1
|
Namuwulya P, Ashraf S, Niebel M, Ssekagiri A, Tushabe P, Kakooza P, Tong L, Bukenya H, Jerome H, Davis C, Birungi M, Turyahabwe I, Mugaga A, Eliku JP, Francis A, Nakabazzi L, Nsubuga F, Katushabe E, Kisakye A, Ampeire I, Nanteza A, Kaleebu P, Bakamutumaho B, Nsamba P, Kazibwe A, da Silva Filipe A, Tweyongyere R, Bwogi J, Thomson EC. Viruses associated with measles-like illnesses in Uganda. J Infect 2024; 88:106148. [PMID: 38588959 PMCID: PMC11060986 DOI: 10.1016/j.jinf.2024.106148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES In this study, we investigated the causes of measles-like illnesses (MLI) in the Uganda national surveillance program in order to inform diagnostic assay selection and vaccination strategies. METHODS We used metagenomic next-generation sequencing (M-NGS) on the Illumina platform to identify viruses associated with MLI (defined as fever and rash in the presence of either cough, coryza or conjunctivitis) in patient samples that had tested IgM negative for measles between 2010 and 2019. RESULTS Viral genomes were identified in 87/271 (32%) of samples, of which 44/271 (16%) contained 12 known viral pathogens. Expected viruses included rubella, human parvovirus B19, Epstein Barr virus, human herpesvirus 6B, human cytomegalovirus, varicella zoster virus and measles virus (detected within the seronegative window-period of infection) and the blood-borne hepatitis B virus. We also detected Saffold virus, human parvovirus type 4, the human adenovirus C2 and vaccine-associated poliovirus type 1. CONCLUSIONS The study highlights the presence of undiagnosed viruses causing MLI in Uganda, including vaccine-preventable illnesses. NGS can be used to monitor common viral infections at a population level, especially in regions where such infections are prevalent, including low and middle income countries to guide vaccination policy and optimize diagnostic assays.
Collapse
Affiliation(s)
| | - Shirin Ashraf
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Marc Niebel
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | | | | | | | - Lily Tong
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Henry Bukenya
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Hanna Jerome
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Chris Davis
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Molly Birungi
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Arnold Mugaga
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Aine Francis
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | | | | | | | | | - Ann Nanteza
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Peninah Nsamba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Anne Kazibwe
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Emma C Thomson
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK; London School of Hygiene and Tropical Medicine (LSHTM), London, UK.
| |
Collapse
|
2
|
Razizadeh MH, Khatami A, Zarei M. Global Status of Bufavirus, Cosavirus, and Saffold Virus in Gastroenteritis: A Systematic Review and Meta-Analysis. Front Med (Lausanne) 2022; 8:775698. [PMID: 35096871 PMCID: PMC8792846 DOI: 10.3389/fmed.2021.775698] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/29/2021] [Indexed: 01/20/2023] Open
Abstract
Background: Bufavirus (BuV), Human Cosavirus (HCoSV), and Saffold (SAFV) virus are three newly discovered viruses and have been suggested as possible causes of gastroenteritis (GE) in some studies. The aim of the present study was to estimate the overall prevalence of viruses and their association with GE. Methods: A comprehensive systematic search was conducted in Scopus, Web of Science, PubMed, and Google scholar between 2007 and 2021 to find studies on the prevalence of BuV, HCoSV, and SAFV viruses. Result: Meta-analysis of the 46 included studies showed the low prevalence of BuV (1.%, 95% CI 0.6-1.5%), HCoSV (0.8%, 95% CI 0.4-1.5%), and SAFV (1.9%, 95% CI 1.1-3.1%) worldwide. Also, no significant association between these viruses and GE was observed. BuV was isolated from patients with GE in Africa, while SAFV was more common in Europe. BuV1 and BuV2 have the same prevalence between the three identified genotypes of BuV. HCoSV-C was the most prevalent genotype of HCoSV, and SAFV2 was the commonest genotype of SAFV. All of these viruses were more prevalent in children older than 5 years of age. Conclusion: This was the first meta-analysis on the prevalence and association of BuV, HCoSV, and SAFV with GE. While no significant association was found between infection with these viruses and GE, we suggest more studies, especially with case-control design and from different geographical regions in order to enhance our knowledge of these viruses.
