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Hou M, Liu G, Meng C, Dong L, Fang Y, Wang L, Wang N, Cai C, Wang H. Circulation patterns and molecular characteristics of respiratory syncytial virus among hospitalized children in Tianjin, China, before and during the COVID-19 pandemic (2017-2022). Virol Sin 2024:S1995-820X(24)00114-7. [PMID: 39067791 DOI: 10.1016/j.virs.2024.07.004] [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: 10/25/2023] [Accepted: 07/24/2024] [Indexed: 07/30/2024] Open
Abstract
Respiratory syncytial virus (RSV) is the main pathogen that causes hospitalization for acute lower respiratory tract infections (ALRIs) in children. With the reopening of communities and schools, the resurgence of RSV in the COVID-19 post-pandemic era has become a major concern. To understand the circulation patterns and genotype variability of RSV in Tianjin before and during the COVID-19 pandemic, a total of 19,531 nasopharyngeal aspirate samples from hospitalized children in Tianjin from July 2017 to June 2022 were evaluated. Direct immunofluorescence and polymerase chain reaction (PCR) were used for screening RSV-positive samples and subtyping, respectively. Further analysis of mutations in the second hypervariable region (HVR2) of the G gene was performed through Sanger sequencing. Our results showed that 16.46% (3,215/19,531) samples were RSV positive and a delayed increase in the RSV infection rates occurred in the winter season from December 2020 to February 2021, with the average RSV-positive rate of 35.77% (519/1,451). The ON1, with H258Q and H266L substitutions, and the BA9, with T290I and T312I substitutions, are dominant strains that alternately circulate every 1-2 years in Tianjin, China, from July 2017 to June 2022. In addition, novel substitutions, such as N296Y, K221T, N230K, V251A in the BA9 genotype, and L226I in the ON1 genotype, emerged during the COVID-19 pandemic. Analysis of clinical characteristics indicated no significant differences between RSV-A and RSV-B groups. This study provides a theoretical basis for clinical prevention and treatment. However, further studies are needed to explore the regulatory mechanism of host immune responses to different lineages of ON1 and BA9 in the future.
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Affiliation(s)
- Mengzhu Hou
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Guangping Liu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Chao Meng
- Department of Medical Laboratory, Tianjin Second People's Hospital, Tianjin, 300192, China
| | - Lili Dong
- Department of Respiratory, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, 300134, China
| | - Yulian Fang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Lu Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Ning Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China.
| | - Hanjie Wang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China.
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Haider SA, Jamal Z, Tahir F, Salman M, Umair M. Genomic characterization of human respiratory syncytial virus circulating in Islamabad, Pakistan, during an outbreak in 2022-2023. Arch Virol 2024; 169:106. [PMID: 38644429 DOI: 10.1007/s00705-024-06036-0] [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: 11/27/2023] [Accepted: 02/26/2024] [Indexed: 04/23/2024]
Abstract
In this study, conducted at the National Institute of Health, Islamabad, during an outbreak of human respiratory syncytial virus (hRSV) from December 2022 to January 2023, the first whole-genome sequences of hRSV isolates from Islamabad, Pakistan, were determined. Out of 10 positive samples, five were sequenced, revealing the presence of two genotypes: RSV-A (GA2.3.5, ON1 strain) and RSV-B (GB5.0.5.a, BA-10 strain). A rare non-synonymous substitution (E232G) in G the protein and N276S in the F protein were found in RSV-A. In RSV-B, the unique mutations K191R, Q209R, and I206M were found in the F protein. These mutations could potentially influence vaccine efficacy and viral pathogenicity. This research underscores the importance of genomic surveillance for understanding RSV diversity and guiding public health responses in Pakistan.
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Affiliation(s)
- Syed Adnan Haider
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan
| | - Zunera Jamal
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan
| | - Faheem Tahir
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan
| | - Massab Umair
- Department of Virology, National Institute of Health, Park Rd, Chak Shahzad, Islamabad, 45500, Pakistan.
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3
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Ono T, Hashimoto K, Kume Y, Chishiki M, Okabe H, Sato M, Norito S, Aso J, Sada M, Mochizuki I, Mashiyama F, Ishibashi N, Suzuki S, Sakuma H, Suwa R, Kawase M, Takeda M, Shirato K, Kimura H, Hosoya M. Molecular Diversity of Human Respiratory Syncytial Virus before and during the COVID-19 Pandemic in Two Neighboring Japanese Cities. Microbiol Spectr 2023; 11:e0260622. [PMID: 37409937 PMCID: PMC10433803 DOI: 10.1128/spectrum.02606-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Human respiratory syncytial viruses (HRSVs) are divided into subgroups A and B, which are further divided based on the nucleotide sequence of the second hypervariable region (HVR) of the attachment glycoprotein (G) gene. Understanding the molecular diversity of HRSV before and during the coronavirus disease 2019 (COVID-19) pandemic can provide insights into the effects of the pandemic on HRSV dissemination and guide vaccine development. Here, we analyzed HRSVs isolated in Fukushima Prefecture from September 2017 to December 2021. Specimens from pediatric patients were collected at two medical institutions in neighboring cities. A phylogenetic tree based on the second HVR nucleotide sequences was constructed using the Bayesian Markov chain Monte Carlo method. HRSV-A (ON1 genotype) and HRSV-B (BA9 genotype) were detected in 183 and 108 specimens, respectively. There were differences in the number of HRSV strains within clusters prevalent at the same time between the two hospitals. The genetic characteristics of HRSVs in 2021 after the COVID-19 outbreak were similar to those in 2019. HRSVs within a cluster may circulate within a region for several years, causing an epidemic cycle. Our findings add to the existing knowledge of the molecular epidemiology of HRSV in Japan. IMPORTANCE Understanding the molecular diversity of human respiratory syncytial viruses during pandemics caused by different viruses can provide insights that can guide public health decisions and vaccine development.
