1
|
Shaheen MNF, Elmahdy EM. Seasonal Prevalence and Detection of Enteric and Respiratory Viruses in Wastewater and Hospitalized Children with Acute Gastroenteritis. Curr Microbiol 2024; 81:337. [PMID: 39223408 DOI: 10.1007/s00284-024-03841-3] [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: 05/27/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024]
Abstract
Human enteric and some respiratory viruses are identified to be involved with acute gastroenteritis that can be shed in feces of infected persons into the environment. Understanding the abundance of these viruses in wastewater is significant when assessing the public health impacts associated with discharge of wastewater into the environment. This study aimed to investigate the prevalence and seasonal variation of human enteric adenovirus (HAdV), Aichi virus (AiV-1), bocavirus (HBoV), and respiratory syndrome coronavirus 2 virus (SARS-CoV-2) in wastewater as well as their prevalence among hospitalized children with acute gastroenteritis. The viruses were detected and quantified with real-time PCR. HAdV was the most detected virus in raw sewage (88.5%), treated sewage (28%), and stool gastroenteritis (74%), followed by HBoV (45.8% for raw sewage, 14.6% for treated sewage, and 55.3% for stool samples). The detection rate of AiV-1 was 59.4%, 19.8%, and 62.6% in raw sewage, treated sewage, and stool samples, respectively. The rate of SARS-CoV-2 detection in raw sewage, treated sewage, and stool samples was 33.3%, 7.3%, and 20.6%, respectively. The viral concentrations ranged between 4.50 × 101 and 8.75 × 107 GC/ml in raw sewage samples, 1.20 × 101 and 5.43 × 106 GC/ml in treated sewage samples, and 4.80 × 101 and 9.88 × 108 GC/gram in stool samples. The overall log means of virus reduction during the wastewater treatment process ranged from 1.68 log10 (HAdV) to 3.31 log10 (AiV-1). The peak prevalence of the four viruses in raw sewage samples occurred during the winter season. This study showed the high detection rates of the four targeted viruses in wastewater and demonstrated that virological surveillance of wastewater in local wastewater treatment plants is a suitable model for epidemiological monitoring of diarrheal and respiratory diseases in middle- and low-resource countries.
Collapse
Affiliation(s)
- Mohamed Nasr Fathi Shaheen
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Centre, Al-Buhouth Street, Dokki, 12622, Cairo, Egypt.
| | - Elmahdy Mohamed Elmahdy
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Centre, Al-Buhouth Street, Dokki, 12622, Cairo, Egypt
| |
Collapse
|
2
|
Kim MG, Yoo B, Min AY, Seo DW, Choi C, Kim SH, Kim SH. Comparative analysis of reverse-transcription-polymerase chain reaction for Aichivirus detection. Food Sci Biotechnol 2024; 33:2807-2814. [PMID: 39184978 PMCID: PMC11339220 DOI: 10.1007/s10068-024-01537-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 08/27/2024] Open
Abstract
Aichivirus-A (AiV-A), a member of the Kobuvirus genus of the family Picornaviridae, was first reported in stool samples of patients with non-bacterial gastroenteritis in Aichi Prefecture, Japan, in 1989. AiV has been reported from in various aquatic environments, such as surface water and sewage, can be transmitted via the fecal-oral route through contaminated water. As AiV is known to acute gastroenteritis worldwide, developing methods for AiV detection from contaminated environments and food is required. In the present study, we established an effective polymerase chain reaction (PCR) method to detect AiV. Various real-time reverse transcription (RT)-PCR and conventional PCR methods for AiV detection were compared, and the limit of detection was confirmed by comparing the sensitivity at varied primer concentrations and PCR conditions. The final detection limits were 102 copy/μL in conventional PCR, and 101 copy/μL in the real-time RT-PCR. The optimized method used in this study might aid in detecting AiV contamination.
Collapse
Affiliation(s)
- Mi-Gyeong Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - Boeun Yoo
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - A Young Min
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - Doo Won Seo
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - Changsun Choi
- School of Food Science and Technology, Chung-Ang University, Ansung, 456-756 South Korea
| | - Seung Hwan Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - Soon Han Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| |
Collapse
|
3
|
Ibrahim C, Hammami S, Khelifi N, Pothier P, Hassen A. Activated sludge and UV-C 254 for Sapovirus, Aichivirus, Astrovirus, and Adenovirus processing. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024; 34:1995-2014. [PMID: 37086061 DOI: 10.1080/09603123.2023.2203906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
In this study, the detection rates of four enteric viruses, Human Astrovirus (HAstVs), Aichivirus (AiVs), Human Adenovirus (HAdVs), and Sapovirus (SaVs) are carried out to assess the virological quality of the treated wastewater. A total of 140 samples was collected from wastewater treatment plant WWTP of Tunis-City. Real-time RT-PCR and conventional RT-PCR results showed high frequencies of detection of the four enteric viruses investigated at the entry and exit of the biological activated sludge procedure and a significant reduction in viral titers after tertiary treatment with UV-C254 irradiation. These results revealed the ineffectiveness of the biological activated sludge treatment in removing viruses and the poor quality of the treated wastewater intended for recycling, agricultural reuse, and safe discharge into the natural environment. The UV-C254 irradiation, selected while considering the non-release of known disinfection by-products because of eventual reactions with the large organic and mineral load commonly present in the wastewater.
Collapse
Affiliation(s)
- Chourouk Ibrahim
- Center of Research and Water Technologies (CERTE), Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Tunisia
- Faculty of Mathematical, Physical and Natural Sciences of Tunis, the University of Tunis El Manar, Tunis, Tunisia
- Microbiology Laboratory, Beja University Hospital, Beja,Tunisia
| | - Salah Hammami
- National School of Veterinary Medicine at Sidi Thabet, University of Manouba, Tunis, Tunisia
| | - Nesserine Khelifi
- Center of Research and Water Technologies (CERTE), Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Tunisia
| | - Pierre Pothier
- National Reference Center for Enteric Viruses, Laboratory of Virology, University Hospital of Dijon, Dijon, France
| | - Abdennaceur Hassen
- Center of Research and Water Technologies (CERTE), Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Tunisia
| |
Collapse
|
4
|
Zamora-Figueroa A, Rosales RE, Fernández R, Ramírez V, Bastardo M, Farías A, Vizzi E. Detection and diversity of gastrointestinal viruses in wastewater from Caracas, Venezuela, 2021-2022. Virology 2024; 589:109913. [PMID: 37924728 DOI: 10.1016/j.virol.2023.109913] [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: 06/14/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023]
Abstract
Gastrointestinal viruses (GIV) are an important cause of childhood morbidity and mortality, particularly in developing countries. Their epidemiological impact in Venezuela during the COVID-19 pandemic remains unclear. GIV can also be detected in domestic sewage. Ninety-one wastewater samples from urban areas of Caracas collected over 12 months and concentrated by polyethylene-glycol-precipitation, were analyzed by multiplex reverse-transcription-PCR for rotavirus/calicivirus/astrovirus and enterovirus/klassevirus/cosavirus, and monoplex-PCR for adenovirus and Aichi virus. The overall frequency of virus detection was 46.2%, fluctuating over months, and peaking in the rainy season. Adenoviruses circulated throughout the year, especially type F41, and predominated (52.7%) over caliciviruses (29.1%) that peaked in the rainy months, rotaviruses (9.1%), cosaviruses (5.5%), astroviruses and enteroviruses (1.8%). Aichi-virus and klassevirus were absent. Rotavirus G9/G12, and P[4]/P[8]/P[14] predominated. The occurrence of GIV in wastewater reflects transmission within the population of Caracas and the persistence of a potential public health risk that needs to be adequately monitored.
Collapse
Affiliation(s)
- Alejandra Zamora-Figueroa
- Laboratorio de Ecología de Microorganismos, Centro de Ecología Aplicada. Instituto de Zoología y Ecología Tropical. Universidad Central de Venezuela, Caracas, Venezuela
| | - Rita E Rosales
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular. Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Rixio Fernández
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular. Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Viviana Ramírez
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular. Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Marjorie Bastardo
- Laboratorio de Ecología de Microorganismos, Centro de Ecología Aplicada. Instituto de Zoología y Ecología Tropical. Universidad Central de Venezuela, Caracas, Venezuela
| | - Alba Farías
- Laboratorio de Ecología de Microorganismos, Centro de Ecología Aplicada. Instituto de Zoología y Ecología Tropical. Universidad Central de Venezuela, Caracas, Venezuela
| | - Esmeralda Vizzi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular. Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela.
| |
Collapse
|
5
|
Mageau A, Ambert-Balay K, Boutolleau D, Schuffenecker I, Burrel S, Kaplon J, Nguyen Quoc S, Uzunov M, Souchet L, de Rougemont A, Roos-Weil D, Baron M. Norovirus and sapovirus infections after allogeneic hematopoietic stem cell transplantation: is it worth it to look for them? Leuk Lymphoma 2023; 64:1295-1303. [PMID: 37165601 DOI: 10.1080/10428194.2023.2211186] [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: 06/06/2022] [Revised: 12/26/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
Norovirus (NoV) and Sapovirus (SaV) are potential causative agents of diarrhea after allogeneic HSCT but little is known in this population. We performed a retrospective analysis by RT-PCR of calicivirus (NoV and SaV), Human adenovirus (HAdV), rotavirus (RV), Aichi virus (AiV), enterovirus (EV), human parechovirus (HPeV) and Human bocavirus (HBoV) in the diarrheal stools of patients after allogeneic HSCT. 49/162 patients had positive viral assays: HAdV (17%), EV (7%), NoV (4.3%), RV and HBoV (3.1% each), SaV (1.9%), AiV (1.2%), HPeV (0.6%). Seven patients were positive for NoV and 3 for SaV. Among viruses-positive samples, the frequency of caliciviruses cases was 7% in the 6 months post-HSCT compared to 40% after (p < 0.0001). The median duration of symptom was 0.7 months but 2 cases, occurring more than one year after HSCT, were chronic, undiagnosed and strongly contributed to morbidity. Systematic testing of caliciviruses appears especially useful in late chronic diarrhea.