Collapse
Affiliation(s)
| | - Alireza Khatami
- Faculty of Medicine, Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Zarei
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| |
Collapse
|
3
|
Chong YM, Chan YF, Jamaluddin MFH, Hasan MS, Pang YK, Ponnampalavanar S, Syed Omar SF, Voon KGL, Sam IC. Detection of respiratory viruses in adults with suspected COVID-19 in Kuala Lumpur, Malaysia. J Clin Virol 2021; 145:105000. [PMID: 34739838 PMCID: PMC8526124 DOI: 10.1016/j.jcv.2021.105000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/05/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022]
Abstract
Background Reports of co-circulation of respiratory viruses during the COVID-19 pandemic and co-infections with SARS-CoV-2 vary. However, limited information is available from developing countries. Objectives We aimed to investigate the incidence of respiratory viruses in adult patients with suspected COVID-19 in Kuala Lumpur, Malaysia. Study Design We collected 198 respiratory samples from adult patients hospitalized with suspected COVID-19 in a single teaching hospital in Kuala Lumpur in February-May 2020 and tested combined oro-nasopharyngeal swabs with the NxTAG Respiratory Pathogen Panel (Luminex) and Allplex RV Essential (Seegene) assays. Forty-five negative samples further underwent viral metagenomics analysis. Results Of the 198 samples, 74 (37.4%) had respiratory pathogens, including 56 (28.3%) with SARS-CoV-2 and 18 (9.1%) positive for other respiratory pathogens. There were five (2.5%) SARS-CoV-2 co-infections, all with rhinovirus/enterovirus. Three samples (6.7%; 3/45) had viruses identified by metagenomics, including one case of enterovirus D68 and one of Saffold virus genotype 6 in a patient requiring ICU care. Most of the COVID-19 patients (91.1%; 51/56) had mild symptoms but 5.4% (3/56) died. Conclusion During the early COVID-19 period, common respiratory viruses other than SARS-CoV-2 only accounted for 9.1% of hospitalization cases with ARI and co-infections with SARS-CoV-2 were rare. Continued surveillance is important to understand the impact of COVID-19 and its associated public health control measures on circulation of other respiratory viruses. Metagenomics can identify unexpected or rare pathogens, such as Saffold virus, which is rarely described in adults.
Collapse
Affiliation(s)
- Yoong Min Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - M Shahnaz Hasan
- Department of Anaesthesiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | | | - Kenny Gah Leong Voon
- Division of Pathology, International Medical University, 57000 Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Medical Microbiology, University of Malaya Medical Centre, 59100 Kuala Lumpur, Malaysia.
| |
Collapse
|
4
|
Vandesande H, Edman K, Rondahl E, Falkeborn T, Serrander L, Lindberg AM. Saffold virus infection in elderly people with acute gastroenteritis in Sweden. J Med Virol 2021; 93:3980-3984. [PMID: 32827319 DOI: 10.1002/jmv.26452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/20/2020] [Indexed: 12/24/2022]
Abstract
Viral gastroenteritis is a major source of morbidity and mortality, predominantly caused by so-called NOROAD viruses (norovirus, rotavirus, and adenovirus). In approximately onethird of all cases, however, the exact etiology is unknown. The in 2007 discovered human cardiovirus Saffold virus (SAFV) may prove to be a plausible candidate to explain this diagnostic gap. This virus, a member of the Picornaviridae family which is closely related to the murine viruses Theiler's murine encephalomyelitis virus and Theravirus, is a widespread pathogen and causes infection early in life. Screening of 238 fecal or vomitus samples obtained from NOROAD-negative, elderly patients with acute gastroenteritis at the University Hospital of Linköping showed that SAFV is present in low abundance (4.6%). Phylogenetic analysis of the VP1 gene revealed a Swedish isolate belonging to the highly common and in Europe widespread SAFV-3 genotype. This genotype is also related to previously reported Asian strains. This study describes the first molecular typing of a Swedish SAFV isolate and is the first report to document the circulation of SAFV among elderly people. The pathogenicity of SAFV is, as of yet, still under debate; further studies are necessary to determine its role in the development of disease.