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Affiliation(s)
- Takashi Ono
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Yohei Kume
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Hisao Okabe
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Masatoki Sato
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Jumpei Aso
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Mitsuru Sada
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Izumi Mochizuki
- Department of Pediatrics, Ohara General Hospital, Fukushima, Fukushima, Japan
| | - Fumi Mashiyama
- Department of Pediatrics, Hoshi General Hospital, Koriyama, Fukushima, Japan
| | - Naohisa Ishibashi
- Department of Pediatrics, Ohara General Hospital, Fukushima, Fukushima, Japan
| | - Shigeo Suzuki
- Department of Pediatrics, Ohara General Hospital, Fukushima, Fukushima, Japan
| | - Hiroko Sakuma
- Department of Pediatrics, Hoshi General Hospital, Koriyama, Fukushima, Japan
| | - Reiko Suwa
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Miyuki Kawase
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Takeda
- Department of Microbiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuya Shirato
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Gunma Paz University, Graduate School of Health Sciences, Takasaki, Gunma, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
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Anandhan G, Narkhede YB, Mohan M, Paramasivam P. Immunoinformatics aided approach for predicting potent cytotoxic T cell epitopes of respiratory syncytial virus. J Biomol Struct Dyn 2023; 41:12093-12105. [PMID: 36935101 DOI: 10.1080/07391102.2023.2191136] [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: 10/18/2022] [Accepted: 12/27/2022] [Indexed: 03/21/2023]
Abstract
Respiratory syncytial virus (RSV) is an infectious viral pathogen that causing serious respiratory infection in adults and neonates. The only approved therapies for RSV are the monoclonal antibodies palivizumab and its derivative motavizumab. Both treatments are expensive and require a hospital setting for administration. A vaccine represents a safe, effective and cheaper alternative for preventing RSV infection. In silico prediction methods have proven to be valuable in speeding up the process of vaccine design. In this study, reverse vaccinology methods were used to predict the cytotoxic T lymphocytes (CTL) epitopes from the entire proteome of RSV strain A. From amongst 3402 predicted binders to 12 high frequency alleles from the Immune Epitope Database (IEDB), 567 had positive processing scores while 327 epitopes were predicted to be immunogenic. A thorough examination of the 327 epitopes for possible antigenicity, allergenicity and toxicity resulted in 95 epitopes with desirable properties. A BLASTp analysis revealed 94 unique and non-homologous epitopes that were subjected to molecular docking across the 12 high frequency alleles. The final dataset of 70 epitopes contained 13 experimentally proven and 57 unique epitopes from a total of 11 RSV proteins. From our findings on selected T-cell-specific RSV antigen epitopes, notably the four epitopes confirmed to exhibit stable binding by molecular dynamics. The prediction pipeline used in this study represents an effective way to screen the immunogenic epitopes from other pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gayathri Anandhan
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, USA
- Vaxigen International Research Center, Coimbatore, Tamil Nadu, India
| | - Premasudha Paramasivam
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, Tamil Nadu, India
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5
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Klivleyeva N, Lukmanova G, Glebova T, Shamenova M, Ongarbayeva N, Saktaganov N, Baimukhametova A, Baiseiit S, Ismagulova D, Kassymova G, Rachimbayeva A, Murzagaliyeva A, Xetayeva G, Isabayeva R, Sagatova M. Spread of Pathogens Causing Respiratory Viral Diseases Before and During CoVID-19 Pandemic in Kazakhstan. Indian J Microbiol 2023; 63:129-138. [PMID: 37168842 PMCID: PMC9972336 DOI: 10.1007/s12088-023-01064-x] [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: 09/22/2022] [Accepted: 02/11/2023] [Indexed: 03/06/2023] Open
Abstract
Analyze clinical samples collected and determine the etiology of viral pathogens and the dynamics of their spread. Acute respiratory viral infections remain one of the key health problems worldwide. They constitute etiologically independent diseases, with similar clinical infection manifestations and a single mechanism for the transmission of pathogens. 4712 nasopharyngeal swabs were collected from people before and during the COVID-19 pandemic with acute respiratory infections that tested negative for COVID-19 and were examined in this study. The collected samples were screened by a real-time polymerase chain reaction on a Rotor-Gene Q6 plex instrument. Statistical processing of the results, tabular, and graphical data were analyzed in the MS Excel. The largest number of the nasopharyngeal swabs were collected from children under 17 years of age (60.75%). In 702 samples (9.85%) pathogens of respiratory infections of non-influenza etiology were detected, including adenovirus, bocavirus, coronavirus, metapneumovirus, paramyxovirus types I–IV, respiratory syncytial virus, and rhinovirus. At the same time, both before and during the COVID-19 pandemic, different influenza virus variants co-circulation (A/H1N1, A/H3N2, and type B) were discovered, with a predominance of viruses with the antigenic formula A/H1N1. The results of the study indicate the need for continuous monitoring of the viral pathogens spread, which will expand the existing knowledge of the viral etiology of respiratory diseases and highlight the importance of viruses in the respiratory infections occurrence.
