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Alkubaisi NA, Aziz IM, Alsaleh AN, Alhetheel AF, Almajhdi FN. Molecular Profiling of Inflammatory Mediators in Human Respiratory Syncytial Virus and Human Bocavirus Infection. Genes (Basel) 2023; 14:genes14051101. [PMID: 37239461 DOI: 10.3390/genes14051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/13/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
Infections due to human respiratory syncytial virus (HRSV) and human bocavirus (HBoV) can mediate the release of several pro-inflammatory cytokines such as IL-6, IL-8, and TNF-α, which are usually associated with disease severity in children. In this study, the change in the expression profile of cytokines and chemokines were determined during HRSV, HBoV, and HRSV coinfection with HBoV in 75 nasopharyngeal aspirates (NPAs) samples, positive real-time reverse transcriptase PCR Assay (rRT-PCR) for HRSV (n = 36), HBoV (n = 23) infection alone or HRSV coinfection with HBoV (n = 16). The samples were collected from hospitalized children. qPCR-based detection revealed that the levels of IL-6, IL-8, IL-10, IL-13, IL-33, and G-CSF were significantly (p < 0.05) greater in patients than in controls. IL-4, IL-17, GM-CSF, and CCL-5 were significantly elevated in children with HRSV coinfection with HBoV than in other groups (p < 0.05). TNF-α, IL-6, IL-8, IL-10, IL-13, and IL-33 in children with HRSV were significantly increased in severe infections compared to mild infections. Whereas, IL-10, IL-13, and IL-33 were significantly increased in severe infection in compared a mild infection in children with HBoV. Further large-scale investigations involving isolates are needed to enhance our knowledge of the association between viral infections and cytokine expression patterns during the different stages of HRSV and HBoV infection.
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Affiliation(s)
- Noorah A Alkubaisi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ibrahim M Aziz
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Asma N Alsaleh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulkarim F Alhetheel
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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ON-1 and BA-IX Are the Dominant Sub-Genotypes of Human Orthopneumovirus A&B in Riyadh, Saudi Arabia. Genes (Basel) 2022; 13:genes13122288. [PMID: 36553555 PMCID: PMC9778264 DOI: 10.3390/genes13122288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
Human orthopneumovirus (HOPV) is the major viral pathogen responsible for lower respiratory tract infections (LRTIs) in infants and young children in Riyadh, Saudi Arabia. Yet, predominant HOPV subtypes circulating in this region and their molecular and epidemiological characteristics are not fully ascertained. A total of 300 clinical samples involving nasopharyngeal aspirates (NPAs), throat swabs, and sputum were collected during winter seasons of 2019/2020 and 2021/2022 for HOPV subtyping and genotyping. Of the 300 samples, HOPV was identified in 55 samples (18.3%) with a distinct predominance of type A viruses (81.8%) compared to type B viruses (18.2%). Importantly, the ON1 strain of HOPV-A and BA-IX strain of HOPV-B groups were found to be responsible for all the infections. Sequence analysis revealed a duplication region within 2nd HVR of G protein gene of ON1 and BA-IX strains. This nucleotide duplication exerted a profound effect on protein length and affinity towards cell receptors. Further, these modifications may aid the HOPV in immune evasion and recurrent infections. Data from this study showed that ON-1 genotype of HOPV-A and BA-IX genotype of HOPV-B were dominant in Riyadh, Saudi Arabia. Further, a duplication of sequence within 2nd HVR of G protein gene was found.
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Respiratory syncytial virus B sequence analysis reveals a novel early genotype. Sci Rep 2021; 11:3452. [PMID: 33568737 PMCID: PMC7876121 DOI: 10.1038/s41598-021-83079-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/22/2021] [Indexed: 02/08/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.