Collapse
Affiliation(s)
- Helena Vandesande
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Kjell Edman
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Elin Rondahl
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tina Falkeborn
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Lena Serrander
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - A Michael Lindberg
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| |
Collapse
|
5
|
López GR, Martinez LM, Freyre L, Freire MC, Vladimirsky S, Rabossi A, Cisterna DM. Persistent Detection of Cosavirus and Saffold Cardiovirus in Riachuelo River, Argentina. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:64-73. [PMID: 33165867 DOI: 10.1007/s12560-020-09451-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/04/2020] [Indexed: 06/11/2023]
Abstract
Cosaviruses (CoSV) and Saffold cardiovirus (SAFV) are novel members of the Picornaviridae family. The Matanza-Riachuelo river basin covers a total area of 2200 km2 with approximately 60 km long. Its last section is called Riachuelo River. The aim of this study was to describe the circulation of both picornaviruses and their relationship with the environmental situation of the Riachuelo River using 274 samples collected from 2005 to 2015. CoSV and SAFV were investigated in samples available by two periods: 2005-2006 and 2014-2015 (103 and 101, respectively). Physicochemical and bacteriological parameters confirmed very high levels of human fecal contamination during the 11 years evaluated. CoSV was detected in 85.7% (66/77) and 65.4% (17/26) of the samples collected in 2005-2006 and 2014-2015 periods, respectively. Species A and D were identified, the first one being widely predominant: 74.1% (20/27) and 75.0% (3/4) in both periods. SAFV virus was detected in 47.1% (32/68) and 52.6% (10/19) in periods 2005-2006 and 2014-2015, respectively. SAFV-6 was the most identified genotype in the entire study, while SAFV-3 was predominant in 2005-2006. The contribution of genotypes 1, 2, 4 and 8 was minor. The high prevalence of CoSV and SAFV suggests that both viruses have been circulating in Argentina at least since 2005. Our results show that a watercourse with high rates of human fecal contamination can become a persistent source of new viruses which capacity to produce human diseases is unknown.
Collapse
Affiliation(s)
- Gabriela Riviello López
- Prefectura Naval Argentina, Av. Eduardo Madero 235 (1106ACC), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Leila Marina Martinez
- Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbran", Av. Velez Sarsfield 563 (1282AFF), Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Freyre
- Prefectura Naval Argentina, Av. Eduardo Madero 235 (1106ACC), Ciudad Autónoma de Buenos Aires, Argentina
| | - María Cecilia Freire
- Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbran", Av. Velez Sarsfield 563 (1282AFF), Ciudad Autónoma de Buenos Aires, Argentina
| | - Sara Vladimirsky
- Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbran", Av. Velez Sarsfield 563 (1282AFF), Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro Rabossi
- IIBBA-CONICET and FIL, Av. Patricias Argentinas 435 (1405BWE), Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniel Marcelo Cisterna
- Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbran", Av. Velez Sarsfield 563 (1282AFF), Ciudad Autónoma de Buenos Aires, Argentina.
| |
Collapse
|
6
|
Identification of Norovirus and Human Parechovirus in Patients With Hand, Foot and Mouth Disease Syndrome. Pediatr Infect Dis J 2019; 38:1079-1084. [PMID: 31568248 DOI: 10.1097/inf.0000000000002459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Hand, foot and mouth disease (HFMD) is caused mostly by enteroviruses. However, other viral agents also can cause similar syndromes, and hence, the infections they cause are often misdiagnosed clinically. To determine non-enterovirus etiologic agents in HFMD-like cases, we screened enterovirus-negative samples collected from the patients who were clinically diagnosed as HFMD in China. METHODS Two hundred enterovirus-negative samples were collected previously in Wenzhou city of Zhejiang province, China. Both high throughput sequencing and RT-PCR were used to screen viral agents. In addition, their clinical features were analyzed. RESULTS Norovirus (NoV) and human parechovirus (HPeV) were identified from 22 (11.00%) and 9 (4.50%) samples, respectively. In addition, the complete genome sequences were recovered from 4 NoV-positive samples, and the VP1/3Dpol gene sequences were recovered from 5 HPeV-positive samples. Phylogenetic analyses of the NoV sequences revealed that they were closely related to those circulated in other regions of China. Notably, 4 genotypes of HPeVs, including HPeV-1, HPeV-4, HPeV-5 and HPeV-14, were found, indicating high genetic diversity of the virus. Frequent recombination between various genotypes was also observed in the HPeVs. Although most of the patients presented with the clinical features of HFMD, 4 patients infected with NoV GII.4 and 3 patients infected with HPeV-1 (1) and HPeV-4 (2) were characterized with diarrhea. Finally, tonsillitis, convulsion and granulocytopenia were observed in 1 NoV GII.4 patient, while liver dysfunction was found in 1 NoV GII.17 patient. CONCLUSIONS These data reveal the variety of agents in the cases clinically diagnosed as HFMD.