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Affiliation(s)
- Nailya Klivleyeva
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Galina Lukmanova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Tatyana Glebova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Mira Shamenova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Nuray Ongarbayeva
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Nurbol Saktaganov
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Assem Baimukhametova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Sagadat Baiseiit
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Dariya Ismagulova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | | | - Almagul Rachimbayeva
- The Almaty Branch of National Center for Expertise, 3 Zhibek Zholy Avenue, Almaty, Kazakhstan
| | - Ardak Murzagaliyeva
- The West Kazakhstan Marat Ospanov Medical University, 68 Maresyev Street, Aktobe, Kazakhstan
| | - Gulzakira Xetayeva
- The Children’s City Clinical Infectious Diseases Hospital, SOPE On REM, ChCCIDH, 299a Baizakova Street, Almaty, Kazakhstan
| | - Rauna Isabayeva
- The Communal State Enterprise Regional Region Clinical Hospital (CSE RCH) of Karaganda Regional Health Department, 41/43 Erubaev Street, Karaganda, Kazakhstan
| | - Madisha Sagatova
- The East Kazakhstan Regional Branch of National Center for Expertise, 17 Independence Avenue, Ust-Kamenogorsk, Kazakhstan
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6
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Chen X, Zhu Y, Wang W, Li C, An S, Lu G, Jin R, Xu B, Zhou Y, Chen A, Li L, Zhang M, Xie Z. A multi-center study on Molecular Epidemiology of Human Respiratory Syncytial Virus from Children with Acute Lower Respiratory Tract Infections in the Mainland of China between 2015 and 2019. Virol Sin 2021; 36:1475-1483. [PMID: 34398429 PMCID: PMC8365132 DOI: 10.1007/s12250-021-00430-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/18/2021] [Indexed: 11/25/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is a major pathogen of acute lower respiratory tract infection among young children. To investigate the prevalence and genetic characteristics of RSV in China, we performed a molecular epidemiological study during 2015-2019. A total of 964 RSV-positive specimens were identified from 5529 enrolled patients during a multi-center study. RSV subgroup A (RSV-A) was the predominant subgroup during this research period except in 2016. Totally, 535 sequences of the second hypervariable region (HVR-2) of the G gene were obtained. Combined with 182 Chinese sequences from GenBank, phylogenetic trees showed that 521 RSV-A sequences fell in genotypes ON1 (512), NA1 (6) and GA5 (3), respectively; while 196 RSV-B sequences fell in BA9 (193) and SAB4 (3). ON1 and BA9 were the only genotypes after December 2015. Genotypes ON1 and BA9 can be separated into 10 and 7 lineages, respectively. The HVR-2 of genotype ON1 had six amino acid changes with a frequency more than 10%, while two substitutions H258Q and H266L were co-occurrences. The HVR-2 of genotype BA9 had nine amino acid substitutions with a frequency more than 10%, while the sequences with T290I and T312I were all from 2018 to 2019. One N-glycosylation site at 237 was identified among ON1 sequences, while two N-glycosylation sites (296 and 310) were identified in the 60-nucleotide duplication region of BA9. To conclusion, ON1 and BA9 were the predominant genotypes in China during 2015-2019. For the genotypes ON1 and BA9, the G gene exhibited relatively high diversity and evolved continuously.