Collapse
Affiliation(s)
- Arthur Mageau
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Katia Ambert-Balay
- Centre National de Référence virus des gastro-entérites, Laboratoire de virologie-sérologie, Plateforme de Biologie Hospitalo-Universitaire, CHU Dijon Bourgogne, Dijon, France
| | - David Boutolleau
- Sorbonne Université, Service de virologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Isabelle Schuffenecker
- Centre National de Référence des Entérovirus et Paréchovirus, Laboratoire de Virologie, Centre de Biologie et de Pathologie Nord, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, France
| | - Sonia Burrel
- Sorbonne Université, Service de virologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Jérome Kaplon
- Centre National de Référence virus des gastro-entérites, Laboratoire de virologie-sérologie, Plateforme de Biologie Hospitalo-Universitaire, CHU Dijon Bourgogne, Dijon, France
| | - Stéphanie Nguyen Quoc
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Madalina Uzunov
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Laetitia Souchet
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Alexis de Rougemont
- Centre National de Référence virus des gastro-entérites, Laboratoire de virologie-sérologie, Plateforme de Biologie Hospitalo-Universitaire, CHU Dijon Bourgogne, Dijon, France
- UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, Dijon, France
| | - Damien Roos-Weil
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| | - Marine Baron
- Sorbonne Université, Service d'hématologie, Groupe hospitalier Pitié-Salpêtrière Charles Foix, APHP, Paris
| |
Collapse
|
6
|
Stockdale SR, Blanchard AM, Nayak A, Husain A, Nashine R, Dudani H, McClure CP, Tarr AW, Nag A, Meena E, Sinha V, Shrivastava SK, Hill C, Singer AC, Gomes RL, Acheampong E, Chidambaram SB, Bhatnagar T, Vetrivel U, Arora S, Kashyap RS, Monaghan TM. RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 14:100205. [PMID: 37193348 PMCID: PMC10150210 DOI: 10.1016/j.lansea.2023.100205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/18/2023]
Abstract
Background The COVID-19 pandemic showcased the power of genomic sequencing to tackle the emergence and spread of infectious diseases. However, metagenomic sequencing of total microbial RNAs in wastewater has the potential to assess multiple infectious diseases simultaneously and has yet to be explored. Methods A retrospective RNA-Seq epidemiological survey of 140 untreated composite wastewater samples was performed across urban (n = 112) and rural (n = 28) areas of Nagpur, Central India. Composite wastewater samples were prepared by pooling 422 individual grab samples collected prospectively from sewer lines of urban municipality zones and open drains of rural areas from 3rd February to 3rd April 2021, during the second COVID-19 wave in India. Samples were pre-processed and total RNA was extracted prior to genomic sequencing. Findings This is the first study that has utilised culture and/or probe-independent unbiased RNA-Seq to examine Indian wastewater samples. Our findings reveal the detection of zoonotic viruses including chikungunya, Jingmen tick and rabies viruses, which have not previously been reported in wastewater. SARS-CoV-2 was detectable in 83 locations (59%), with stark abundance variations observed between sampling sites. Hepatitis C virus was the most frequently detected infectious virus, identified in 113 locations and co-occurring 77 times with SARS-CoV-2; and both were more abundantly detected in rural areas than urban zones. Concurrent identification of segmented virus genomic fragments of influenza A virus, norovirus, and rotavirus was observed. Geographical differences were also observed for astrovirus, saffold virus, husavirus, and aichi virus that were more prevalent in urban samples, while the zoonotic viruses chikungunya and rabies, were more abundant in rural environments. Interpretation RNA-Seq can effectively detect multiple infectious diseases simultaneously, facilitating geographical and epidemiological surveys of endemic viruses that could help direct healthcare interventions against emergent and pre-existent infectious diseases as well as cost-effectively and qualitatively characterising the health status of the population over time. Funding UK Research and Innovation (UKRI) Global Challenges Research Fund (GCRF) grant number H54810, as supported by Research England.
Collapse
Affiliation(s)
| | - Adam M. Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Amit Nayak
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Aliabbas Husain
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Rupam Nashine
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Hemanshi Dudani
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - C. Patrick McClure
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Alexander W. Tarr
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Aditi Nag
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Ekta Meena
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Vikky Sinha
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Sandeep K. Shrivastava
- Centre for Innovation, Research & Development, Dr. B. Lal Clinical Laboratory Pvt. Ltd., Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Andrew C. Singer
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Rachel L. Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, United Kingdom
| | - Edward Acheampong
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, United Kingdom
- Department of Statistics and Actuarial Science, University of Ghana, P.O. Box, LG 115, Legon, Ghana
| | - Saravana B. Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, 570015, KA, India
| | - Tarun Bhatnagar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- National Institute of Traditional Medicine, Indian Council of Medical Research, Belagavi, 590010, India
- Virology and Biotechnology Division, ICMR-National Institute for Research in Tuberculosis, Chennai, 600031, India
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Rajpal Singh Kashyap
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Tanya M. Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| |
Collapse
|
7
|
Lanrewaju AA, Enitan-Folami AM, Sabiu S, Edokpayi JN, Swalaha FM. Global public health implications of human exposure to viral contaminated water. Front Microbiol 2022; 13:981896. [PMID: 36110296 PMCID: PMC9468673 DOI: 10.3389/fmicb.2022.981896] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/05/2022] [Indexed: 01/08/2023] Open
Abstract
Enteric viruses are common waterborne pathogens found in environmental water bodies contaminated with either raw or partially treated sewage discharge. Examples of these viruses include adenovirus, rotavirus, noroviruses, and other caliciviruses and enteroviruses like coxsackievirus and polioviruses. They have been linked with gastroenteritis, while some enteric viruses have also been implicated in more severe infections such as encephalitis, meningitis, hepatitis (hepatitis A and E viruses), cancer (polyomavirus), and myocarditis (enteroviruses). Therefore, this review presents information on the occurrence of enteric viruses of public health importance, diseases associated with human exposure to enteric viruses, assessment of their presence in contaminated water, and their removal in water and wastewater sources. In order to prevent illnesses associated with human exposure to viral contaminated water, we suggest the regular viral monitoring of treated wastewater before discharging it into the environment. Furthermore, we highlight the need for more research to focus on the development of more holistic disinfection methods that will inactivate waterborne viruses in municipal wastewater discharges, as this is highly needed to curtail the public health effects of human exposure to contaminated water. Moreover, such a method must be devoid of disinfection by-products that have mutagenic and carcinogenic potential.
Collapse
Affiliation(s)
| | | | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, South Africa
| | - Joshua Nosa Edokpayi
- Water and Environmental Management Research Group, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa
| | - Feroz Mahomed Swalaha
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, South Africa
| |
Collapse
|
8
|
Chen BC, Huang TS, Huang NY, Chen CS, Chen YS, Chang TH. Low Seroprevalence of Aichi Virus Infection in Taiwan. Pathogens 2021; 10:pathogens10050553. [PMID: 34063639 PMCID: PMC8147638 DOI: 10.3390/pathogens10050553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 11/16/2022] Open
Abstract
Aichi virus (AiV) belongs to the genus Kobuvirus of the family Picornaviridae; it is a single-stranded positive-sense RNA virus without an envelope. AiV causes acute gastroenteritis, abdominal pain, nausea, vomiting, and fever. Low incidence and high seroprevalence of AiV infections have been reported in several regions of the world; however, little was known on the prevalence of AiV infections in Taiwan. This study described the first two cases of AiV infection and analyzed AiV seroprevalence in Taiwan. A total of 700 sera were collected from a single hospital in southern Taiwan. The neutralization assay was employed to assess AiV neutralization antibodies in the serum. The test identified 48 positive cases, with a seroprevalence of 6.86%. Results also showed a gradual increase in AiV seroprevalence rate with age. Compared with other countries, Taiwan had a relatively low AiV seroprevalence, suggesting a low incidence of or sporadic AiV infections.
Collapse
Affiliation(s)
- Bao-Chen Chen
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan; (B.-C.C.); (T.-S.H.); (N.-Y.H.); (C.-S.C.)
| | - Tsi-Shu Huang
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan; (B.-C.C.); (T.-S.H.); (N.-Y.H.); (C.-S.C.)
| | - Nuan-Ya Huang
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan; (B.-C.C.); (T.-S.H.); (N.-Y.H.); (C.-S.C.)
| | - Chiao-Shan Chen
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan; (B.-C.C.); (T.-S.H.); (N.-Y.H.); (C.-S.C.)
| | - Yao-Shen Chen
- Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan
- Faculty of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Correspondence: (Y.-S.C.); (T.-H.C.)
| | - Tsung-Hsien Chang
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei 11490, Taiwan
- Correspondence: (Y.-S.C.); (T.-H.C.)
| |
Collapse
|
9
|
Sadiq A, Yinda CK, Deboutte W, Matthijnssens J, Bostan N. Whole genome analysis of Aichivirus A, isolated from a child, suffering from gastroenteritis, in Pakistan. Virus Res 2021; 299:198437. [PMID: 33901591 DOI: 10.1016/j.virusres.2021.198437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/30/2021] [Accepted: 04/20/2021] [Indexed: 11/19/2022]
Abstract
Viruses are the primary cause of acute gastroenteritis in children all over the world. Understanding the emergence and genetic variation of these viruses may help to prevent infections. Aichivirus (AiV) is a member of the Kobuvirus genus, which currently contains six officially recognized species: Aichivirus A-F. The species AiV A contains six types including Aichivirus 1 (AiV 1) and eventually, three genotypes have been identified in the human AiV 1 (named A to C). The present study describes the identification and sequencing of the polyprotein gene of a human AiV 1 strain PAK419 via NGS in Pakistani children with acute gastroenteritis. Our study strain PAK419 was classified as AiV 1 genotype A, most commonly found in Japan and Europe, and closely related to non-Japanese and European strains on the phylogenetic tree. PAK419 showed 95-98 % nucleotide sequence identity with strains isolated from Ethiopia (ETH/2016/P4), Australia (FSS693) and China (Chshc7). On phylogenetic observation PAK419 formed a distinct cluster in the AiV 1 genotype A with the above mentioned and other human AiV strains detected around the world (Germany, Brazil, Japan, Thailand, Korea and Vietnam). The data clearly showed that Pakistani AiV strains and human strains identified from all over the world are distinct from Aichivirus strains found in bovine, swine, canine, feline, caprine, ferret, bat, and environmental samples. The distinguishing characteristics of the AiV genome showed a lower probability of inter-genotypic recombination events, which may support the lack of AiV serotypes. PAK419 also had a high content of C nucleotide (37.4 %), as found in previous studies, which could also restrict the possible genetic variation of AiV. This study demonstrate the power of NGS in uncovering unknown gastroenteric etiological agents circulating in the population.