Collapse
|
7
|
Abstract
BACKGROUND Saffold virus (SAFV) is a novel human cardiovirus that was identified in 2007. Recently, SAFV has been isolated from nasal and stool specimens of infants presenting with respiratory and gastrointestinal symptoms and from cerebrospinal fluid (CSF) specimens of children with central nervous system infection. However, little is known regarding clinical characteristics of SAFV in children. METHODS We reviewed 5412 specimens from the database of the infectious agents surveillance system in Niigata prefecture, Japan, between January 2006 and December 2013, and identified SAFV-infected patients. Subsequently, we retrospectively reviewed their medical records and evaluated their clinical characteristics. RESULTS We identified 9 SAFV-infected patients (median age: 5 years; range: 2-16 years). Seven patients were diagnosed with pharyngitis, one with meningitis and one with fever of unknown origin. Dominant symptoms were high fever, appetite loss and headache. The median duration of the fevers was 2 days in patients with pharyngitis; however, the patient with meningitis remained febrile for 5 days. All blood tests available in this case series revealed leukocytosis with a predominance of neutrophils. CSF profiles showed mild lymphocytic pleocytosis. All patients recovered fully without complications. CONCLUSIONS A few clinical characteristics of SAFV infection were clarified, including high fever of short duration in patients with pharyngitis, and neutrophil-dominant leukocytosis. The clinical course and CSF profiles of a case of meningitis were similar to those of other aseptic meningitis. SAFV needs to be included in the differential diagnosis of pharyngitis or meningitis when commonly identified viruses are not identified in such patients.
Collapse
|
8
|
Lindner K, Ludwig M, Bootz F, Reber U, Safavieh Z, Eis-Hübinger AM, Herberhold S. Frequent detection of Saffold cardiovirus in adenoids. PLoS One 2019; 14:e0218873. [PMID: 31269055 PMCID: PMC6608973 DOI: 10.1371/journal.pone.0218873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/11/2019] [Indexed: 01/15/2023] Open
Abstract
Saffold virus (SAFV) is classified into the Cardiovirus genus of the Picornaviridae family. Up to now, eleven genotypes have been identified however, their clinical significance remains unclear. Here, we investigated the presence of SAFV in asymptomatic patients admitted for adenoidectomy. A total of 70 adenoid tissue samples were collected from children with clinical symptoms caused by hypertrophy of adenoids but without symptoms of airway infection. Samples were investigated for SAFV by RT-nested PCR and sequence analysis. Eleven of 70 (15.7%) samples were positive for SAFV. Nasopharyngeal swabs were available from 45 children just before surgery. SAFV was rarely found and only in children with SAFV-positive adenoids 2/8. Our findings indicate that the presence of SAFV seems to be more frequent in adenoid tissue than expected. This could support the notion of a longer than previously anticipated persistence of SAFV nucleic acids in the respiratory tract and possibly a chronic infection. Further investigations are necessary to establish the role of SAFV infection in humans.
Collapse
Affiliation(s)
- Kira Lindner
- ENT Department, Head and Neck Surgery, University of Bonn, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Friedrich Bootz
- ENT Department, Head and Neck Surgery, University of Bonn, Bonn, Germany
| | - Ulrike Reber
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | - Anna Maria Eis-Hübinger
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- * E-mail: (AMEH); (SH)
| | - Stephan Herberhold
- ENT Department, Head and Neck Surgery, University of Bonn, Bonn, Germany
- * E-mail: (AMEH); (SH)
| |
Collapse
|
9
|
Zhou F, Chen X, Chen G, Yan J, Xiao Y. Identification of SAA and ACTB as potential biomarker of patients with severe HFMD using iTRAQ quantitative proteomics. Clin Biochem 2019; 67:1-6. [PMID: 30817906 DOI: 10.1016/j.clinbiochem.2019.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 02/01/2019] [Accepted: 02/24/2019] [Indexed: 12/19/2022]
Abstract
Hand, foot and mouth disease (HFMD) is an infectious disease caused by a variety of enterovirus infections, and the most common types of virus infections are the newenterovirus71 (EV71) and coxsackievirus A group 16 (CoxA16). A small fraction of HFMD will cause further severe HFMD. A rapid and accurate diagnosis biomarker of severe HFMD is important for the timely treatment. In the study, we conducted a clinical biomarker discovery study using iTRAQ combined with MS. Serum proteome alterations in severe HFMD group (n = 32) and health control group (n = 32) were analyzed. 47 proteins were upregulated (fold change > 1.5) between the severe HFMD group and HC group. The identified proteins were classified into different groups according to the molecular function, biology processes, cellular component. During the up-regulated proteins, serum amyloid A (SAA) and human β-actin (ACTB), were confirmed in the serum of the severe HFMD and HC by ELISA assay. SAA and ACTB levels were significantly higher in the sever HFMD patients (P < .01), consistent with iTRAQ-LC-MS/MS analysis. In summary, Our results showed that SAA and human β-actin (ACTB) may be served as a potential biomarker of the clinical diagnosis of severe HFMD.