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Affiliation(s)
- Xiangpeng Chen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wei Wang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Changchong Li
- The 2nd Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Shuhua An
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Gen Lu
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Rong Jin
- Guiyang Maternal and Child Health Hospital, Guiyang, 550003, China
| | - Baoping Xu
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 10045, China
| | - Yunlian Zhou
- The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Aihuan Chen
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Lei Li
- Yinchuan Maternal and Child Health Care Hospital, Yinchuan, 750001, China
| | - Meng Zhang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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7
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Next-generation sequencing of human respiratory syncytial virus subgroups A and B genomes. J Virol Methods 2021; 299:114335. [PMID: 34673119 DOI: 10.1016/j.jviromet.2021.114335] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/17/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022]
Abstract
Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Whole genome sequencing of HRSV offers enhanced resolution of strain variability for epidemiological surveillance and provides genomic information essential for antiviral and vaccine development. A 10-amplicon one-step RT-PCR assay and a 20-amplicon nested RT-PCR assay with enhanced sensitivity were developed to amplify whole HRSV genomes from samples containing high and low viral loads, respectively. Ninety-six HRSV-positive samples comprised of 58 clinical specimens and 38 virus isolates with Ct values ≤ 24 were amplified successfully using the 10-amplicon one-step RT-PCR method and multiplexed in a single MiSeq run. Genome coverage exceeded 99.3% for all 96 samples. The 20-amplicon nested RT-PCR NGS method was used to generate >99.6% HRSV full-length genome for 72 clinical specimens with Ct values ranging from 24 to 33. Phylogenetic analysis of the genome sequences obtained from the 130 clinical specimens revealed a wide diversity of HRSV genotypes demonstrating methodologic robustness.
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8
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Yu JM, Fu YH, Peng XL, Zheng YP, He JS. Genetic diversity and molecular evolution of human respiratory syncytial virus A and B. Sci Rep 2021; 11:12941. [PMID: 34155268 PMCID: PMC8217232 DOI: 10.1038/s41598-021-92435-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023] Open
Abstract
Human respiratory syncytial viruses (RSVs) are classified into two major groups (A and B) based on antigenic differences in the G glycoprotein. To investigate circulating characteristics and phylodynamic history of RSV, we analyzed the genetic variability and evolutionary pattern of RSVs from 1977 to 2019 in this study. The results revealed that there was no recombination event of intergroup. Single nucleotide polymorphisms (SNPs) were observed through the genome with the highest occurrence rate in the G gene. Five and six sites in G protein of RSV-A and RSV-B, respectively, were further identified with a strong positive selection. The mean evolutionary rates for RSV-A and -B were estimated to be 1.48 × 10–3 and 1.92 × 10–3 nucleotide substitutions/site/year, respectively. The Bayesian skyline plot showed a constant population size of RSV-A and a sharp expansion of population size of RSV-B since 2005, and an obvious decrease 5 years later, then became stable again. The total population size of RSVs showed a similar tendency to that of RSV-B. Time-scaled phylogeny suggested a temporal specificity of the RSV-genotypes. Monitoring nucleotide changes and analyzing evolution pattern for RSVs could give valuable insights for vaccine and therapy strategies against RSV infection.
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Affiliation(s)
- Jie-Mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yuan-Hui Fu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Xiang-Lei Peng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yan-Peng Zheng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Jin-Sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.
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9
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The burden of Respiratory Syncytial Virus (RSV) infection in the Middle East and North Africa (MENA) region across age groups: A systematic review. Vaccine 2021; 39:3803-3813. [PMID: 34099329 DOI: 10.1016/j.vaccine.2021.05.076] [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: 02/17/2021] [Revised: 05/02/2021] [Accepted: 05/21/2021] [Indexed: 11/22/2022]
Abstract
Respiratory Syncytial Virus (RSV) is a common respiratory virus that generally causes a mild illness in children and adults or severe symptoms with complications in infants and the elderly, particularly in the presence of underlying comorbidities. While epidemiological data about this virus are available globally, data from the Middle East and North Africa (MENA) region are still scarce. For this reason, we conducted a systematic review to determine the burden of RSV disease in the MENA region by searching the available literature up until September 2018. A total of 1242 studies were retrieved of which 90 were included in the review. Most of the included studies were conducted in subjects aged 0-18 years with the majority being in children below 3 years of age, while only 2 studies included exclusively adults above 18 years of age. RSV infection rates varied greatly between different studies on hospitalized subjects and ranged between 4% and 82%, while the range was smaller in studies on outpatient subjects (between 6% and 36%). When calculating the RSV infection rates in the hospitalized subjects with different inclusion criteria, we found that it was 19%, 70%, and 33% among subjects admitted with Acute Respiratory Infections (ARIs), Acute Lower Respiratory Infections (ALRIs), and bronchiolitis, respectively. RSV infections were most common during the winter season. With regards to complications, intensive care unit admissions ranged between 1% and 15%, while the need for mechanical ventilation ranged between 1% and 10%. The overall RSV related mortality rate across all age groups in studies included in our review was 1.9%. This review identifies several limitations in the existing data and under-representation of the adult population. Future studies should be providing more evidence on the RSV burden in adults and children with comorbidities in order to better assess the potential impact of future preventive strategies in the MENA region.