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Kang HM, Park KC, Park J, Kil HR, Yang EA. Circulating Respiratory Syncytial Virus Genotypes and Genetic Variability of the G Gene during 2017 and 2018/2019 Seasonal Epidemics Isolated from Children with Lower Respiratory Tract Infections in Daejeon, Korea. J Korean Med Sci 2020; 35:e422. [PMID: 33350185 PMCID: PMC7752254 DOI: 10.3346/jkms.2020.35.e422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a major pathogen causing respiratory tract infections in infants and young children. The aim of this study was to confirm the genetic evolution of RSV causing respiratory infections in children at Daejeon in Korea, through G gene analysis of RSV-A and RSV-B strains that were prevalent from 2017 to 2019. METHODS Pediatric patients admitted for lower respiratory tract infections at The Catholic University of Korea Daejeon St. Mary's Hospital in the 2017 and 2018/2019 RSV seasonal epidemics, who had RSV detected via multiplex polymerase chain reaction (PCR) were included. The nucleic acid containing RSV-RNA isolated from each of the patients' nasal discharge during standard multiplex PCR testing was stored. The G gene was sequenced and phylogenetic analysis was performed using MEGA X program and the genotype was confirmed. RESULTS A total of 155 specimens including 49 specimens from 2017 and 106 specimens from 2018-2019 were tested. The genotype was confirmed in 18 specimens (RSV-A:RSV-B = 4:14) from 2017 and 8 specimens (RSV-A:RSV-B = 7:1) from 2018/2019. In the phylogenetic analysis, all RSV-A type showed ON1 genotype and RSV-B showed BA9 genotype. CONCLUSION RSV-B belonging to BA9 in 2017, and RSV-A belonging to ON1 genotype in 2018/2019 was the most prevalent circulating genotypes during the two RSV seasons in Daejeon, Korea.
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Affiliation(s)
- Hyun Mi Kang
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ki Cheol Park
- Clinical Research Institute, Daejeon St. Mary's Hospital, The Catholic University of Korea, Daejeon, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hong Ryang Kil
- Department of Pediatrics, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Eun Ae Yang
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Pediatrics, Daejeon St. Mary's Hospital, The Catholic University of Korea, Daejeon, Korea.
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Dominance of the ON1 Genotype of RSV-A and BA9 Genotype of RSV-B in Respiratory Cases from Jeddah, Saudi Arabia. Genes (Basel) 2020; 11:genes11111323. [PMID: 33182267 PMCID: PMC7695323 DOI: 10.3390/genes11111323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/10/2023] Open
Abstract
Human respiratory syncytial virus (HRSV) is a main cause of hospital admission for lower respiratory tract infection. In previous studies from Saudi Arabia, higher prevalence of the NA1 genotype in group A was observed from Riyadh and Taif. This study recruited respiratory cases from Jeddah during January to December, 2017. RSV represented 13.4% in the recruited cases with 64% of them belonging to group A and 36% to group B. All group A cases in this study were ON1 type characterized by duplication of 72 nucleotides, 24 amino acids in the C-terminal in the second hypervariable region of the G gene. In addition, for group B all of the cases were clustered under BA9, which had uniquely characterized as duplication of 60 nucleotides in the G protein. Our sequences showed similarity with earlier sequences from Saudi Arabia, Kuwait, Thailand, South Africa, Spain, the USA and Cyprus. Some amino acid substitutions in the investigated sequences would cause a change in potential O-glycosylation and N-glycosylation profiles from prototype ON1. The predominance of the ON1 and BA9 genotype of RSV-A in Jeddah compared to previous Saudi studies showing predominance of the NA1 genotype for group A. This difference in genotype prevalence could be due to fast spread of the ON1 genotype worldwide or due to the flux of travelers through Jeddah during hajj/umrah compared to Riyadh and Taif. This shift in genotype distribution requires continuous surveillance for genetic characterization of circulating respiratory infections including RSV. These findings may contribute to the understanding of RSV evolution and to the potential development of a vaccine against RSV.
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Jerbi A, Fodha I, Ben Hamida-Rebai M, Ben Hadj Fredj M, Ataoui I, Bennour H, Abroug S, Khlifa M, Mathlouthi J, Mahdhaoui N, Boussetta K, Trabelsi A. Molecular characterization of respiratory syncytial virus circulating in Tunisia between 2015 and 2018. J Med Microbiol 2020; 69:1203-1212. [PMID: 32755531 DOI: 10.1099/jmm.0.001240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Respiratory syncytial virus (RSV) is the most frequently identified viral agent in children with lower respiratory tract infection (LRTI). No data are available to date regarding RSV genotypes circulating in Tunisia.Aim. The aim of the present study was to investigate the genetic variability of the glycoprotein G gene in Tunisian RSV strains.Methodology. Nasopharyngeal aspirates were collected from infants hospitalized for LRTI in five Tunisian hospitals. All specimens were screened for RSV by a direct immunofluorescence assay (DIFA). To molecularly characterize Tunisian RSV strains, a phylogenetic analysis was conducted. Randomly selected positive samples were subjected to reverse transcription PCR amplifying the second hyper-variable region (HVR2) of the G gene.Results. Among a total of 1417 samples collected between 2015 and 2018, 394 (27.8 %) were positive for RSV by DIFA. Analysis of 61 randomly selected RSV strains revealed that group A RSV (78.7 %) predominated during the period of study as compared to group B RSV (21.3 %). The phylogenetic analysis showed that two genotypes of RSV-A were co-circulating: the ON1 genotype with a 72-nt duplication in HVR2 of the G gene was predominant (98.0 % of RSV-A strains), while one RSV-A strain clustered with the NA1 genotype (2.0 %). Concerning Tunisian group B RSV strains, all sequences contained a 60-nt insertion in HVR2 and a clustered BA10 genotype.Conclusion. These data suggest that RSV-A genotype ON1 and RSV-B genotype BA10, both with duplications in the G gene, were widely circulating in the Central coastal region of Tunisia between 2015 and 2018.