Collapse
Affiliation(s)
- Fangye Zhou
- Fujian Medical University Teaching Hospital, First Hospital of Putian, China
| | - Xianqian Chen
- Fujian Medical University Teaching Hospital, First Hospital of Putian, China.
| | - Guoxian Chen
- Fujian Medical University Teaching Hospital, First Hospital of Putian, China
| | - Junhua Yan
- Fujian Medical University Teaching Hospital, First Hospital of Putian, China
| | - Yupeng Xiao
- Fujian Medical University Teaching Hospital, First Hospital of Putian, China
| |
Collapse
|
10
|
Recombination Located over 2A-2B Junction Ribosome Frameshifting Region of Saffold Cardiovirus. Viruses 2018; 10:v10100520. [PMID: 30249971 PMCID: PMC6213509 DOI: 10.3390/v10100520] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/26/2018] [Accepted: 09/04/2018] [Indexed: 01/15/2023] Open
Abstract
Here we report the nearly full-length genome of a recombinant Saffold virus strain (SAFV-BR-193) isolated from a child with acute gastroenteritis. Evolutionary analysis performed using all available near-full length Saffold picornavirus genomes showed that the breakpoint found in the Brazilian strain (SAFV-BR-193) is indeed a recombination hotspot. Notably, this hotspot is located just one nucleotide after the ribosomal frameshift GGUUUUU motif in the SAFV genome. Empirical studies will be necessary to determine if this motif also affects the binding affinity of RNA-dependent RNA-polymerase (RdRp) and therefore increases the changes of RdRp swap between molecules during the synthesis of viral genomes.
Collapse
|
11
|
Prevalence of human cosavirus and saffold virus with an emergence of saffold virus genotype 6 in patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, 2014–2016. INFECTION GENETICS AND EVOLUTION 2017; 53:1-6. [DOI: 10.1016/j.meegid.2017.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/02/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022]
|
12
|
Zhu T, Lu QB, Zhang SY, Wo Y, Zhuang L, Zhang PH, Zhang XA, Wei W, Liu W. Molecular epidemiology of WU polyomavirus in hospitalized children with acute respiratory tract infection in China. Future Microbiol 2017; 12:481-489. [PMID: 28481120 DOI: 10.2217/fmb-2016-0144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
AIM To explore the molecular epidemiology and clinical characteristics of Washington University polyomavirus (WUPyV) infection in pediatric patients with acute respiratory tract infections in China. MATERIALS & METHODS A laboratory surveillance was performed to recruit pediatric patients with acute respiratory tract infections. WUPyV was detected using real-time PCR and complete genome was sequenced for randomly selected positive nasopharyngeal aspirate. RESULTS Altogether 122 (7.5%) of 1617 children found to be infected with WUPyV and 88 (72.1%) were coinfected with other viruses during 2012-2015. The phylogenetic analysis showed that 14 strains from our study formed two new clusters (Id and IIIc) within the Branch I and Branch III, respectively. CONCLUSION WUPyV is persistently circulating in China. Surveillance on WUPyV infection in wider areas and long persistence is warranted.