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10
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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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Morse SS, Qureshi H. Acute respiratory infections in the WHO Eastern Mediterranean Region: Time to get better data to guide better preparedness. J Infect Public Health 2020; 13:375-376. [PMID: 32164979 DOI: 10.1016/j.jiph.2020.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
| | - Huma Qureshi
- Pakistan Health Research Council, Islamabad, Pakistan
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Li W, Wu K, Liu Y, Yang Y, Wang W, Li X, Zhang Y, Zhang Q, Zhou R, Tang H. Molecular cloning of SLC35D3 and analysis of its role during porcine intramuscular preadipocyte differentiation. BMC Genet 2020; 21:20. [PMID: 32087688 PMCID: PMC7036214 DOI: 10.1186/s12863-020-0822-0] [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: 10/18/2018] [Accepted: 02/04/2020] [Indexed: 11/10/2022] Open
Abstract
Background Solute carrier family 35 (SLC35) is one of a large number of membrane transporter protein families. Member D3 of this family is thought to be involved in adipose deposition and metabolic control. Results We obtained 2238 bp cDNA of porcine SLC35D3, it contains a 1272 bp ORF, encoding a 423 amino acid polypeptide, and a 966 bp 3′ UTR. BLAST results revealed that the amino acid sequence of porcine SLC35D3 had the closest phylogenetic relationship with members of the genus Ovis aries. Further bioinformatics analysis showed that the SLC35D3 protein contains 8 transmembrane domains, and that there is no signal peptide structure. The secondary structure of the protein mainly contains 37.12% α-helixes, 7.8% in β-folds, and 33.57% random coils. mRNA expression analysis showed that SLC35D3 is expressed in lung, liver, heart, spleen, kidney, longissimus dorsi muscle (LDM), leaf fat (LF), and subcutaneous adipose tissue (SAT). To examine the effects of SLC35D3 expression on fat synthesis and catabolism, SLC35D3-siRNA was transfected into cultured intramuscular adipocytes. SLC35D3 silenced cells showed increased expression of genes related to fat synthesis, and increased deposition of intramuscular fat (IMF), abundance of lipid droplets, and the level of free fatty acid (FFA) in the culture medium. In contrast, the siRNA decreased the expression genes involved in fat catabolism. Conclusions Our results demonstrate that silenced SLC35D3 results in increased adipogenic processes in pig intramuscular adipocytes. These data represent the first exploration of SLC35D3 expression in swine, and provide valuable insights into the functions of SLC35D3 in adipocyte differentiation.
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Affiliation(s)
- Wentong Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, 271018, People's Republic of China.,The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Keliang Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Ying Liu
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Yalan Yang
- School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China
| | - Wenwen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, 271018, People's Republic of China
| | - Xiuxiu Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, 271018, People's Republic of China
| | - Yanmin Zhang
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, 271018, People's Republic of China
| | - Rong Zhou
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Hui Tang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, 271018, People's Republic of China.
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Zhao T, Ye Z, Wang B, Cui Y, Nie Y, Yang B, Chen K, Zhang H, Hu F, Yu F. Virus isolation and genotype identification of human respiratory syncytial virus in Guizhou Province, China. Braz J Infect Dis 2019; 23:427-434. [PMID: 31734172 PMCID: PMC9428243 DOI: 10.1016/j.bjid.2019.10.007] [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: 06/24/2019] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 11/30/2022] Open
Abstract
To investigate the genetic variation and molecular epidemiology characteristics of Human Respiratory Syncytial Virus (HRSV) in Guizhou Province, nasopharyngeal aspirates were collected from patients with acute respiratory infection (ARI) in Guizhou Provincial People's Hospital, from December 2017 to March 2018, and inoculated to Hep-2 cells to isolate HRSV. Cells that showed cytopathic effect (CPE) were then confirmed by indirect immunofluorescence assay and reverse transcription. The sequence of the PCR products was determined for HRSV isolates, and the genetic variation was analyzed. Out of 196 nasopharyngeal aspirate samples, HRSV were isolated in 39. The second hypervariable region at the 3′ terminal of glycoprotein gene (HVR2) sequence analysis showed that subgroup A was dominant. Seventy-nine percent of the isolates belonged to subgroup A, ON1 genotype, and 21 % belonged to subgroup B, BA9 genotype, which indicates that the dominant HRSV circulating in Guizhou Province was subgroup A, genotype ON1, co-circulating with a less prevalent subgroup B, genotype BA9.
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Affiliation(s)
- Ting Zhao
- Guizhou University, Medical College, Guiyang, China; Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina.