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Affiliation(s)
- Amira Jerbi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Imene Fodha
- Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Meriam Ben Hamida-Rebai
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Mouna Ben Hadj Fredj
- Faculty of Sciences and Techniques, University of Kairouan, Kairouan, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Imene Ataoui
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Haifa Bennour
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Saoussen Abroug
- Pediatric Unit, Sahloul University Hospital, Sousse, Tunisia
| | - Monia Khlifa
- Pediatric Unit, Regional Hospital of Msaken, Sousse, Tunisia
| | - Jihen Mathlouthi
- Neonatology Unit, University Hospital Farhat Hached, Sousse, Tunisia
| | - Nabiha Mahdhaoui
- Neonatology Unit, University Hospital Farhat Hached, Sousse, Tunisia
| | - Khedija Boussetta
- Paediatrics B Department, Children's Hospital of Tunis, Tunis, Tunisia
| | - Abdelhalim Trabelsi
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Research Laboratory for Epidemiology and Immunogenetics of Viral Infections (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
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Al-Hassinah S, Parveen S, Somily AM, AlSaadi MM, Alamery SF, Haq SH, Alsenaidy HA, Ahmed A. Evolutionary analysis of the ON1 genotype of subtype a respiratory syncytial virus in Riyadh during 2008-16. INFECTION GENETICS AND EVOLUTION 2019; 79:104153. [PMID: 31881360 DOI: 10.1016/j.meegid.2019.104153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/05/2019] [Accepted: 12/20/2019] [Indexed: 01/07/2023]
Abstract
Respiratory syncytial virus is a leading cause of acute respiratory tract infection (ARI) in children worldwide. Limited information is available on molecular epidemiology of respiratory syncytial virus (RSV) from Saudi Arabia. An attempt was made to identify and characterize RSV strains in nasopharyngeal aspirates collected from hospitalized symptomatic ARI pediatric patients with <5 years of age from Riyadh, Saudi Arabia during 2016. All the samples (n = 100) were tested for RSV by real time PCR. The RSV strains were characterized by sequencing of the second hypervariable region of G protein gene. The study sequences along with the previously reported strains from Saudi Arabia were assessed for mutational, glycosylation, phylogenetic, selection pressure and entropy analyses. Fifty percent of the nasopharyngeal aspirates were positive for RSV. The RSVA (72%) predominated as compared to RSVB (24%) during the study. The study RSVA strains (n = 29) clustered into NA1 and ON1 genotypes whereas all the RSVB sequences (n = 5) were in BA genotype by phylogenetic analysis. Interestingly, 97% of RSVA sequences (n =28) clustered into ON1 genotype with 72 bp duplication in the G protein gene. Numerous mutations, variable N-/O-glycosylation sites and purifying selections were observed in the ON1 genotype. Positive selection with high entropy value was observed for three codons in ON1 (247, 262 and 274 amino acids) indicating higher probability of variations at these positions. Our study shows the progressive emergence and predominance of the ON1 genotype in Riyadh, Saudi Arabia during 2008-16. ON1 genotype almost replaced the previously circulating RSVA strains in this region during this period. Contribution of host genetic and immune factors towards disease severity of the ON1 genotype needs to be investigated in future studies. RSV surveillance in future elaborate investigations are needed in this region to understand its disease burden, evolutionary trajectory and circulation dynamics warranting steps towards vaccine development.