Collapse
Affiliation(s)
- Asma Sadiq
- Department of Biosciences, COMSATS University (CUI), Park Road, Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan
| | - Claude Kwe Yinda
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ward Deboutte
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Nazish Bostan
- Department of Biosciences, COMSATS University (CUI), Park Road, Tarlai Kalan, Chak Shahzad, Islamabad, 45550, Pakistan.
| |
Collapse
|
10
|
Upfold NS, Luke GA, Knox C. Occurrence of Human Enteric Viruses in Water Sources and Shellfish: A Focus on Africa. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:1-31. [PMID: 33501612 PMCID: PMC7837882 DOI: 10.1007/s12560-020-09456-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/16/2020] [Indexed: 05/02/2023]
Abstract
Enteric viruses are a diverse group of human pathogens which are primarily transmitted by the faecal-oral route and are a major cause of non-bacterial diarrhoeal disease in both developed and developing countries. Because they are shed in high numbers by infected individuals and can persist for a long time in the environment, they pose a serious threat to human health globally. Enteric viruses end up in the environment mainly through discharge or leakage of raw or inadequately treated sewage into water sources such as springs, rivers, dams, or marine estuaries. Human exposure then follows when contaminated water is used for drinking, cooking, or recreation and, importantly, when filter-feeding bivalve shellfish are consumed. The human health hazard posed by enteric viruses is particularly serious in Africa where rapid urbanisation in a relatively short period of time has led to the expansion of informal settlements with poor sanitation and failing or non-existent wastewater treatment infrastructure, and where rural communities with limited or no access to municipal water are dependent on nearby open water sources for their subsistence. The role of sewage-contaminated water and bivalve shellfish as vehicles for transmission of enteric viruses is well documented but, to our knowledge, has not been comprehensively reviewed in the African context. Here we provide an overview of enteric viruses and then review the growing body of research where these viruses have been detected in association with sewage-contaminated water or food in several African countries. These studies highlight the need for more research into the prevalence, molecular epidemiology and circulation of these viruses in Africa, as well as for development and application of innovative wastewater treatment approaches to reduce environmental pollution and its impact on human health on the continent.
Collapse
Affiliation(s)
- Nicole S Upfold
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Garry A Luke
- Centre for Biomolecular Sciences, School of Biology, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews, Scotland, KY16 9ST, UK
| | - Caroline Knox
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
| |
Collapse
|
11
|
Dastjerdi A, Benfield C, Everest D, Stidworthy MF, Zell R. Novel enteric viruses in fatal enteritis of grey squirrels. J Gen Virol 2021; 101:746-750. [PMID: 32459620 DOI: 10.1099/jgv.0.001431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Astro- and kobuviruses infect both humans and animals. Here, we report on the disease history, detection and genomic characterization of novel astro- and kobuviruses from fatal diarrhoea of two juvenile grey squirrels. The virus particles had enterovirus-like morphology and a diameter of 28-32 nm. Next-generation sequencing confirmed astro- and kobuviruses and sequence analysis revealed typical astrovirus and picornavirus genome organizations. The astrovirus ORF2 sequence clustered with a clade of unassigned astroviruses, with marmot and rodent mamastroviruses as closest relatives. For the kobuvirus, divergences greater than 49.4 % for P1 and 43.5 % in the non-structural proteins indicated a novel species. However, phylogenetic analysis of the 3D polymerase showed that it clustered with that of the newly classified ludopivirus A1, suggesting a previous recombination event in the evolution of the kobuvirus. Our data provide further insights into the diversity of astro- and kobuviruses and broaden the spectrum of viruses infecting grey squirrels.
Collapse
Affiliation(s)
- Akbar Dastjerdi
- Animal and Plant Health Agency (APHA) - Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - Camilla Benfield
- Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
| | - David Everest
- Animal and Plant Health Agency (APHA) - Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - Mark F Stidworthy
- International Zoo Veterinary Group, Station House, Parkwood Street, Keighley, West Yorkshire, BD21 4NQ, UK
| | - Roland Zell
- Section for Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich-Schiller-Universität Jena, Hans-Knöll-Str. 2, Germany
| |
Collapse
|
12
|
Kebe O, Fernandez-Garcia MD, Fall A, Dia H, Bidalot M, Ambert-Balay K, Ndiaye K. Prevalence and Genetic Diversity of Aichi Virus 1 from Urban Wastewater in Senegal. Intervirology 2021; 64:96-101. [PMID: 33440372 DOI: 10.1159/000512130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 09/24/2020] [Indexed: 11/19/2022] Open
Abstract
Aichi virus 1 (AiV-1) has been proposed as a causative agent of human gastroenteritis. In this study, raw, decanted, and treated wastewater samples from a wastewater treatment plant in an urban area of Dakar, Senegal, were collected. AiV-1 was detected in raw (70%, 14/20), decanted (68.4%, 13/19), and treated (59.3%, 16/27) samples, revealing a noticeable resistance of AiV-1 to chlorine-based treatment. Phylogenetic analysis revealed that all sequences clustered within genotype B. Our study presents the first report on the detection of AiV-1 in the environment of Dakar and constitutes indirect evidence of virus circulation in the population.
Collapse
Affiliation(s)
- Ousmane Kebe
- Laboratory of Enteric Viruses, Virology Unit, Institut Pasteur, Dakar, Senegal
| | | | - Amary Fall
- Laboratory of Enteric Viruses, Virology Unit, Institut Pasteur, Dakar, Senegal
| | - Hamet Dia
- Laboratory of Enteric Viruses, Virology Unit, Institut Pasteur, Dakar, Senegal
| | - Maxime Bidalot
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Biology and Pathology, University Hospital Dijon, Bourgogne, Dijon, France
| | - Katia Ambert-Balay
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Biology and Pathology, University Hospital Dijon, Bourgogne, Dijon, France
| | - Kader Ndiaye
- Laboratory of Enteric Viruses, Virology Unit, Institut Pasteur, Dakar, Senegal
| |
Collapse
|
13
|
Kumthip K, Khamrin P, Yodmeeklin A, Maneekarn N. Prevalence and Genetic Characterization of Aichivirus in Environmental Waters in Thailand. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:342-349. [PMID: 33044663 DOI: 10.1007/s12560-020-09445-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Aichivirus 1 (AiV-1) is an enteric virus that has been documented to be the causative agent of diarrhea in humans. It is transmitted by fecal-oral route, through person-to-person contact, consumption of contaminated food or water, or recreation of contaminated water. AiV-1 is highly prevalent in water samples and has been proposed as a potential indicator of fecal contamination in water reservoirs. This study aimed to investigate the prevalence and genetic diversity of AiV-1 in environmental water samples in Thailand. A total of 126 samples were collected monthly from November 2016 to July 2018 from various sources of environmental water including irrigation water, reservoir, river, and wastewater. The presence of AiV-1 was detected by RT-nested PCR of the 3CD region and further analyzed by phylogenetic analysis. The AiV-1 was detected in 28 out of 126 (22.2%) of tested samples. A high frequency of AiV-1 detection was in wastewater (52.4%). All 28 AiV-1 strains detected in this study belonged to the genotype B and were closely related to AiV strains detected previously in environmental waters and in humans worldwide. This study demonstrated, for the first time, the contamination of AiV-1 in various sources of water samples in Thailand and provided a better insight into the prevalence of AiV-1 in environmental waters and its potential risk of human health.
Collapse
Affiliation(s)
- Kattareeya Kumthip
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, 50200, Thailand
- Emerging and Re-emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, 50200, Thailand
- Emerging and Re-emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, 50200, Thailand
- Emerging and Re-emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Emerging and Re-emerging Diarrheal Viruses Cluster, Chiang Mai University, Chiang Mai, Thailand.
| |
Collapse
|
14
|
Sobhy NM, Armién AG, Wünschmann A, Muldoon D, Goyal SM, Mor SK. Detection and molecular characterization of kobuvirus from diarrheic goats in Minnesota. J Vet Diagn Invest 2020; 32:873-879. [PMID: 33140709 DOI: 10.1177/1040638720949475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Kobuvirus infections are common among humans, rodents, carnivores, pigs, and ruminants. We report herein the complete genome sequence of a novel caprine kobuvirus (MN604700) from diarrheic kids in Minnesota. Whole-genome sequencing revealed a kobuvirus genome of 8,139 nt with a single ORF region encoding a polyprotein of 2,480 amino acids. Further analysis revealed nt substitutions along the genome compared with that of the caprine kobuvirus reference strain, with 93% identity. Phylogenetic analysis indicated that the clade of the caprine kobuvirus was most closely related to porcine kobuviruses rather than bovine or ovine kobuviruses. Using primers designed from this genome, caprine kobuvirus was identified in the stools of other goats. Sanger sequencing of PCR products indicated 3D and VP1 gene nucleotides of this latter strain were 95% and 91% identical with those of MN604700, respectively. There were 35 and 101 nt substitutions in 3D and VP1 genes, respectively. Findings of kobuvirus over a 2-y period may indicate an endemic state, which needs further research. In addition, screening for kobuviruses over large geographic areas is needed to identify the evolutionary connections among different strains.
Collapse
Affiliation(s)
- Nader M Sobhy
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN.,Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, Egypt
| | - Aníbal G Armién
- California Animal Health and Food Safety Laboratory System, University of California-Davis, Davis, CA
| | - Arno Wünschmann
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN
| | - Dean Muldoon
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN
| | - Sagar M Goyal
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN
| | - Sunil K Mor
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN
| |
Collapse
|
15
|
Abstract
BACKGROUND Initially, detection and isolation of Aichivirus as a new member of Picornaviridae family was documented in Japan. Aichivirus species belongs to genus Kobuvirus, including 3 genotypes A, B and C. In previous studies, it has been suggested that Aichivirus infect humans by fecal-oral route. To establish an investigation for the occurrence of Aichivirus among pediatric patients involved to acute gastroenteritis, we developed a reverse transcription quantitative polymerase chain reaction assay for detection and quantification of Aichivirus in stool specimens. MATERIAL AND METHODS In this study, a total of 160 stool samples from September 2018 to May 2019 were collected from pediatric patients presenting with acute gastroenteritis in Karaj hospital, Iran. After viral RNA extraction, the reverse transcription quantitative polymerase chain reaction was performed to amplify the 3CD junction region of Aichivirus genome and viral load was assessed. Aichivirus genomic RNA was detected in 13/160 (8.1%) of stool samples. The highest Aichivirus detection rate was in December (30.7%). The maximum viral load was determined to be 3.9 × 10 copies/g in one sample obtained from a 1-month-old patient. The co-infection of Aichivirus with salivirus and saffold virus was also assessed by reverse transcription quantitative polymerase chain reaction, among which frequent mixed infections by 2 or more viruses were identified. CONCLUSIONS This is the first documentation of Aichivirus detection in stool samples that demonstrates Aichivirus has been circulating among Iranian pediatric patients.