| | - Zhixu Ye
- Guizhou University, Guizhou Provincial People's Hospital, Department of Pediatrics, Guiyang, China; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
| | - Binlin Wang
- People's Hospital of QianNan, Department of Clinical Labotatory, Guizhou Province, China
| | - Yuxia Cui
- Guizhou University, Guizhou Provincial People's Hospital, Department of Pediatrics, Guiyang, China
| | - Yingjie Nie
- Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
| | - Bin Yang
- Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
| | - Kun Chen
- Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
| | - Hua Zhang
- Guizhou University, Guizhou Provincial People's Hospital, Department of Clinical Laboratory, Guiyang, China
| | - Fangfang Hu
- Guizhou University, Guizhou Provincial People's Hospital, Department of Clinical Laboratory, Guiyang, China
| | - Fuxun Yu
- Guizhou University, Guizhou Provincial People's Hospital, Department of Central Laboratory, GuiyangChina; Guizhou Provincial People's Hospital, NHC Key Laboratory of Pulmonary Immunological Diseases, Guiyang, China
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Epidemiology of respiratory syncytial virus infections in Chennai, south India. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2019. [DOI: 10.1016/j.cegh.2018.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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15
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Molecular characterization of circulating respiratory syncytial virus genotypes in Pakistani children, 2010-2013. J Infect Public Health 2019; 13:438-445. [PMID: 31229412 DOI: 10.1016/j.jiph.2019.05.014] [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: 09/13/2018] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Data on the viral etiology of acute lower respiratory infections are scarce in Pakistan. Human respiratory syncytial virus (RSV) is an important cause of morbidity in children but no effective vaccine or antiviral therapy is currently available. As vaccines are expected to become available in the future, it is important to understand the epidemiology of locally prevalent RSV subtypes. This study aimed to define the molecular epidemiology of RSV (A and B) genotypes in Pakistani children under 5 years. METHODS World Health Organization case definitions for influenza-like illness (ILI) and severe acute respiratory illness (SARI) were used for case selection. Children under 5 years who presented with ILI or SARI at tertiary care hospitals from all provinces/regions, including the eight influenza sentinel sites, during October-April each year between 2010 and 2013 were enrolled. Demographic and clinical data of the children were recorded and nasopharyngeal/throat swabs taken for analysis. All samples were tested for RSV A and B using real-time polymerase chain reaction for non-influenza respiratory viruses. Specific oligonucleotide primers for RSV A and B were used for subtyping and sequencing of the G protein, followed by phylogenetic analysis. RESULTS A total of 1941 samples were included. RSV was detected in 472 (24%) children, with RSV A detected in 367 (78%) and RSV B in 105 (22%). The G protein of all RSV A strains clustered in the NA1/GA2 genotype while RSV B strains carried the signature 60 nucleotide duplication and were assigned to three BA genotypes: BA-9, BA-10 and the new BA-13 genotype. CONCLUSIONS This study highlights the importance of RSV as a viral etiologic agent of acute respiratory infections in children in Pakistan, and the diversity of RSV viruses. Continued molecular surveillance for early detection of prevalent and newly emerging genotypes is needed to understand the epidemiology of RSV infections in Pakistan.
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Hindupur A, Menon T, Dhandapani P. Genetic diversity of human respiratory syncytial virus in children with acute respiratory infections in Chennai, South India. Indian J Med Microbiol 2019; 37:248-254. [PMID: 31745027 DOI: 10.4103/ijmm.ijmm_19_193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Introduction Human respiratory syncytial virus (HRSV) an RNA virus belonging to Pneumoviridae family, is an important cause of acute respiratory infections (ARIs) in young children. HRSV circulates as two subgroups A and B, which are further categorised into several genotypes. New genotypes may replace existing ones over successive epidemic seasons and multiple genotypes may cocirculate in the same community rendering it important to monitor them at the molecular level. The present study assessed the circulating genotypes of HRSV in Chennai. Materials and Methods Two hundred and sixty-seven children with ARI were recruited during the study from April 2016 to March 2018 for detecting HRSV A and B by real-time reverse transcription-polymerase chain reaction. Phylogeny and selection pressure analysis were done. Results Fifty-seven of the 267 samples (21.3%) were positive for HRSV, of which 7.1% and 14.2% were HRSV A and B, respectively, indicating that HRSV B was the major subgroup circulating in Chennai. Peak activity of HRSV was observed during the monsoon and winter months. Phylogenetic analysis of 2nd hypervariable region (HVR) of attachment glycoprotein gene (G gene) revealed that the HRSV A strains belonged to ON1 and HRSV B strains belonged to BA9 genotypes. Several unique amino acid substitutions were observed among the study strains. The Shannon entropy plot revealed that the HRSV A strains from our study have a high potential for amino acid substitutions in the 2nd HVR of G gene. Conclusion This study underlines the genetic diversity of HRSV and emphasises the need for continued molecular surveillance for infection management and prevention strategies.