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Affiliation(s)
- Sarah Al-Hassinah
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ali M Somily
- Department of Microbiology, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Muslim Mohammed AlSaadi
- Department of Pediatrics, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Salman Fareeh Alamery
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia; Centre of Excellence in Biotechnology Research, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Samina Haider Haq
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Anwar Ahmed
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia; Centre of Excellence in Biotechnology Research, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.
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Farrag MA, Amer HM, Aziz IM, Alsaleh AN, Almajhdi FN. The emergence of subgenotype ON-1 of Human orthopneumovirus type A in Riyadh, Saudi Arabia: A new episode of the virus epidemiological dynamic. J Med Virol 2019; 92:1133-1140. [PMID: 31777964 DOI: 10.1002/jmv.25643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/25/2019] [Indexed: 12/28/2022]
Abstract
Lower respiratory tract infections caused by Human orthopneumovirus are still a threat to the pediatric population worldwide. To date, the molecular epidemiology of the virus in Saudi Arabia has not been adequately charted. In this study, a total of 205 nasopharyngeal aspirate samples were collected from hospitalized children with lower respiratory tract symptoms during the winter seasons of 2014/15 and 2015/16. Human orthopneumovirus was detected in 89 (43.4%) samples, of which 56 (27.3%) were positive for type A and 33 (16.1%) were positive for type B viruses. The fragment that spans the two hypervariable regions (HVR1 and HVR2) of the G gene of Human orthopneumovirus A was amplified and sequenced. Sequence and phylogenetic analyses have revealed a genotype shift from NA1 to ON-1, which was prevalent during the winter seasons of 2007/08 and 2008/09. Based on the intergenotypic p-distance values, ON-1 was reclassified as a subgenotype of the most predominant genotype GA2. Three conserved N-glycosylation sites were observed in the HVR2 of Saudi ON-1 strains. The presence of a 23 amino acid duplicated region in ON-1 strains resulted in a higher number of O-glycosylation sites as compared to other genotypes. The data presented in this report outlined the replacement of NA1 and NA2 subgenotypes in Saudi Arabia with ON-1 within 7 to 8 years. The continuous evolution of Human orthopneumovirus through point mutations and nucleotide duplication may explain its ability to cause recurrent infections.
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Affiliation(s)
- Mohamed A Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Haitham M Amer
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Ibrahim M Aziz
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Asma N Alsaleh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Farrag MA, Hamed ME, Amer HM, Almajhdi FN. Epidemiology of respiratory viruses in Saudi Arabia: toward a complete picture. Arch Virol 2019; 164:1981-1996. [PMID: 31139937 PMCID: PMC7087236 DOI: 10.1007/s00705-019-04300-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
Acute lower respiratory tract infection is a major health problem that affects more than 15% of the total population of Saudi Arabia each year. Epidemiological studies conducted over the last three decades have indicated that viruses are responsible for the majority of these infections. The epidemiology of respiratory viruses in Saudi Arabia is proposed to be affected mainly by the presence and mobility of large numbers of foreign workers and the gathering of millions of Muslims in Mecca during the Hajj and Umrah seasons. Knowledge concerning the epidemiology, circulation pattern, and evolutionary kinetics of respiratory viruses in Saudi Arabia are scant, with the available literature being inconsistent. This review summarizes the available data on the epidemiology and evolution of respiratory viruses. The demographic features associated with Middle East respiratory syndrome-related coronavirus infections are specifically analyzed for a better understanding of the epidemiology of this virus. The data support the view that continuous entry and exit of pilgrims and foreign workers with different ethnicities and socioeconomic backgrounds in Saudi Arabia is the most likely vehicle for global dissemination of respiratory viruses and for the emergence of new viruses (or virus variants) capable of greater dissemination.
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Affiliation(s)
- Mohamed A Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455QA6, Riyadh, 11451, Saudi Arabia
| | - Maaweya E Hamed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455QA6, Riyadh, 11451, Saudi Arabia
| | - Haitham M Amer
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455QA6, Riyadh, 11451, Saudi Arabia.
