filtration), and the various tools and chemical reagents used to separate PV from other viruses and pathogens in water samples (microporous glass, pads, polyethylene glycol [PEG]/dextran, PEG/sodium chloride, NanoCeram/ViroCap, and ester membranes). The advantages and disadvantages of each method are considered, and the geographical areas where they are currently used are discussed. Several methods have demonstrated the ability to concentrate and recover PVs from environmental samples. The details of the particular sampling conditions and locations should be considered carefully in method selection.
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Affiliation(s)
- Graciela Matrajt
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Washington
| | | | | | - John Scott Meschke
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Washington
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25
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Zhou NA, Fagnant-Sperati CS, Shirai JH, Sharif S, Zaidi SZ, Rehman L, Hussain J, Agha R, Shaukat S, Alam M, Khurshid A, Mujtaba G, Salman M, Safdar RM, Mahamud A, Ahmed J, Khan S, Kossik AL, Beck NK, Matrajt G, Asghar H, Bandyopadhyay AS, Boyle DS, Meschke JS. Evaluation of the bag-mediated filtration system as a novel tool for poliovirus environmental surveillance: Results from a comparative field study in Pakistan. PLoS One 2018; 13:e0200551. [PMID: 30011304 PMCID: PMC6047795 DOI: 10.1371/journal.pone.0200551] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/28/2018] [Indexed: 01/06/2023] Open
Abstract
Poliovirus (PV) environmental surveillance (ES) plays an important role in the global eradication program and is crucial for monitoring silent PV circulation especially as clinical cases decrease. This study compared ES results using the novel bag-mediated filtration system (BMFS) with the current two-phase separation method. From February to November 2016, BMFS and two-phase samples were collected concurrently from twelve sites in Pakistan (n = 117). Detection was higher in BMFS than two-phase samples for each Sabin-like (SL) PV serotype (p<0.001) and wild PV type 1 (WPV1) (p = 0.065). Seventeen sampling events were positive for WPV1, with eight discordant in favor of BMFS and two in favor of two-phase. A vaccine-derived PV type 2 was detected in one BMFS sample but not the matched two-phase. After the removal of SL PV type 2 (SL2) from the oral polio vaccine in April 2016, BMFS samples detected SL2 more frequently than two-phase (p = 0.016), with the last detection by either method occurring June 12, 2016. More frequent PV detection in BMFS compared to two-phase samples is likely due to the greater effective volume assayed (1620 mL vs. 150 mL). This study demonstrated that the BMFS achieves enhanced ES for all PV serotypes in an endemic country.
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Affiliation(s)
- Nicolette Angela Zhou
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Christine Susan Fagnant-Sperati
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Jeffry Hiroshi Shirai
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | | | | | - Lubna Rehman
- National Institute of Health, Islamabad, Pakistan
| | | | - Rahim Agha
- World Health Organization, Islamabad, Pakistan
- National Emergency Operations Center, Islamabad, Pakistan
| | | | - Masroor Alam
- National Institute of Health, Islamabad, Pakistan
| | | | | | | | - Rana Muhammed Safdar
- National Institute of Health, Islamabad, Pakistan
- National Emergency Operations Center, Islamabad, Pakistan
| | - Abdirahman Mahamud
- World Health Organization, Islamabad, Pakistan
- National Emergency Operations Center, Islamabad, Pakistan
| | - Jamal Ahmed
- World Health Organization, Islamabad, Pakistan
- National Emergency Operations Center, Islamabad, Pakistan
| | - Sadaf Khan
- PATH, Seattle, WA, United States of America
| | - Alexandra Lynn Kossik
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Nicola Koren Beck
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Graciela Matrajt
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | | | | | | | - John Scott Meschke
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
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26
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Fagnant CS, Toles M, Zhou NA, Powell J, Adolphsen J, Guan Y, Ockerman B, Shirai JH, Boyle DS, Novosselov I, Meschke JS. Development of an elution device for ViroCap virus filters. ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:574. [PMID: 29046968 PMCID: PMC5648745 DOI: 10.1007/s10661-017-6258-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Environmental surveillance of waterborne pathogens is vital for monitoring the spread of diseases, and electropositive filters are frequently used for sampling wastewater and wastewater-impacted surface water. Viruses adsorbed to electropositive filters require elution prior to detection or quantification. Elution is typically facilitated by a peristaltic pump, although this requires a significant startup cost and does not include biosafety or cross-contamination considerations. These factors may pose a barrier for low-resource laboratories that aim to conduct environmental surveillance of viruses. The objective of this study was to develop a biologically enclosed, manually powered, low-cost device for effectively eluting from electropositive ViroCap™ virus filters. The elution device described here utilizes a non-electric bilge pump, instead of an electric peristaltic pump or a positive pressure vessel. The elution device also fully encloses liquids and aerosols that could contain biological organisms, thereby increasing biosafety. Moreover, all elution device components that are used in the biosafety cabinet are autoclavable, reducing cross-contamination potential. This device reduces costs of materials while maintaining convenience in terms of size and weight. With this new device, there is little sample volume loss due to device inefficiency, similar virus yields were demonstrated during seeded studies with poliovirus type 1, and the time to elute filters is similar to that required with the peristaltic pump. The efforts described here resulted in a novel, low-cost, manually powered elution device that can facilitate environmental surveillance of pathogens through effective virus recovery from ViroCap filters while maintaining the potential for adaptability to other cartridge filters.
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Affiliation(s)
| | | | - Nicolette Angela Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA
| | - Jacob Powell
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA, 98195, USA
| | - John Adolphsen
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA, 98195, USA
| | - Yifei Guan
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA, 98195, USA
| | - Byron Ockerman
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA, 98195, USA
| | - Jeffry Hiroshi Shirai
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA
| | - David S Boyle
- PATH, 2201 Westlake Ave., Suite 200, Seattle, WA, 98121, USA
| | - Igor Novosselov
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA, 98195, USA
| | - John Scott Meschke
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA.
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