Collapse
Affiliation(s)
- Teng Zhu
- Graduate School of Anhui Medical University, Hefei 230032, PR China.,State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Qing-Bin Lu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing 100191, PR China.,Beijing Key Laboratory of Toxicological Research & Risk Assessment for Food Safety, Beijing 100191, PR China
| | - Shu-Yan Zhang
- Department of Developmental Biology, Affiliated Bayi Children's Hospital, PLA Army General Hospital, Beijing 100700, PR China
| | - Ying Wo
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Lu Zhuang
- Department of Developmental Biology, Affiliated Bayi Children's Hospital, PLA Army General Hospital, Beijing 100700, PR China
| | - Pan-He Zhang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Xiao-Ai Zhang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| | - Wei Wei
- Department of Epidemiology, Tong Zhou Institute of Infectious Disease & Epidemiology, Beijing 101113, PR China
| | - Wei Liu
- Graduate School of Anhui Medical University, Hefei 230032, PR China.,State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, PR China
| |
Collapse
|
13
|
Analysis of Aichi virus and Saffold virus association with pediatric acute gastroenteritis. J Clin Virol 2016; 87:37-42. [PMID: 27992789 DOI: 10.1016/j.jcv.2016.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/28/2022]
Abstract
BACKGROUND Aichi virus (AiV) and Saffold virus (SAFV) have been reported in children with acute gastroenteritis and respiratory disease worldwide; however, their causative role in acute gastroenteritis remains ambiguous. OBJECTIVES To assess the clinical association of AiV and SAFV with acute gastroenteritis in the pediatric population. STUDY DESIGN A case-control study involving 461 paired stool samples from pediatric cases with diarrhea and healthy controls was conducted in China. Quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) was used to screen AiV and SAFV. RESULTS In the 461 paired samples, AiV and SAFV were more prevalent among asymptomatic children than children with acute gastroenteritis (0.87% vs. 0.43% and 2.8% vs. 1.5%, respectively), with no significant differences between groups (p=0.142 and p=0.478, respectively). Cox regression model analysis revealed no correlation between AiV (odds ratio, OR=2.24; 95% confidence interval, CI, 0.76-6.54) or SAFV infection (OR=1.36; 95% CI, 0.86-2.15) and diarrhea. High viral loads were found in both AiV- and SAFV-positive groups, with no significant difference in viral load between the groups (p=0.507 and p=0.677, respectively). No other known enteric pathogens were found in the AiV-positive samples but common in SAFV-positive cases. Phylogenetic analysis revealed that all 6 AiV subjects clustered with genotype B. All 7 SAFV-positive cases and 8 of 13 SAFV-positive controls were genotyped successfully; the genotypes identified included SAFV-1, SAFV-2 SAFV-3, and SAFV-6. CONCLUSION Our study revealed no association of these viruses in acute gastroenteritis in children. These viruses may have the ability to replicate in humans; however, the infections are usually asymptomatic.
Collapse
|
14
|
Tan SZK, Prabakaran M. Immunohistochemical insights into Saffold virus infection of the brain of juvenile AG129 mice. Virol J 2016; 13:191. [PMID: 27887630 PMCID: PMC5123230 DOI: 10.1186/s12985-016-0654-8] [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: 04/27/2016] [Accepted: 11/21/2016] [Indexed: 11/28/2022] Open
Abstract
Background Saffold Virus (SAFV) is a human cardiovirus that is suspected of causing infection of the central nervous system (CNS) in children. While recent animal studies have started to elucidate the pathogenesis of SAFV, very little is known about the mechanisms behind it. Method In this study, we attempted to elucidate some of the mechanisms of the pathogenesis of SAFV in the brain of a juvenile mouse model by using immunohistochemical methods. Results We first showed that SAFV is able to infect both neuronal and glial cells in the brain of 2 week-old AG129 mice. We then showed that SAFV is able to induce apoptosis in both neuronal and glial cells in the brain. Lastly, we showed that SAFV infection does not show any signs of gross demyelination in the brain. Conclusion Overall, our results provide important insights into the mechanisms of SAFV in the brain. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0654-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shawn Zheng Kai Tan
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore.