Collapse
|
16
|
Rivadulla E, Romalde JL. A Comprehensive Review on Human Aichi Virus. Virol Sin 2020; 35:501-516. [PMID: 32342286 PMCID: PMC7223127 DOI: 10.1007/s12250-020-00222-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/28/2020] [Indexed: 12/16/2022] Open
Abstract
Although norovirus, rotavirus, adenovirus and Astrovirus are considered the most important viral agents transmitted by food and water, in recent years other viruses, such as Aichi virus (AiV), have emerged as responsible for gastroenteritis outbreaks associated with different foods. AiV belongs to the genus Kobuvirus of the family Picornaviridae. It is a virus with icosahedral morphology that presents a single stranded RNA genome with positive sense (8280 nucleotides) and a poly (A) chain. AiV was first detected from clinical samples and in recent years has been involved in acute gastroenteritis outbreaks from different world regions. Furthermore, several studies conducted in Japan, Germany, France, Tunisia and Spain showed a high prevalence of AiV antibodies in adults (between 80% and 99%), which is indicative of a large exposure to this virus. The aim of this review is to bring together all the discovered information about the emerging pathogen human Aichi virus (AiV), discussing the possibles routes of transmission, new detection techniques and future research. Although AiV is responsible for a low percentage of gastroenteritis outbreaks, the high seroprevalence shown by human populations indicates an evident role as an enteric agent. The low percentage of AiV detection could be explained by the fact that the pathogen is more associated to subclinical infections. Further studies will be needed to clarify the real impact of AiV in human health and its importance as a causative gastroenteritis agent worldwide.
Collapse
Affiliation(s)
- Enrique Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain.
| |
Collapse
|
17
|
Northill JA, Simmons RJ, Genge D, Moore FA. Molecular characterization of the first reported Aichivirus A in Australia. Access Microbiol 2020; 2:acmi000099. [PMID: 33005865 PMCID: PMC7523624 DOI: 10.1099/acmi.0.000099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/20/2019] [Indexed: 11/28/2022] Open
Abstract
A novel real-time reverse transcription polymerase chain reaction (RT-rPCR) assay was developed to detect Aichivirus A (AiV-A) based on four complete genomes. The assay successfully detected AiV-A in a sample from a patient with acute gastroenteritis in January 2008. Screening of 756 samples submitted for norovirus testing during May 2008 detected a further 23 AiV-A-positive samples from 18 individual patients. Genotyping using novel primers targeting the 3C–3D junction region identified AiV-A genotype B. Further sequencing of the VP1 region supported the 3C–3D result. All three assays proved useful to support foodborne outbreak investigations. This is the first report of AiV-A detection in Australia.
Collapse
Affiliation(s)
- Judith A. Northill
- Public Health Virology, Forensic and Scientific Services, Coopers Plains, QLD, Australia
| | - Russell J. Simmons
- Public Health Virology, Forensic and Scientific Services, Coopers Plains, QLD, Australia
| | - Doris Genge
- Public Health Virology, Forensic and Scientific Services, Coopers Plains, QLD, Australia
| | - Frederick A. Moore
- Public Health Virology, Forensic and Scientific Services, Coopers Plains, QLD, Australia
| |
Collapse
|
18
|
Shaheen MNF, Abd El-Daim SE, Ahmed NI, Elmahdy EM. Environmental monitoring of Aichi virus and human bocavirus in samples from wastewater treatment plant, drain, and River Nile in Egypt. JOURNAL OF WATER AND HEALTH 2020; 18:30-37. [PMID: 32129184 DOI: 10.2166/wh.2019.075] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Wastewater plays a major role in water pollution causing transmission of several viral pathogens, including Aichi virus (AiV) and human bocavirus (HBoV), associated with gastrointestinal illness in humans. In this study, we investigated the presence of AiV and HBoV in aquatic, sludge, sediment matrices collected from Abu-Rawash wastewater treatment plant (WWTP), El-Rahawy drain, Rosetta branch of the River Nile in Egypt by conventional polymerase chain reaction (PCR). AiV RNA was detected in 16.6% (2/12), 8.3% (1/12), 8.3% (1/12), 22% (16/72), 12.5% (3/24), 4% (1/24), and 0/24 (0%) of untreated raw sewage, treated sewage, sewage sludge, drainage water, drain sediment, river water, and river sediment, respectively. On the other hand, HBoV DNA was detected in 41.6% (5/12), 25% (3/12), 16.6% (2/12), 48.6% (35/72), 29% (7/24), 3/24 (12.5%), 4% (1/24) of untreated raw sewage, treated raw sewage, sewage sludge, drainage water, drain sediment, river water, and river sediment, respectively. This study provides data on the presence of these viruses in various types of water samples that are valuable to environmental risk assessment. In addition, the current study demonstrates the importance of environmental monitoring as an additional tool to investigate the epidemiology of AiV and HBoV circulating in a given community.
Collapse
Affiliation(s)
- Mohamed N F Shaheen
- Environmental Virology Laboratory, Water Pollution Research Department, Environmental Research Division, National Research Centre, Al-Buhouth Street, 12622 Dokki, Giza, Egypt E-mail:
| | - Sahar E Abd El-Daim
- Environmental Virology Laboratory, Water Pollution Research Department, Environmental Research Division, National Research Centre, Al-Buhouth Street, 12622 Dokki, Giza, Egypt E-mail:
| | - Nehal I Ahmed
- Environmental Virology Laboratory, Water Pollution Research Department, Environmental Research Division, National Research Centre, Al-Buhouth Street, 12622 Dokki, Giza, Egypt E-mail:
| | - Elmahdy M Elmahdy
- Environmental Virology Laboratory, Water Pollution Research Department, Environmental Research Division, National Research Centre, Al-Buhouth Street, 12622 Dokki, Giza, Egypt E-mail:
| |
Collapse
|
19
|
Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
Collapse
Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| |
Collapse
|
20
|
Epidemiology of Aichi virus in fecal samples from outpatients with acute gastroenteritis in Northwestern Spain. J Clin Virol 2019; 118:14-19. [PMID: 31382225 DOI: 10.1016/j.jcv.2019.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/21/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND In recent years, Aichi virus (AiV) has been involved in acute viral gastroenteritis outbreaks. However, the common pathogenesis of AiV releases more in subclinical infections underestimating the impact of AiV in human health. OBJECTIVES The present study describes the presence and genetic diversity of AiV in patients with gastroenteritis in Northwestern Spain. STUDY DESIGN A total of 2667 stool samples, obtained between July 2010 and June 2011, from diarrheic outpatients were studied for detection and molecular characterization of AiV using PCR techniques followed by sequencing and phylogenetic analyses. RESULTS The virus was detected in 124 (5.0%) of the samples among all age groups. Coinfections were also detected, from the 124 positive samples, 72 (58.1%) were positive only for AiV, whereas mixed contaminations with Norovirus genogroup I or genogroup II, Sapovirus, or other enteric pathogens were detected in 52 (41.9%) samples. A total of 70 positive samples could be genotyped, being characterized as genotype A (58.6%) or B (41.4%). AiV was detected from August to April, being the highest number of AiV positive samples detected during autumn and winter seasons. CONCLUSIONS This survey remarks the importance of emerging enteric viruses in patients who require medical assistance, and offers more information about the real importance of AiV as gastroenteritis agent.
Collapse
|
21
|
Onosi O, Upfold NS, Jukes MD, Luke GA, Knox C. The First Molecular Detection of Aichi Virus 1 in Raw Sewage and Mussels Collected in South Africa. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:96-100. [PMID: 30560489 DOI: 10.1007/s12560-018-9362-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 12/12/2018] [Indexed: 05/18/2023]
Abstract
Aichi virus 1 (AiV-1) has a worldwide distribution and is associated with gastroenteritis in humans. In this study, raw sewage and mussel samples were analyzed for the presence of AiV-1 using reverse transcription-PCR (RT-PCR). Amplification and sequencing of the 3CD and VP1 genomic regions followed by phylogenetic analysis using selected genome sequences revealed the presence of AiV-1, genotype B. The results highlight the importance of further screening to evaluate the prevalence and epidemiology of this clinically important virus in South Africa.
Collapse
Affiliation(s)
- Oikwathaile Onosi
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Nicole S Upfold
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
| | - Michael D Jukes
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Garry A Luke
- Centre for Biomolecular Sciences, School of Biology, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews, Scotland, KY16 9ST, UK
| | - Caroline Knox
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| |
Collapse
|
22
|
Hata A, Hanamoto S, Ihara M, Shirasaka Y, Yamashita N, Tanaka H. Comprehensive Study on Enteric Viruses and Indicators in Surface Water in Kyoto, Japan, During 2014-2015 Season. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:353-364. [PMID: 30151619 DOI: 10.1007/s12560-018-9355-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
Certain enteric viruses that are present in the water environment are potential risk factors of waterborne infections. To better understand the impact of viruses in water, both enteric viruses and their potential indicators should be comparatively investigated. In this study, occurrences of GI- and GII-noroviruses (NoVs), sapovirus (SaV), rotavirus (RoV), Aichi virus 1 (AiV-1), enterovirus (EV), and pepper mild mottle virus (PMMoV) were quantitatively determined in surface water samples in Japan. Additionally, the genotype distribution of GI- and GII-NoVs was determined using a next-generation amplicon sequencing. PMMoV was the most abundant virus regardless of season and location, indicating its usefulness as an indicator for the viral contamination of water. Other potential indicators, AiV and EV, were less abundant than GII-NoV. Viruses other than PMMoV showed seasonality, i.e., EV and other viruses (NoVs, SaV, RoV, and AiV-1) became prevalent during summer and winter, respectively. SaV showed a relatively high abundance at a location that was affected by untreated wastewater. Regarding NoV genotypes, GI.1, GI.2, GI.4, GI.5, GI.6, GII.3, GII.4, GII.6, and GII.17 were found from the surface water samples. GII.4 and GII.17 seemed to have contributed to the high abundance of GII-NoV in the samples. Interestingly, GII.17 strains became prevalent in the water samples before becoming prevalent among gastroenteritis patients in Japan. These findings provide further insights into the properties of viruses as contaminants in the water environment.
Collapse
Affiliation(s)
- Akihiko Hata
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan.