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Affiliation(s)
- Anusha Hindupur
- Department of Microbiology, Dr. AL Mudaliar PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| | - Thangam Menon
- Department of Microbiology, Dr. AL Mudaliar PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| | - Prabu Dhandapani
- Department of Microbiology, Dr. AL Mudaliar PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
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Gimferrer L, Vila J, Piñana M, Andrés C, Rodrigo-Pendás JA, Peremiquel-Trillas P, Codina MG, C Martín MD, Esperalba J, Fuentes F, Rubio S, Campins-Martí M, Pumarola T, Antón A. Virological surveillance of human respiratory syncytial virus A and B at a tertiary hospital in Catalonia (Spain) during five consecutive seasons (2013-2018). Future Microbiol 2019; 14:373-381. [PMID: 30860397 DOI: 10.2217/fmb-2018-0261] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
AIM Human respiratory syncytial virus (HRSV) is the main cause of respiratory tract infections among infants. MATERIALS & METHODS In the present study, the molecular epidemiology of HRSV detected from 2013 to 2017 has been described. RESULTS A 10% of collected samples were laboratory confirmed for HRSV. Patients under 2 years of age were the main susceptible population to respiratory syncytial virus disease, but an increasingly number of confirmed patients over 65 years of age was reported. Epidemics usually started in autumn and ended in spring. Both HRSV groups co-circulated every season, but the HRSV-B was the most predominant. HRSV-A and HRSV-B strains mainly belonged to ON1 and BA9 genotypes, respectively. CONCLUSION The present study reports recent data about the genetic diversity of circulating HRSV in Spain.
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Affiliation(s)
- Laura Gimferrer
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jorgina Vila
- Paediatric Hospitalisation Unit, Department of Paediatrics, Hospital Universitari Maternoinfantil Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Piñana
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Cristina Andrés
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José A Rodrigo-Pendás
- Preventive Medicine & Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Paula Peremiquel-Trillas
- Preventive Medicine & Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María G Codina
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María Del C Martín
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juliana Esperalba
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francisco Fuentes
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Susana Rubio
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Magda Campins-Martí
- Preventive Medicine & Epidemiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Andrés Antón
- Respiratory Virus Unit, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
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Naz R, Gul A, Javed U, Urooj A, Amin S, Fatima Z. Etiology of acute viral respiratory infections common in Pakistan: A review. Rev Med Virol 2019; 29:e2024. [PMID: 30548740 PMCID: PMC7169323 DOI: 10.1002/rmv.2024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 01/22/2023]
Abstract
Respiratory infections, especially those of the lower respiratory tract, remain a foremost cause of mortality and morbidity of children greater than 5 years in developing countries including Pakistan. Ignoring these acute-level infections may lead to complications. Particularly in Pakistan, respiratory infections account for 20% to 30% of all deaths of children. Even though these infections are common, insufficiency of accessible data hinders development of a comprehensive summary of the problem. The purpose of this study was to determine the prevalence rate in various regions of Pakistan and also to recognize the existing viral strains responsible for viral respiratory infections through published data. Respiratory viruses are detected more frequently among rural dwellers in Pakistan. Lower tract infections are found to be more lethal. The associated pathogens comprise respiratory syncytial virus (RSV), human metapneumovirus (HMPV), coronavirus, enterovirus/rhinovirus, influenza virus, parainfluenza virus, adenovirus, and human bocavirus. RSV is more dominant and can be subtyped as RSV-A and RSV-B (BA-9, BA-10, and BA-13). Influenza A (H1N1, H5N1, H3N2, and H1N1pdm09) and Influenza B are common among the Pakistani population. Generally, these strains are detected in a seasonal pattern with a high incidence during spring and winter time. The data presented include pneumonia, bronchiolitis, and influenza. This paper aims to emphasise the need for standard methods to record the incidence and etiology of associated pathogens in order to provide effective treatment against viral infections of the respiratory tract and to reduce death rates.
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Affiliation(s)
- Riffat Naz
- Department of Bioinformatics and BiotechnologyInternational Islamic UniversityIslamabadPakistan
| | - Asma Gul
- Department of Bioinformatics and BiotechnologyInternational Islamic UniversityIslamabadPakistan
| | - Urooj Javed
- Department of Bioinformatics and BiotechnologyInternational Islamic UniversityIslamabadPakistan
| | - Alina Urooj
- Department of Bioinformatics and BiotechnologyInternational Islamic UniversityIslamabadPakistan
| | - Sidra Amin
- Department of Bioinformatics and BiotechnologyInternational Islamic UniversityIslamabadPakistan
| | - Zareen Fatima
- Department of Bioinformatics and BiotechnologyInternational Islamic UniversityIslamabadPakistan
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Obodai E, Odoom JK, Adiku T, Goka B, Wolff T, Biere B, Schweiger B, Reiche J. The significance of human respiratory syncytial virus (HRSV) in children from Ghana with acute lower respiratory tract infection: A molecular epidemiological analysis, 2006 and 2013-2014. PLoS One 2018; 13:e0203788. [PMID: 30199549 PMCID: PMC6130863 DOI: 10.1371/journal.pone.0203788] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/27/2018] [Indexed: 12/01/2022] Open
Abstract
Background Acute lower respiratory tract infection (ALRI) is a leading cause of childhood morbidity and mortality in developing countries. Globally, human respiratory syncytial virus (HRSV) is the most common pathogen of ALRI in infants and children. However, age-stratified HRSV disease burden data are largely absent from Africa, which is a key gap in informing an evidence-based recommendation for the introduction of an HRSV vaccine by the WHO. Methods This study investigated the presence of HRSV in respiratory specimens from 552 children <5 years old with ALRI from Accra, Ghana in 2006 and 2013–2014 by real-time PCR. Of HRSV-positive samples the second hypervariable region of the viral G protein gene was sequenced and analyzed for phylogeny, characteristic amino acid substitutions, and potential glycosylation patterns. Further, HRSV infections have been characterized by age, symptoms and timely occurrence. Results HRSV was observed in 23% (127/552) of the children with ALRI, with the highest incidence in infants younger than one year (33%, 97/295, p = 0.013). Within the observed seasonal circulation time of HRSV from June (mid-wet season) to December (beginning of the dry season) the incidence of ALRI due to HRSV was as high as 46% (125/273). HRSV disease was significantly associated with (broncho-) pneumonia, bronchiolitis, LRTI, and difficulty in breathing. Phylogenetic characterization of HRSV strains from Ghana identified the circulation of the currently worldwide prevailing genotypes ON1 and BA9, and shows evidence of an independent molecular evolution of ON1 and BA9 strains in Ghana resulting in potentially new subgenotypes within ON1 and BA9, provisionally named ON1.5, ON1.6, and BA9-IV. Conclusion This study addresses important knowledge gaps in the forefront of introducing the HRSV vaccine by providing information on the molecular evolution and incidence of HRSV in Accra (Ghana, Africa).