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Co-Circulation of 72bp Duplication Group A and 60bp Duplication Group B Respiratory Syncytial Virus (RSV) Strains in Riyadh, Saudi Arabia during 2014. PLoS One 2016; 11:e0166145. [PMID: 27835664 PMCID: PMC5106011 DOI: 10.1371/journal.pone.0166145] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/23/2016] [Indexed: 01/10/2023] Open
Abstract
Respiratory syncytial virus (RSV) is an important viral pathogen of acute respiratory tract infection (ARI). Limited data are available on molecular epidemiology of RSV from Saudi Arabia. A total of 130 nasopharyngeal aspirates were collected from children less than 5 years of age with ARI symptoms attending the Emergency Department at King Khalid University Hospital and King Fahad Medical City, Riyadh, Saudi Arabia between October and December, 2014. RSV was identified in the 26% of the hospitalized children by reverse transcriptase PCR. Group A RSV (77%) predominated during the study as compared to group B RSV (23%). The phylogenetic analysis of 28 study strains clustered group A RSV in NA1 and ON1 genotypes and group B viruses in BA (BA9) genotype. Interestingly, 26% of the positive samples clustered in genotypes with duplication in the G protein gene (ON1 for group A and BA for group B). Both the genotypes showed enhanced O-linked glycosylation in the duplicated region, with 10 and 2 additional sites in ON1 and BA respectively. Selection pressure analysis revealed purifying selection in both the ON1 and BA genotypes. One codon each in the ON1 (position 274) and BA genotypes (position 219) were positively selected and had high entropy values indicating variations at these amino acid positions. This is the first report describing the presence of ON1 genotype and the first report on co-circulation of two different genotypes of RSV with duplication in the G protein gene from Saudi Arabia. The clinical implications of the simultaneous occurrence of genotypes with duplication in G protein gene in a given population especially in the concurrent infections should be investigated in future. Further, the ongoing surveillance of RSV in this region will reveal the evolutionary trajectory of these two genotypes with duplication in G protein gene from largest country in the Middle East.
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11
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Malasao R, Okamoto M, Chaimongkol N, Imamura T, Tohma K, Dapat I, Dapat C, Suzuki A, Saito M, Saito M, Tamaki R, Pedrera-Rico GAG, Aniceto R, Quicho RFN, Segubre-Mercado E, Lupisan S, Oshitani H. Molecular Characterization of Human Respiratory Syncytial Virus in the Philippines, 2012-2013. PLoS One 2015; 10:e0142192. [PMID: 26540236 PMCID: PMC4635013 DOI: 10.1371/journal.pone.0142192] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/19/2015] [Indexed: 12/12/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of acute lower respiratory tract infections in infants and children worldwide. We performed molecular analysis of HRSV among infants and children with clinical diagnosis of severe pneumonia in four study sites in the Philippines, including Biliran, Leyte, Palawan, and Metro Manila from June 2012 to July 2013. Nasopharyngeal swabs were collected and screened for HRSV using real-time polymerase chain reaction (PCR). Positive samples were tested by conventional PCR and sequenced for the second hypervariable region (2nd HVR) of the G gene. Among a total of 1,505 samples, 423 samples were positive for HRSV (28.1%), of which 305 (72.1%) and 118 (27.9%) were identified as HRSV-A and HRSV-B, respectively. Two genotypes of HRSV-A, NA1 and ON1, were identified during the study period. The novel ON1 genotype with a 72-nucleotide duplication in 2nd HVR of the G gene increased rapidly and finally became the predominant genotype in 2013 with an evolutionary rate higher than the NA1 genotype. Moreover, in the ON1 genotype, we found positive selection at amino acid position 274 (p<0.05) and massive O- and N-glycosylation in the 2nd HVR of the G gene. Among HRSV-B, BA9 was the predominant genotype circulating in the Philippines. However, two sporadic cases of GB2 genotype were found, which might share a common ancestor with other Asian strains. These findings suggest that HRSV is an important cause of severe acute respiratory infection among children in the Philippines and revealed the emergence and subsequent predominance of the ON1 genotype and the sporadic detection of the GB2 genotype. Both genotypes were detected for the first time in the Philippines.