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Seiya Hanamoto
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
- Water Quality Research Team, Public Works Research Institute, 1-6 Minamihara, Tsukuba, Ibaraki, 305-8516, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Yuya Shirasaka
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Naoyuki Yamashita
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
- Course of Rural Engineering, Department of Science and Technology for Biological Resources and Environment, Faculty of Agriculture, Graduate School of Agriculture Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| |
Collapse
|
23
|
Kumthip K, Khamrin P, Ushijima H, Maneekarn N. Molecular epidemiology of classic, MLB and VA astroviruses isolated from <5 year-old children with gastroenteritis in Thailand, 2011-2016. INFECTION GENETICS AND EVOLUTION 2018; 65:373-379. [PMID: 30153477 DOI: 10.1016/j.meegid.2018.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/20/2018] [Accepted: 08/23/2018] [Indexed: 12/23/2022]
Abstract
This study aimed to investigate the molecular epidemiology and genetic diversity of astrovirus circulating in pediatric patients with acute gastroenteritis in Thailand. A total of 2034 fecal specimens collected between 2011 and 2016 from children hospitalized with acute gastroenteritis were analyzed for astrovirus infection using RT-PCR and nucleotide sequencing techniques. Overall, 54 samples were positive for astrovirus (2.6%). About half of the virus-positive samples (57.4%) were co-infection cases, mainly with rotavirus or norovirus. Genotyping revealed that three major clades, classic human astrovirus (HAstV) and newly emerging MLB and VA astroviruses co-circulated in the study population. At least seven different genotypes were identified and HAstV1 was the most predominant genotype detected (50%), followed by MLB1 (16.7%), HAstV4 (11.1%), HAstV5 and HAstV8 (7.4% each), MLB2 and VA2 (3.7% each). This study provided a useful information and contributed to molecular epidemiology of astroviruses including the novel MLB and VA astoviruses have been characterized and reported for the first time in Thailand.
Collapse
Affiliation(s)
- Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand.
| |
Collapse
|
24
|
Thongprachum A, Fujimoto T, Takanashi S, Saito H, Okitsu S, Shimizu H, Khamrin P, Maneekarn N, Hayakawa S, Ushijima H. Detection of nineteen enteric viruses in raw sewage in Japan. INFECTION GENETICS AND EVOLUTION 2018; 63:17-23. [PMID: 29753903 DOI: 10.1016/j.meegid.2018.05.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 04/18/2018] [Accepted: 05/09/2018] [Indexed: 11/19/2022]
Abstract
One-year surveillance for enteric viruses in raw sewage was conducted in Kansai area, central part of Japan from July 2015 to June 2016. The raw sewage was collected monthly from an inlet polluted pool and was concentrated by polyethylene glycol (PEG) precipitation. Twelve sewage samples were screened for nineteen kinds of enteric viruses by using RT-PCR method and further analyzed by nucleotide sequencing. Twelve enteric viruses were found in the investigative sewage samples. Rotavirus A and norovirus GI and GII with several genotypes were detected all year round. Interestingly, norovirus GII.17 (Kawasaki-like strain) and rotavirus G2 that caused the outbreaks in Japan last epidemic season were also found in sewage. Moreover, adenovirus, astrovirus, sapovirus, bocavirus, human parechovirus, enterovirus, Aichi virus, Saffold virus and salivirus were also detected. Enterovirus D68 was detected only in the same month as those of enterovirus D68 outbreak in Japan. The rotavirus B and C, hepatitis A and E viruses, human cosavirus, bufavirus and rosavirus were not detected in this surveillance. The study provides the information on the enteric viruses contaminated in raw sewage, which is valuable for risk assessment. Our results imply that the viruses detected in sewage may be associated with infections in the Japanese population.
Collapse
Affiliation(s)
- Aksara Thongprachum
- Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand; Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tsuguto Fujimoto
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Saito
- Akita Prefectural Research Center for Public Health and Environment, Akita, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
25
|
Kitajima M, Rachmadi AT, Iker BC, Haramoto E, Gerba CP. Temporal variations in genotype distribution of human sapoviruses and Aichi virus 1 in wastewater in Southern Arizona, United States. J Appl Microbiol 2018; 124:1324-1332. [PMID: 29377502 DOI: 10.1111/jam.13712] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 01/21/2023]
Abstract
AIMS To investigate the molecular epidemiology, especially temporal variations in genotype distribution, of sapoviruses and Aichi virus 1 (AiV-1) in Arizona, United States, by examining wastewater. METHODS AND RESULTS A total of 26 wastewater samples (13 influent and 13 effluent) were collected monthly from a wastewater treatment plant and viral strains were identified through nested reverse transcription-PCR followed by cloning and sequencing analysis. Identified sapovirus strains were classified into seven genotypes belonging to three genogroups (GI, GII, and GV): GI.1, GI.2, GI.3, GII.1, GII.2, GII.8 and GV.1, with a clear temporal shift. The majority of AiV-1 strains identified from the wastewater samples were classified into genotype B, and genotype A strains were identified in only two samples. CONCLUSIONS We identified a number of sapovirus and AiV-1 strains belonging to multiple genotypes in wastewater samples collected over a 13-month period. Our results suggested a temporal shift in prevalent genotypes in the community. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study elucidating the genotype distribution of human sapoviruses and AiV-1 in wastewater in the United States. Wastewater surveillance is especially useful for understanding molecular epidemiology of viruses that are less commonly tested in clinical diagnosis, including sapoviruses and AiV-1.
Collapse
Affiliation(s)
- M Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - A T Rachmadi
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - B C Iker
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, USA
| | - E Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Kofu, Yamanashi, Japan
| | - C P Gerba
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, USA
| |
Collapse
|
26
|
Alcalá AC, Pérez K, Blanco R, González R, Ludert JE, Liprandi F, Vizzi E. Molecular detection of human enteric viruses circulating among children with acute gastroenteritis in Valencia, Venezuela, before rotavirus vaccine implementation. Gut Pathog 2018; 10:6. [PMID: 29483944 PMCID: PMC5822563 DOI: 10.1186/s13099-018-0232-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/18/2018] [Indexed: 01/15/2023] Open
Abstract
Background The role of rotavirus as main etiologic agent of diarrhea has been well documented worldwide, including in Venezuela. However, information about the prevalence of gastrointestinal viruses such as calicivirus, adenovirus and astrovirus is limited and the contribution of other agents as Aichi virus and klassevirus is largely unknown. To explore the etiological spectrum of diarrhea associated with agents other than rotaviruses, 227 stool samples from children under 5 years old with acute gastroenteritis, collected in Valencia (Venezuela) from 2001 to 2005, and previously tested as rotavirus-negative, were analyzed for caliciviruses, adenoviruses, astroviruses, Aichi viruses, klasseviruses, picobirnaviruses and enteroviruses by specific RT-PCRs. Results At least one viral agent was detected in 134 (59%) of the samples analyzed, mainly from children under 24 months of age and most of them belonging to the lowest socioeconomic status. Overall, enterovirus was identified as the most common viral agent (37.9%), followed by calicivirus (23.3%), adenovirus (11.5%), astrovirus (3.5%), klassevirus (1.3%) and Aichi virus (0.4%), while no picobirnavirus was detected. Klasseviruses were found during 2004 and 2005 and Aichi viruses only in 2005, indicating their circulation in Venezuela; meanwhile, the rest of the viruses were detected during the whole study period. Coinfections with two or more viruses were found in 39 (29.1%) of the infected children, most under 24 months of age. Adenovirus was involved as the coinfecting agent in at least 46.9% of the cases, but no differences concerning socio-demographic variables were observed between the coinfected and the single infected children. Conclusions The results show that various enteric viruses, including enteroviruses, caliciviruses and adenoviruses, accounted for a significant proportion of infantile diarrhea cases in Venezuela before rotavirus vaccine implementation. In addition, emerging viruses as Aichi virus and klassevirus were found, indicating the need to continue monitoring their spreading into the communities. Efforts are needed to develop more accurate methods to identify the major causes of diarrhea and to provide tools for more effective preventive measures.
Collapse
Affiliation(s)
- Ana C Alcalá
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela.,4Present Address: Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Mexico, D.F. Mexico
| | - Kriss Pérez
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela
| | - Ruth Blanco
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela
| | - Rosabel González
- 3Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico, D.F. Mexico
| | - Juan E Ludert
- Instituto Autónomo de Biomedicina Dr. Jacinto Convit-MPPS, Caracas, Venezuela
| | - Ferdinando Liprandi
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela
| | - Esmeralda Vizzi
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela
| |
Collapse
|
27
|
Terio V, Bottaro M, Di Pinto A, Fusco G, Barresi T, Tantillo G, Martella V. Occurrence of Aichi virus in retail shellfish in Italy. Food Microbiol 2018; 74:120-124. [PMID: 29706327 DOI: 10.1016/j.fm.2018.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/05/2018] [Accepted: 02/15/2018] [Indexed: 11/25/2022]
Abstract
AiV-1 is considered an emerging human enteric pathogens and foodborne transmission has been documented as an important source of exposure for humans, chiefly in relation to non-safe, risky food habits. We surveyed the presence of AiV-1 in retail shellfish, including oysters and mussles, identifying the virus in 3/170 (1.8%) of the analysed samples. The AiV-1 positive samples were of different geographic origin. Upon sequence analysis of a portion of the 3CD junction region, two AiV strains identified from harvesting areas in Northern Italy were characterised as genotype B and displayed 99-100% identity at the nucleotide level to other AiV-1 strains detected in sewages in Central Italy in 2012, suggesting that such strains are stably circulating in Italian ecosystems. Interestingly, a strain identified from mussles harvested in Southern Italy could not be characterised firmly, as inferred in the Bayesian analysis and by sequence comparison, indicating that different AiV strains are also circulating in Italy. Viral contamination in retail shellfish challenges the microbiological guidelines for food control and requires the development and optimization of additional diagnostic and prevention strategies.
Collapse
Affiliation(s)
- Valentina Terio
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy.
| | - Marilisa Bottaro
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Angela Di Pinto
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Division of Caserta, Via Jervolino n. 19, 81029, Caserta, Italy
| | - Teodosio Barresi
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Giuseppina Tantillo
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Vito Martella
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| |
Collapse
|
28
|
Lee S, Hata A, Yamashita N, Tanaka H. Evaluation of Virus Reduction by Ultrafiltration with Coagulation-Sedimentation in Water Reclamation. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:453-463. [PMID: 28455611 DOI: 10.1007/s12560-017-9301-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/25/2017] [Indexed: 06/07/2023]
Abstract
The evaluation of virus reduction in water reclamation processes is essential for proper assessment and management of the risk of infection by enteric viruses. Ultrafiltration (UF) with coagulation-sedimentation (CS) is potentially effective for efficient virus removal. However, its performance at removing indigenous viruses has not been evaluated. In this study, we evaluated the reduction of indigenous viruses by UF with and without CS in a pilot-scale water reclamation plant in Okinawa, Japan, by measuring the concentration of viruses using the real-time polymerase chain reaction (qPCR). Aichi virus (AiV) and pepper mild mottle virus (PMMoV) were targeted in addition to the main enteric viruses of concern for risk management, namely, norovirus (NoV) genogroups I and II (GI and GII) and rotavirus (RoV). PMMoV, which is a plant pathogenic virus and is present at high concentrations in water contaminated by human feces, has been suggested as a useful viral indicator. We also investigated the reduction of a spiked model virus (F-specific RNA bacteriophage MS2) to measure the effect of viral inactivation by both qPCR and plaque assay. Efficiencies of removal of NoV GI, NoV GII, RoV, and AiV by UF with and without CS were >0.5 to 3.7 log10, although concentrations were below the detection limit in permeate water. PMMoV was the most prevalent virus in both feed and permeate water following UF, but CS pretreatment could not significantly improve its removal efficiency (mean removal efficiency: UF, 3.1 log10; CS + UF, 3.4 log10; t test, P > 0.05). CS increased the mean removal efficiency of spiked MS2 by only 0.3 log10 by qPCR (t-test, P > 0.05), but by 2.8 log10 by plaque assay (t-test, P < 0.01). This difference indicates that the virus was inactivated during CS + UF. Our results suggest that PMMoV could be used as an indicator of removal efficiency in water reclamation processes, but cultural assay is essential to understanding viral fate.