| |
Collapse
|
15
|
Intracerebral Inoculation of Mouse-Passaged Saffold Virus Type 3 Affects Cerebellar Development in Neonatal Mice. J Virol 2016; 90:10007-10021. [PMID: 27581974 DOI: 10.1128/jvi.00864-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/22/2016] [Indexed: 01/04/2023] Open
Abstract
Saffold virus (SAFV), a human cardiovirus, is occasionally detected in infants with neurological disorders, including meningitis and cerebellitis. We recently reported that SAFV type 3 isolates infect cerebellar glial cells, but not large neurons, in mice. However, the impact of this infection remained unclear. Here, we determined the neuropathogenesis of SAFV type 3 in the cerebella of neonatal ddY mice by using SAFV passaged in the cerebella of neonatal BALB/c mice. The virus titer in the cerebellum increased following the inoculation of each of five passaged strains. The fifth passaged strain harbored amino acid substitutions in the VP2 (H160R and Q239R) and VP3 (K62M) capsid proteins. Molecular modeling of the capsid proteins suggested that the VP2-H160R and VP3-K62M mutations alter the structural dynamics of the receptor binding surface via the formation of a novel hydrophobic interaction between the VP2 puff B and VP3 knob regions. Compared with the original strain, the passaged strain showed altered growth characteristics in human-derived astroglial cell lines and greater replication in the brains of neonatal mice. In addition, the passaged strain was more neurovirulent than the original strain, while both strains infected astroglial and neural progenitor cells in the mouse brain. Intracerebral inoculation of either the original or the passaged strain affected brain Purkinje cell dendrites, and a high titer of the passaged strain induced cerebellar hypoplasia in neonatal mice. Thus, infection by mouse-passaged SAFV affected cerebellar development in neonatal mice. This animal model contributes to the understanding of the neuropathogenicity of SAFV infections in infants. IMPORTANCE Saffold virus (SAFV) is a candidate neuropathogenic agent in infants and children, but the neuropathogenicity of the virus has not been fully elucidated. Recently, we evaluated the pathogenicity of two clinical SAFV isolates in mice. Similar to other neurotropic picornaviruses, these isolates showed mild infectivity of glial and neural progenitor cells, but not of large neurons, in the cerebellum. However, the outcome of this viral infection in the cerebellum has not been clarified. Here, we examined the tropism of SAFV in the cerebellum. We obtained an in vivo-passaged strain from the cerebella of neonatal mice and examined its genome and its neurovirulence in the neonatal mouse brain. The passaged virus showed high infectivity and neurovirulence in the brain, especially the cerebellum, and affected cerebellar development. This unique neonatal mouse model will be helpful for elucidating the neuropathogenesis of SAFV infections occurring early in life.
Collapse
|
16
|
Tan SZK, Tan MZY, Prabakaran M. Saffold virus, an emerging human cardiovirus. Rev Med Virol 2016; 27. [PMID: 27723176 PMCID: PMC7169152 DOI: 10.1002/rmv.1908] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 08/23/2016] [Accepted: 08/30/2016] [Indexed: 01/16/2023]
Abstract
Saffold virus (SAFV) is an emerging human cardiovirus that has been shown to be ubiquitous. Initial studies of SAFV focused on respiratory and gastrointestinal infection; however, it has also recently been associated with diverse clinical symptoms including the endocrine, cardiovascular, and neurological systems. Given the systemic nature of SAFV, and its high prevalence, understanding its pathogenicity and clinical impact is of utmost importance. This comprehensive review highlights and discusses recent developments in epidemiology, human pathogenicity, animal, and molecular studies related to SAFV. It also provides detailed insights into the neuropathogenicity of SAFV. We argue that human studies have been confounded by coinfections and therefore require support from robust molecular and animal research. Thereby, we aim to provide foresight into further research to better understand this emerging virus.
Collapse
Affiliation(s)
- Shawn Zheng Kai Tan
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore, Singapore, Republic of Singapore
| | - Mark Zheng Yi Tan
- Critical Care Unit, Central Manchester Foundation NHS Trust, Manchester, UK
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore, Singapore, Republic of Singapore
| |
Collapse
|
17
|
Kotani O, Naeem A, Suzuki T, Iwata-Yoshikawa N, Sato Y, Nakajima N, Hosomi T, Tsukagoshi H, Kozawa K, Hasegawa H, Taguchi F, Shimizu H, Nagata N. Neuropathogenicity of Two Saffold Virus Type 3 Isolates in Mouse Models. PLoS One 2016; 11:e0148184. [PMID: 26828718 PMCID: PMC4734772 DOI: 10.1371/journal.pone.0148184] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/14/2016] [Indexed: 12/11/2022] Open
Abstract
Objective Saffold virus (SAFV), a picornavirus, is occasionally detected in children with acute flaccid paralysis, meningitis, and cerebellitis; however, the neuropathogenicity of SAFV remains undetermined. Methods The virulence of two clinical isolates of SAFV type 3 (SAFV-3) obtained from a patient with aseptic meningitis (AM strain) and acute upper respiratory inflammation (UR strain) was analyzed in neonatal and young mice utilizing virological, pathological, and immunological methods. Results The polyproteins of the strains differed in eight amino acids. Both clinical isolates were infective, exhibited neurotropism, and were mildly neurovirulent in neonatal ddY mice. Both strains pathologically infected neural progenitor cells and glial cells, but not large neurons, with the UR strain also infecting epithelial cells. UR infection resulted in longer inflammation in the brain and spinal cord because of demyelination, while the AM strain showed more infectivity in the cerebellum in neonatal ddY mice. Additionally, young BALB/c mice seroconverted following mucosal inoculation with the UR, but not the AM, strain. Conclusions Both SAFV-3 isolates had neurotropism and mild neurovirulence but showed different cell tropisms in both neonatal and young mouse models. This animal model has the potential to recapitulate the potential neuropathogenicity of SAFV-3.