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Affiliation(s)
| | - Michiko Okamoto
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | | | - Kentaro Tohma
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Isolde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Clyde Dapat
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akira Suzuki
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mayuko Saito
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, Philippines
| | - Raita Tamaki
- Tohoku-RITM Collaborating Research Center on Emerging and Reemerging Diseases, Muntinlupa City, Philippines
| | | | - Rapunzel Aniceto
- Eastern Visayas Regional Medical Center, Tacloban City, Philippines
| | | | | | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, Philippines
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Retrospective phylogenetic analysis of circulating BA genotype of human respiratory syncytial virus with 60 bp duplication from New Delhi, India during 2007-2010. Virusdisease 2015; 26:276-281. [PMID: 26645038 DOI: 10.1007/s13337-015-0283-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022] Open
Abstract
Human respiratory syncytial virus (hRSV) is the most common viral pathogen of acute lower respiratory tract infection in infants and young children. The G protein of hRSV is the trans-membrane glycoprotein that is involved in the attachment of virion with the host cell. The nasopharyngeal aspirates were subjected to RT-PCR for the second hypervariable region of the G protein gene in the present investigation. Sequencing and phylogenetic analysis revealed that all the study strains clustered within the BA genotype. The study sequences further clustered in BA-9, BA-7, BA-10 and BA-12 subgroups within the BA genotype. The G proteins of the study sequences were predicted to encode 312 and 319 amino acids. Three different N-linked glycosylation sites were observed in the deduced 93-100 amino acid region. There were 40-43 serine and threonine residues that are the potential O-linked glycosylation sites. The non-synonymous/synonymous (dN/dS) ratio was less than one indicating negative selection pressure for amino acid change in the analyzed region of the G protein. The present investigation provides information on circulating strains of BA genotype from New Delhi, India. Further elaborate investigations of the BA viruses from different regions of the world will establish the basis of the rapid global spread and evolutionary pattern of this expanding genotype.
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Gimferrer L, Andrés C, Campins M, Codina MG, Rodrigo JA, Melendo S, Martin MC, Fuentes F, Saiz MR, Esperalba J, Bruguera A, Vilca LM, Armadans L, Pumarola T, Antón A. Circulation of a novel human respiratory syncytial virus Group B genotype during the 2014-2015 season in Catalonia (Spain). Clin Microbiol Infect 2015; 22:97.e5-97.e8. [PMID: 26408279 DOI: 10.1016/j.cmi.2015.09.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/11/2015] [Indexed: 10/23/2022]
Abstract
Human respiratory syncytial virus (HRSV) is one of the most common viral aetiological agents in the youngest population. In the present study a novel HRSV-B BA genotype is first described based on the phylogenetic analysis of the coding hypervariable region 2 sequences of G protein from strains detected during the 2014-2015 season. Among all strains detected in the last season, 44% belonged to this new genotype. Therefore, it highlights the importance of a continuous HRSV surveillance to monitor the emergence and spread of new genotypes or variants with genetic changes that may affect antigenic and tropism features.
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Affiliation(s)
- L Gimferrer
- Virology Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - C Andrés
- Virology Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M Campins
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M G Codina
- Virology Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J A Rodrigo
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - S Melendo
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M C Martin
- Virology Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - F Fuentes
- Virology Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M R Saiz
- Virology Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Esperalba
- Virology Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - A Bruguera
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - L M Vilca
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - L Armadans
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - T Pumarola
- Virology Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - A Antón
- Virology Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain.
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Functional Analysis of the 60-Nucleotide Duplication in the Respiratory Syncytial Virus Buenos Aires Strain Attachment Glycoprotein. J Virol 2015; 89:8258-66. [PMID: 26018171 DOI: 10.1128/jvi.01045-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/25/2015] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED There are two subgroups of respiratory syncytial virus (RSV), A and B, and within each subgroup, isolates are further divided into clades. Several years ago, multiple subgroup B isolates which contained a duplication of 60 nucleotides in the glycoprotein (G) gene were described. These isolates were given a new clade designation of BA based on the site of isolation, Buenos Aires, Argentina. BA RSV strains have since become the predominant circulating clade of RSV B viruses. We hypothesized that the duplicated region in G serves to enhance the function of G in the virus life cycle. We generated recombinant viruses that express a consensus BA G gene or a consensus BA G gene lacking the duplication (GΔdup). We determined that the duplicated region functions during virus attachment to cells. Additionally, we showed that in vitro, the virus containing the duplication has a fitness advantage compared to the virus without the duplication. Our data demonstrate that the duplicated region in the BA strain G protein augments virus attachment and fitness. IMPORTANCE Respiratory syncytial virus (RSV) is an important pathogen for infants for which there is no vaccine. Different strains of RSV circulate from year to year, and the predominating strains change over time. Subgroup B RSV strains with a duplication in the attachment glycoprotein (G) emerged and then became the dominant B genotype. We found that a recombinant virus harboring the duplication bound more efficiently to cells and was more fit than a recombinant strain lacking the duplication. Our work advances a mechanism for an important natural RSV mutation.
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