Collapse
Affiliation(s)
- Suntae Lee
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan.
| | - Akihiko Hata
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Naoyuki Yamashita
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| |
Collapse
|
29
|
Haramoto E, Kitajima M. Quantification and Genotyping of Aichi Virus 1 in Water Samples in the Kathmandu Valley, Nepal. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:350-353. [PMID: 28185207 DOI: 10.1007/s12560-017-9283-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/02/2017] [Indexed: 05/27/2023]
Abstract
Aichi virus 1 genomes were detected by quantitative PCR in groundwater from shallow dug (10/22) and tube wells (1/15), river water (14/14), and sewage (1/1), with the maximum concentration of 4.0 × 109 copies/l. Nucleotide sequencing analysis demonstrated the prevalence of genotype B in the virus positive samples.
Collapse
Affiliation(s)
- Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| |
Collapse
|
30
|
Ibrahim C, Hammami S, Mejri S, Mehri I, Pothier P, Hassen A. Detection of Aichi virus genotype B in two lines of wastewater treatment processes. Microb Pathog 2017; 109:305-312. [PMID: 28596124 DOI: 10.1016/j.micpath.2017.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/11/2017] [Accepted: 06/01/2017] [Indexed: 11/28/2022]
Abstract
Enteric viruses are released in important quantities into the environment where they can persist for a very long time. At very low doses, they can cause human gastroenteritis, and are responsible for a substantial number of waterborne diseases. The aims of this study were multiple: firstly, to study the circulation of Aichi viruses (AiV) in wastewater sampled at the scale of a pilot wastewater treatment plant; secondly, to evaluate the performance of two wastewater treatment procedures, as natural oxidizing lagoons and rotating Biodisks, concerning the AiV removal; and finally, to determine the different type of AiV genotype found during this study. Hence, the pilot wastewater treatment plant is principally irrigated by the wastewater of three neighbouring clinics. Wastewater samples were collected during 2011 from the two lines of biological treatment procedures. AiV detection in wastewater were achieved using the Reverse Transcription Polymerase Chain Reaction (RT-PCR) technique, and the identification of AiV genotype was realized by the direct sequencing of PCR products. The result revealed that AiV strains were identified in 50% (n = 51) of the wastewater samples. A significant increase of the AiV detection frequency was registered from upstream to downstream of the five ponds constituting the natural oxidizing lagoon process, and at the exit of the rotating Biodisks procedure. All detected AiV strains showed the highest nucleotide sequence identity to genotype B that has been recently observed in patients in Asia. This finding represented the first Tunisian survey that revealed and mentioned the first detection of AiV genotype B in sewage and by the same argued for a noticeable resistance or survival of this type of virus in the two lines of treatment considered.
Collapse
Affiliation(s)
- Chourouk Ibrahim
- Centre of Research and Water Technologies (CERTE), Laboratory of Treatment and Wastewater Valorisation, 8020, Techno Park of Borj-Cedria, Tunisia; Faculty of Mathematical, Physical and Natural Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia.
| | - Salah Hammami
- National School of Veterinary Medicine at Sidi Thabet, 2020 Tunis, University of Manouba, Tunisia.
| | - Selma Mejri
- Veterinary Research Institute of Tunisia, Laboratory of Virology, 1006, La Rabta, Tunis, Tunisia.
| | - Ines Mehri
- Centre of Research and Water Technologies (CERTE), Laboratory of Treatment and Wastewater Valorisation, 8020, Techno Park of Borj-Cedria, Tunisia.
| | - Pierre Pothier
- National Reference Centre for Enteric Viruses, Laboratory of Virology, University Hospital of Dijon, 21070 Dijon, France.
| | - Abdennaceur Hassen
- Centre of Research and Water Technologies (CERTE), Laboratory of Treatment and Wastewater Valorisation, 8020, Techno Park of Borj-Cedria, Tunisia.
| |
Collapse
|
31
|
Portes SAR, Volotão EDM, Rocha MS, Rebelo MC, Xavier MDPTP, Assis RMD, Rose TL, Miagostovich MP, Leite JPG, Carvalho-Costa FA. A non-enteric adenovirus A12 gastroenteritis outbreak in Rio de Janeiro, Brazil. Mem Inst Oswaldo Cruz 2017; 111:403-6. [PMID: 27223654 PMCID: PMC4909040 DOI: 10.1590/0074-02760160030] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/09/2016] [Indexed: 11/22/2022] Open
Abstract
A gastroenteritis outbreak that occurred in 2013 in a low-income community in Rio de
Janeiro was investigated for the presence of enteric viruses, including species A
rotavirus (RVA), norovirus (NoV), astrovirus (HAstV), bocavirus (HBoV), aichivirus
(AiV), and adenovirus (HAdV). Five of nine stool samples (83%) from patients were
positive for HAdV, and no other enteric viruses were detected. Polymerase chain
reaction products were sequenced and subjected to phylogenetic analysis, which
revealed four strains and one strain of non-enteric HAdV-A12 and HAdV-F41,
respectively. The HAdV-A12 nucleotide sequences shared 100% nucleotide similarity.
Viral load was assessed using a TaqMan real-time PCR assay. Stool samples that were
positive for HAdV-A12 had high viral loads (mean 1.9 X 107 DNA copies/g
stool). All four patients with HAdV-A12 were < 25 months of age and had symptoms
of fever and diarrhoea. Evaluation of enteric virus outbreaks allows the
characterisation of novel or unique diarrhoea-associated viruses in regions where RVA
vaccination is routinely performed.
Collapse
Affiliation(s)
- Silvana Augusta Rodrigues Portes
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro RJ , Brasil, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Eduardo de Mello Volotão
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro RJ , Brasil, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Monica Simões Rocha
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro RJ , Brasil, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Maria Cristina Rebelo
- Laboratório Central de Saúde Pública, Laboratório Central de Saúde Pública, Rio de Janeiro RJ , Brasil, Laboratório Central de Saúde Pública, Rio de Janeiro, RJ, Brasil
| | - Maria da Penha Trindade Pinheiro Xavier
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro RJ , Brasil, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Rosane Maria de Assis
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro RJ , Brasil, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Tatiana Lundgren Rose
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro RJ , Brasil, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Marize Pereira Miagostovich
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro RJ , Brasil, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - José Paulo Gagliardi Leite
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro RJ , Brasil, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Filipe Anibal Carvalho-Costa
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro RJ , Brasil, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil.,Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Escritório Técnico Regional Fiocruz Piauí, Teresina PI , Brasil, Fundação Oswaldo Cruz, Escritório Técnico Regional Fiocruz Piauí, Teresina, PI, Brasil
| |
Collapse
|
32
|
Molecular detection of kobuviruses in livestock in Northern Ireland and the Republic of Ireland. Arch Virol 2017; 162:1275-1279. [DOI: 10.1007/s00705-017-3223-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
|
33
|
|
34
|
Thongprachum A, Khamrin P, Pham NTK, Takanashi S, Okitsu S, Shimizu H, Maneekarn N, Hayakawa S, Ushijima H. Multiplex RT-PCR for rapid detection of viruses commonly causing diarrhea in pediatric patients. J Med Virol 2016; 89:818-824. [PMID: 27735999 DOI: 10.1002/jmv.24711] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2016] [Indexed: 01/16/2023]
Abstract
Multiplex RT-PCR method using five sets of panel primers was developed for the detection of diarrheal viruses, including rotavirus A, B, and C, adenovirus, astrovirus, norovirus GI and GII, sapovirus, Aichi virus, parechovirus, enterovirus, cosavirus, bocavirus, and Saffold virus. The sensitivity of the method was evaluated and tested with 751 fecal specimens collected from Japanese children with acute diarrhea. Several kinds of viruses were detected in 528 out of 751 (70.3%) fecal specimens. Mixed-infection with different viruses in clinical specimens could also be effectively detected. The method proved to be reliable with highly sensitive and specific and useful for routine diagnosis. J. Med. Virol. 89:818-824, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Aksara Thongprachum
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Disease, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
35
|
Shigemoto N, Hisatsune Y, Toukubo Y, Tanizawa Y, Shimazu Y, Takao S, Tanaka T, Noda M, Fukuda S. Detection of gastroenteritis viruses among pediatric patients in Hiroshima Prefecture, Japan, between 2006 and 2013 using multiplex reverse transcription PCR-based assays involving fluorescent dye-labeled primers. J Med Virol 2016; 89:791-800. [PMID: 27736008 DOI: 10.1002/jmv.24714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2016] [Indexed: 12/15/2022]
Abstract
Multiplex reverse transcription (RT)-polymerase chain reaction (PCR)-based assays involving fluorescent dye-labeled primers were modified to detect 10 types of gastroenteritis viruses by adding two further assays to a previously developed assay. Then, these assays were applied to clinical samples, which were collected between January 2006 and December 2013. All 10 types of viruses were effectively detected in the multiplex RT-PCR-based assays. In addition, various viral parameters, such as the detection rates and age distributions of each viral type, were examined. The frequency and types of mixed infections were also investigated. Among the 186 virus-positive samples, genogroup II noroviruses were found to be the most common type of virus (32.7%), followed by group A rotaviruses (10.6%) and parechoviruses (10.3%). Mixed infections were observed in 37 samples, and many of them were detected in patients who were less than 2 years old. These observations showed that the multiplex RT-PCR-based assays involving fluorescent dye-labeled primers were able to effectively detect the viruses circulating among pediatric acute gastroenteritis patients and contributed to the highly specific and sensitive diagnosis of gastroenteritis. J. Med. Virol. 89:791-800, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Naoki Shigemoto
- Center for Public Health and Environment, Hiroshima Prefectural Technology Research Institute, Minami-ku, Hiroshima, Japan
| | - Yuri Hisatsune
- Center for Public Health and Environment, Hiroshima Prefectural Technology Research Institute, Minami-ku, Hiroshima, Japan
| | - Yasushi Toukubo
- Center for Public Health and Environment, Hiroshima Prefectural Technology Research Institute, Minami-ku, Hiroshima, Japan
| | - Yukie Tanizawa
- Center for Public Health and Environment, Hiroshima Prefectural Technology Research Institute, Minami-ku, Hiroshima, Japan
| | - Yukie Shimazu
- Center for Public Health and Environment, Hiroshima Prefectural Technology Research Institute, Minami-ku, Hiroshima, Japan
| | - Shinichi Takao
- Center for Public Health and Environment, Hiroshima Prefectural Technology Research Institute, Minami-ku, Hiroshima, Japan
| | | | - Mamoru Noda
- Division of Biomedical Food Research, National Institute of Health Sciences, Setagaya-ku, Tokyo, Japan
| | - Shinji Fukuda
- Department of Human Nutrition, Faculty of Contemporary Life Science, Chugokugakuen University, Kita-ku, Okayama, Japan
| |
Collapse
|
36
|
Sewlikar S, D'Souza DH. Survival of hepatitis A virus and Aichi virus in cranberry-based juices at refrigeration (4 °C). Food Microbiol 2016; 62:251-255. [PMID: 27889156 DOI: 10.1016/j.fm.2016.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 09/07/2016] [Accepted: 10/02/2016] [Indexed: 12/01/2022]
Abstract
Viral foodborne illness continues to be a health-concern globally, with numerous fruit and juice outbreaks of Hepatitis A virus (HAV) reported worldwide. Aichi virus (AiV) is an emerging pathogen with limited epidemiological data. Both, HAV and AiV are resistant to low pH and can survive under adverse environmental conditions leading to transmission ease. The objective of this study was to evaluate the survival of HAV and AiV in commercially-available cranberry-based juices (Cranberry juice cocktail, CJ and a 100% juice with cranberry, MJ) over 21 days at refrigeration (4 °C). Equal volumes of juice was mixed with each virus individually (final titer of 6 log PFU/mL) and stored at refrigeration over 21 days. At each time interval, the inoculated juices were serially diluted in cell culture media and infectious virus survival was determined by standard plaque assays. Each experiment was carried out in duplicate and replicated thrice. Reductions of 0.72 ± 0.06 (after day 1) to 2.3 ± 0.18 log PFU/mL (after day 21) and 0.63 ± 0.02 (after day 1) to 1.84 ± 0.14 log PFU/mL (after day 21) were obtained for AiV with MJ and CJ, respectively. Reductions ranging from 0.67 ± 0.03 (after day 1) to 1.09 ± 0.1 log PFU/mL (after day 21) and 0.93 ± 0.27 (after day1) to 1.49 ± 0.18 log PFU/mL (after day 21) were obtained for HAV at refrigeration in MJ and CJ, respectively. HAV showed greater survival than AiV in these juices over refrigerated storage. These results provide survival data of HAV and AiV in cranberry-based juices that can be used in risk-modeling and risk assessment studies.