Collapse
Affiliation(s)
- Osamu Kotani
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Virology and Viral Infections, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Asif Naeem
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takushi Hosomi
- The Public Health Institute of Kochi Prefecture, Kochi, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Gunma, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Gunma, Japan
| | - Hideki Hasegawa
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Fumihiro Taguchi
- Department of Virology and Viral Infections, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail:
| |
Collapse
|
18
|
Linsuwanon P, Poovorawan Y, Li L, Deng X, Vongpunsawad S, Delwart E. The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses. PLoS One 2015; 10:e0135573. [PMID: 26288145 PMCID: PMC4545796 DOI: 10.1371/journal.pone.0135573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 07/24/2015] [Indexed: 01/21/2023] Open
Abstract
Hand, foot, and mouth disease (HFMD) affects infant and young children. A viral metagenomic approach was used to identify the eukaryotic viruses in fecal samples from 29 Thai children with clinical diagnosis of HFMD collected during the 2012 outbreak. These children had previously tested negative by PCR for enterovirus 71 and coxsackievirus A16 and A6. Deep sequencing revealed nine virus families: Picornaviridae, Astroviridae, Parvoviridae, Caliciviridae, Paramyxoviridae, Adenoviridae, Reoviridae, Picobirnaviridae, and Polyomaviridae. The highest number of viral sequences belonged to human rhinovirus C, astrovirus-MLB2, and coxsackievirus A21. Our study provides an overview of virus community and highlights a broad diversity of viruses found in feces from children with HFMD.
Collapse
Affiliation(s)
- Piyada Linsuwanon
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| |
Collapse
|
19
|
Lin TL, Lin TH, Chiu SC, Huang YP, Ho CM, Lee CC, Wu HS, Lin JH. Molecular epidemiological analysis of Saffold cardiovirus genotype 3 from upper respiratory infection patients in Taiwan. J Clin Virol 2015; 70:7-13. [PMID: 26305811 DOI: 10.1016/j.jcv.2015.06.100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Saffold cardiovirus (SAFV) belongs to the Cardiovirus genus of Picornaviridae family, and may be a relevant new human pathogen; Thus far, eleven genotypes have been identified. The SAFV type 3 (SAFV-3) is thought to be the major genotype and is detected relatively frequently in children with acute gastroenteritis and respiratory illness. The epidemiology and pathogenicity of SAFV-3 remain unclear. OBJECTIVES To investigate the genomic and epidemiologic profiles of SAFV-3 infection in Taiwan. STUDY DESIGN Virus was detected in respiratory samples from children suffering for URI. SAFV-3 isolates were detected by isolation on cell culture and IF assay. The molecular typing was performed by RT-PCR and was sequenced to compare with reference strains available in the NCBI GeneBank. Serum samples were collected from 2005 to 2013 in Taiwan for seroprevalence investigation. RESULTS A total of 226 specimens collected from children with URIs, 22 (9.73%) were positive for SAFV-3. The majority of SAFV-3 infections were found in children less than 6 years of age (14 of 22, 63.6%). Genetic analysis of VP1 coding region of Taiwanese isolates shown an 83.2-97.7% difference from other available SAFV-3 sequences in NCBI GenBank. Phylogenetic analysis revealed there is three genetic groups of SAFV-3 co-circulated in Taiwan during the study period. In addition, seroprevalence investigation results indicated that SAFV-3 infection occurs early in life and 43.7-77.8% of children aged between 6 months to 9 years old, had neutralizing antibodies against SAFV-3. CONCLUSION SAFV-3 may have circulated in Taiwan for some time and it appears to be one of the etiological agents responsible for URIs in children.
Collapse
Affiliation(s)
- Tsuey-Li Lin
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Ting-Han Lin
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Shu-Chun Chiu
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Yuan-Pin Huang
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Cheng-Mao Ho
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Chia-Chi Lee
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Ho-Sheng Wu
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan; School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan.
| | - Jih-Hui Lin
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan.
| |
Collapse
|