Collapse
Affiliation(s)
- Snigdha Sewlikar
- The University of Tennessee-Knoxville, Department of Food Science and Technology, 2600 River Drive, Knoxville, TN 37966, USA
| | - Doris H D'Souza
- The University of Tennessee-Knoxville, Department of Food Science and Technology, 2600 River Drive, Knoxville, TN 37966, USA.
| |
Collapse
|
37
|
Ayouni S, Estienney M, Hammami S, Neji Guediche M, Pothier P, Aouni M, Belliot G, de Rougemont A. Cosavirus, Salivirus and Bufavirus in Diarrheal Tunisian Infants. PLoS One 2016; 11:e0162255. [PMID: 27631733 PMCID: PMC5025138 DOI: 10.1371/journal.pone.0162255] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/21/2016] [Indexed: 11/17/2022] Open
Abstract
Three newly discovered viruses have been recently described in diarrheal patients: Cosavirus (CosV) and Salivirus (SalV), two picornaviruses, and Bufavirus (BuV), a parvovirus. The detection rate and the role of these viruses remain to be established in acute gastroenteritis (AGE) in diarrheal Tunisian infants. From October 2010 through March 2012, stool samples were collected from 203 children <5 years-old suffering from AGE and attending the Children's Hospital in Monastir, Tunisia. All samples were screened for CosV, SalV and BuV as well as for norovirus (NoV) and group A rotavirus (RVA) by molecular biology. Positive samples for the three screened viruses were also tested for astrovirus, sapovirus, adenovirus, and Aichi virus, then genotyped when technically feasible. During the study period, 11 (5.4%) samples were positive for one of the three investigated viruses: 2 (1.0%) CosV-A10, 7 (3.5%) SalV-A1 and 2 (1.0%) BuV-1, whereas 71 (35.0%) children were infected with NoV and 50 (24.6%) with RVA. No mixed infections involving the three viruses were found, but multiple infections with up to 4 classic enteric viruses were found in all cases. Although these viruses are suspected to be responsible for AGE in children, our data showed that this association was uncertain since all infected children also presented infections with several enteric viruses, suggesting here potential water-borne transmission. Therefore, further studies with large cohorts of healthy and diarrheal children will be needed to evaluate their clinical role in AGE.
Collapse
Affiliation(s)
- Siwar Ayouni
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France.,Faculté de Pharmacie, Université de Monastir, Monastir, Tunisie
| | - Marie Estienney
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France
| | - Sabeur Hammami
- Service de Pédiatrie, Hôpital Universitaire Fattouma-Bourguiba, Monastir, Tunisie.,Faculté de Médicine, Université de Monastir, Monastir, Tunisie
| | - Mohamed Neji Guediche
- Service de Pédiatrie, Hôpital Universitaire Fattouma-Bourguiba, Monastir, Tunisie.,Faculté de Médicine, Université de Monastir, Monastir, Tunisie
| | - Pierre Pothier
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, Dijon, France
| | - Mahjoub Aouni
- Faculté de Pharmacie, Université de Monastir, Monastir, Tunisie
| | - Gael Belliot
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, Dijon, France
| | - Alexis de Rougemont
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, Dijon, France
| |
Collapse
|
38
|
Chuchaona W, Khamrin P, Yodmeeklin A, Kumthip K, Saikruang W, Thongprachum A, Okitsu S, Ushijima H, Maneekarn N. Detection and characterization of Aichi virus 1 in pediatric patients with diarrhea in Thailand. J Med Virol 2016; 89:234-238. [PMID: 27420653 DOI: 10.1002/jmv.24630] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2016] [Indexed: 11/06/2022]
Abstract
Kobuvirus is a newly discovered virus that belongs to the Kobuvirus genus in Picornaviridae family, which comprised of three species including Aichivirus A, Aichivirus B, and Aichivirus C. The kobuvirus isolated from human has been classified as Aichi virus 1 and belongs to Aichivirus A species. The present study aimed to assess the epidemiology and to perform molecular characterization of Aichi virus 1 in children admitted to hospitals with acute gastroenteritis in Chiang Mai, Thailand. A total of 923 fecal specimens collected from January, 2011 to December, 2013 were screened for the presence of Aichi virus 1 by RT semi-nested PCR. Out of 923 fecal specimens tested, Aichi virus 1 was detected with the prevalence of 2.6% (24/923). Of these, 0.3% (3/923) was genotype A and 2.3% (21/923) were genotype B. It is interesting to note that the genotype A showed the nucleotide sequence closely related to the Aichi virus reference strain isolated from sewage in Tunisia, while genotype B was most closely related to other human Aichi virus B reference strains. The results suggest that Aichi virus 1 of both genotypes A and B are circulating in pediatric patients in Thailand. J. Med. Virol. 89:234-238, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Watchaporn Chuchaona
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Wilaiporn Saikruang
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| | - Aksara Thongprachum
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shoko Okitsu
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Faculty of Medicine, Department of Microbiology, Chiang Mai University, Chiang Mai, Thailand
| |
Collapse
|
39
|
Prevalence and Genetic Diversity of Enteric Viruses in Children with Diarrhea in Ouagadougou, Burkina Faso. PLoS One 2016; 11:e0153652. [PMID: 27092779 PMCID: PMC4836733 DOI: 10.1371/journal.pone.0153652] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 04/01/2016] [Indexed: 02/06/2023] Open
Abstract
Enteric viruses are a major cause of diarrhea in children, especially those under five years old. Identifying the viral agents is critical to the development of effective preventive measures. This study aimed to determine the prevalence and genetic diversity of common enteric viruses in children under five years old in Burkina Faso. Stool samples from children with (n = 263) and without (n = 50) diarrhea disorders were collected in Ouagadougou, Burkina Faso from November 2011 to September 2012. Rotavirus, norovirus, sapovirus, astrovirus, adenovirus and Aichivirus A were detected using real-time or end-point (RT-)PCR. Rotavirus strains were G and P genotyped by multiplex RT-PCR and other viral strains were characterized by sequencing of viral subgenomic segements. At least one viral agent was detected in 85.6% and 72% of the symptomatic and asymptomatic patients, respectively. Rotavirus (63.5%), adenovirus (31.2%) and genogroup II norovirus (18.2%) were the most prevalent viruses in symptomatic patients, but only rotavirus and genogroup II norovirus were significantly associated with diarrhea (OR: 7.9, 95%CI: 3.7-17; OR: 3.5, 95%CI: 1-11.7, respectively). Sapovirus (10.3%), astrovirus (4.9%), genogroup I norovirus (2.7%) and Aichivirus A (0.8%) were less prevalent. The predominant genotype of rotavirus was G9P[8] (36.5%), and the predominant norovirus strain was GII.4 variant 2012 (71.4%). Among sapovirus, the genogroup II (87.5%) predominated. Astrovirus type 1 (41.7%) was the most frequent astrovirus identified. Aichivirus A belonged to the three genotypes (A, B and C). Enteric adenoviruses type 40 and 41 were identified in 10.2% and 5.1% respectively. Several cases of co-infections were detected. The results highlight the high prevalence and the high diversity of enteric viruses in Burkinabe children.
Collapse
|
40
|
Burutarán L, Lizasoain A, García M, Tort LFL, Colina R, Victoria M. Detection and Molecular Characterization of Aichivirus 1 in Wastewater Samples from Uruguay. FOOD AND ENVIRONMENTAL VIROLOGY 2016; 8:13-17. [PMID: 26456918 DOI: 10.1007/s12560-015-9217-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/03/2015] [Indexed: 06/05/2023]
Abstract
Aichivirus 1 (AiV-1) is an enteric virus with 30 nm in diameter, belonging to the genus Kobuvirus in the Picornaviridae family being a causative agent of gastroenteritis in humans. The transmission is via the fecal-oral route, through person to person contact, recreation in contaminated waters, or through the consumption of contaminated food or water. The aim of this study was to determine the frequency and the molecular characterization of AiV-1 in wastewater from Uruguay. Biweekly collections from March 2011 to February 2012 were performed in the cities of Bella Unión, Salto, Paysandú, and Fray Bentos, northwestern region of Uruguay. A total of 96 samples were collected; viruses were concentrated by ultracentrifugation, and AiV-1 was detected by using a nested PCR with primers directed to a conserved region (3CD junction) of the viral genome. A high frequency of AiV-1 (n = 54) was observed at all the cities analyzed mainly in the colder months of the year. AiV-1 was not evidenced as an appropriate viral fecal indicator since when compared with other previously detected enteric viruses, no correlation was observed. All 13 characterized AiV-1 belonged to the genotype B after the phylogenetic analysis performed with the sequences obtained from the first round PCR amplicon. This study demonstrates that AiV-1 is a frequently detected enteric viruses present in wastewater and excreted by infected persons in the northwestern region of Uruguay.
Collapse
Affiliation(s)
- L Burutarán
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte, CENUR del Noroeste, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - A Lizasoain
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte, CENUR del Noroeste, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - M García
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte, CENUR del Noroeste, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - L F L Tort
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte, CENUR del Noroeste, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - R Colina
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte, CENUR del Noroeste, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - M Victoria
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Regional Norte, CENUR del Noroeste, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay.
| |
Collapse
|
41
|
|
42
|
|
43
|
Bozkurt H, D'Souza DH, Davidson PM. Thermal Inactivation of Foodborne Enteric Viruses and Their Viral Surrogates in Foods. J Food Prot 2015; 78:1597-617. [PMID: 26219377 DOI: 10.4315/0362-028x.jfp-14-487] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Foodborne viruses, in particular human norovirus and hepatitis A virus, are the most common causes of food-associated infections and foodborne illness outbreaks around the world. Since it is currently not possible to cultivate human noroviruses and the wild-type strain of hepatitis A virus in vitro, the use of a variety of viral surrogates is essential to determine appropriate thermal processing conditions to reduce the risk associated with their contamination of food. Therefore, the objectives of this review are to (i) present pertinent characteristics of enteric foodborne viruses and their viral surrogates, (ii) discuss the viral surrogates currently used in thermal inactivation studies and their significance and value, (iii) summarize available data on thermal inactivation kinetics of enteric viruses, (iv) discuss factors affecting the efficacy of thermal treatment, (v) discuss suggested mechanisms of thermal inactivation, and (vi) provide insights on foodborne enteric viruses and viral surrogates for future studies and industrial applications. The overall goal of this review is to contribute to the development of appropriate thermal processing protocols to ensure safe food for human consumption.
Collapse
Affiliation(s)
- Hayriye Bozkurt
- Department of Food Science and Technology, University of Tennessee, 2605 River Drive, Knoxville, Tennessee 37996-4591, USA
| | - Doris H D'Souza
- Department of Food Science and Technology, University of Tennessee, 2605 River Drive, Knoxville, Tennessee 37996-4591, USA
| | - P Michael Davidson
- Department of Food Science and Technology, University of Tennessee, 2605 River Drive, Knoxville, Tennessee 37996-4591, USA.
| |
Collapse
|
44
|
Kitajima M, Gerba CP. Aichi virus 1: environmental occurrence and behavior. Pathogens 2015; 4:256-68. [PMID: 25996404 PMCID: PMC4493473 DOI: 10.3390/pathogens4020256] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 11/30/2022] Open
Abstract
Aichi virus 1 (AiV-1), belonging to the genus Kobuvirus in the family Picornaviridae, has been proposed as a causative agent of human gastroenteritis potentially transmitted by fecal-oral routes through contaminated food or water. AiV-1 is globally distributed and has been detected in various types of environmental samples, such as sewage, river water, groundwater, and shellfish. Recent environmental studies revealed that this virus could be detected in higher frequency and greater abundance than other human enteric viruses. These findings suggest that AiV-1 could potentially be an appropriate indicator of viral contamination in the environment because of its high prevalence in water environments as well as structural and genetic similarity with some of the other important enteric viruses. Further studies on the occurrence and fate of AiV-1 in environments, even in combination with clinical studies of many regions, are needed for a better understanding of their epidemiology, temporal and geographical distribution, environmental stability, and potential health risks to humans.
Collapse
Affiliation(s)
- Masaaki Kitajima
- Department of Soil, Water and Environmental Science, The University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA.
| | - Charles P Gerba
- Department of Soil, Water and Environmental Science, The University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA.
| |
Collapse
|
45
|
Thongprachum A, Takanashi S, Kalesaran AFC, Okitsu S, Mizuguchi M, Hayakawa S, Ushijima H. Four-year study of viruses that cause diarrhea in Japanese pediatric outpatients. J Med Virol 2015; 87:1141-8. [DOI: 10.1002/jmv.24155] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Aksara Thongprachum
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
| | - Angela F. C. Kalesaran
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
| | - Shoko Okitsu
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
| | - Masashi Mizuguchi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
| | - Satoshi Hayakawa
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine; The University of Tokyo; Tokyo Japan
- Division of Microbiology; Department of Pathology and Microbiology; Nihon University School of Medicine; Tokyo Japan
| |
Collapse
|
46
|
Infection of farmed pigs with porcine kobuviruses in Italy. Arch Virol 2015; 160:1533-6. [PMID: 25809018 DOI: 10.1007/s00705-015-2397-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/08/2015] [Indexed: 12/18/2022]
Abstract
Two-hundred eight swine fecal samples from six Italian farms were tested using a kobuvirus-specific RT-PCR with primers that amplify a region within the 3D gene. All farms were kobuvirus positive, with prevalence rates ranging between 24 % and 84 %. Overall, 57.5 % of asymptomatic pigs and 49.7 % of animals with diarrhea were positive for kobuvirus. Sequence analysis showed a different predominant strain circulating on each farm and indicated that the strains detected were related to both European and Asiatic strains. A possible pathogenic role of kobuvirus should be investigated further, since infections with this virus occur frequently in pigs of different ages.
Collapse
|
47
|
Hirneisen K, Reith J, Wei J, Hoover D, Hicks D, Pivarnik L, Kniel K. Comparison of pressure inactivation of caliciviruses and picornaviruses in a model food system. INNOV FOOD SCI EMERG 2014. [DOI: 10.1016/j.ifset.2014.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Yip CCY, Lo KL, Que TL, Lee RA, Chan KH, Yuen KY, Woo PCY, Lau SKP. Epidemiology of human parechovirus, Aichi virus and salivirus in fecal samples from hospitalized children with gastroenteritis in Hong Kong. Virol J 2014; 11:182. [PMID: 25326707 PMCID: PMC4283143 DOI: 10.1186/1743-422x-11-182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Emerging human picornaviruses, including human parechovirus (HPeV), Aichi virus (AiV) and salivirus (SalV) were found to be associated with gastroenteritis, but their roles in enteric infections are not fully understood. In addition, no report on the circulation of these viruses in Hong Kong is available. The objective of this study was to investigate the prevalence and genetic diversity of HPeV, AiV and SalV in fecal samples from hospitalized children with gastroenteritis in Hong Kong. METHODS Fecal samples from hospitalized children with gastroenteritis were subject to detection of HPeV, AiV and SalV by RT-PCR using consensus primers targeted to their 5'UTRs. Positive samples were subject to capsid and/or 3CD region analysis for genotype determination. The epidemiology of HPeV, AiV and SalV infections was analyzed. RESULTS Among 1,708 fecal samples subjected to RT-PCR using primers targeted to 5'UTR of HPeV, AiV and SalV, viruses were detected in 55 samples, with 50 positive for HPeV only, 3 positive for AiV only, 1 positive for both HPeV and AiV, and 1 positive for both HPeV and SalV. Phylogenetic analysis of the partial VP1 gene of the 33 HPeV strains revealed the presence of genotypes of HPeV- 1, 3, 4, 5, 7, 10, among which HPeV-1 was the predominant genotype circulating in our population. The peak activity of HPeV infection was in fall. Of the 3 children with AiV infection, the 3 AiV strains were found to belong to genotype A based on the phylogenetic analysis of their partial VP1 and 3CD regions. The genotype of a SalV strain detected in this study could not be determined. Co-detection of different pathogens was observed in 24 samples (43.6%) of 55 fecal samples positive for HPeV, AiV and SalV. CONCLUSIONS HPeV, AiV and SalV were detected in fecal samples of hospitalized children with gastroenteritis in Hong Kong, with the former having the highest prevalence. HPeV-1 was the predominant genotype among HPeVs, while genotype A was the predominant genotype among AiVs in this study.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, Hong Kong.
| | | |
Collapse
|
49
|
Detection of diarrheal viruses circulating in adult patients in Thailand. Arch Virol 2014; 159:3371-5. [PMID: 25078389 PMCID: PMC7087097 DOI: 10.1007/s00705-014-2191-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/19/2014] [Indexed: 11/18/2022]
Abstract
A total of 332 fecal specimens collected during January-December 2008 from adult patients with diarrhea were screened for group A and C rotaviruses, noroviruses GI and GII, sapovirus, Aichi virus, human parechovirus, enterovirus, adenovirus and astrovirus by RT-multiplex PCR. The detection rate for diarrheal viruses was 4.2 %. Adenovirus and enterovirus were equally detected as the most predominant viruses, with prevalence of 1.2 %, followed by Aichi virus (0.9 %) and norovirus GII (0.6 %). Mixed infection with norovirus GII and human parechovirus was also detected (0.3 %). This study provides epidemiological data for a wide variety of diarrheal viruses circulating in adult patients with diarrhea in Chiang Mai, Thailand.
Collapse
|
50
|
Yahiro T, Wangchuk S, Tshering K, Bandhari P, Zangmo S, Dorji T, Tshering K, Matsumoto T, Nishizono A, Söderlund-Venermo M, Ahmed K. Novel human bufavirus genotype 3 in children with severe diarrhea, Bhutan. Emerg Infect Dis 2014; 20:1037-9. [PMID: 24856373 PMCID: PMC4036752 DOI: 10.3201/eid2006.131430] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We identified a new genotype of bufavirus, BuV3, in fecal samples (0.8%) collected to determine the etiology of diarrhea in children in Bhutan. Norovirus GII.6 was detected in 1 sample; no other viral diarrheal pathogens were detected, suggesting BuV3 as a cause of diarrhea. This study investigates genetic diversity of circulating BuVs.
Collapse
|