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Affiliation(s)
- Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
| | - John Kofi Odoom
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Theophilus Adiku
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Volta Region, Ghana
| | - Bamenla Goka
- Department of Child Health, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Thorsten Wolff
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Barbara Biere
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Brunhilde Schweiger
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Janine Reiche
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
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Okamoto M, Dapat CP, Sandagon AMD, Batangan-Nacion LP, Lirio IC, Tamaki R, Saito M, Saito-Obata M, Lupisan SP, Oshitani H. Molecular Characterization of Respiratory Syncytial Virus in Children With Repeated Infections With Subgroup B in the Philippines. J Infect Dis 2018; 218:1045-1053. [PMID: 29722817 PMCID: PMC6107742 DOI: 10.1093/infdis/jiy256] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/01/2018] [Indexed: 11/26/2022] Open
Abstract
Background Human respiratory syncytial virus (RSV) is the leading cause of severe acute respiratory infection in infants and young children, which is characterized by repeated infections. However, the role of amino acid substitutions in repeated infections remains unclear. Hence, this study aimed to elucidate the genetic characteristics of RSV in children with repeated infections using molecular analyses of F and G genes. Methods We conducted a cohort study of children younger than 5 years in the Philippines. We collected nasopharyngeal swabs from children with acute respiratory symptoms and compared F and G sequences between initial and subsequent RSV infections. Results We examined 1802 children from May 2014 to January 2016 and collected 3471 samples. Repeated infections were observed in 25 children, including 4 with homologous RSV-B reinfections. Viruses from the 4 pairs of homologous reinfections had amino acid substitutions in the G protein mostly at O-glycosylation sites, whereas changes in the F protein were identified at antigenic sites V (L173S) and θ (Q209K), considered essential epitopes for the prefusion conformation of the F protein. Conclusions Amino acid substitutions in G and F proteins of RSV-B might have led to antigenic changes, potentially contributing to homologous reinfections observed in this study.
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Affiliation(s)
- Michiko Okamoto
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Clyde P Dapat
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Ann Marie D Sandagon
- Tohoku-Research Institute for Tropical Medicine Collaborating Research Center on Emerging and Reemerging Infectious Diseases
| | | | - Irene C Lirio
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Raita Tamaki
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Mayuko Saito
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Mariko Saito-Obata
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Tohoku-Research Institute for Tropical Medicine Collaborating Research Center on Emerging and Reemerging Infectious Diseases
| | - Socorro P Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Hitoshi Oshitani
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
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Bayrakdar F, Kocabas CN, Altas AB, Kavuncuoglu HG, Cosgun Y, Mısırlıoglu ED, Durmaz I, Korukluoglu G, Ozkul A. Genetic variability human respiratory syncytial virus subgroups A and B in Turkey during six successive epidemic seasons, 2009-2015. J Med Virol 2017; 90:456-463. [PMID: 29077212 PMCID: PMC7166824 DOI: 10.1002/jmv.24983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/12/2017] [Indexed: 01/10/2023]
Abstract
Human respiratory syncytial virus (HRSV) is most important viral respiratory pathogen of acute lower respiratory tract infections in infants and young children worldwide. The circulating pattern and genetic characteristics in the HRSV attachment glycoprotein gene were investigated in Turkey during six consecutive seasons from 2009 to 2015. HRSVA was dominant in the all epidemic seasons except 2011‐2012 season. Partial sequences of the HVR2 region of the G gene of 479 HRSVA and 135 HRSVB were obtained. Most Turkish strains belonged to NA1, ON1, and BA9, which were the predominant genotypes circulating worldwide. Although three novel genotypes, TR‐A, TR‐BA1, and TR‐BA2, were identified, they were not predominant. Clinical data were available for 69 HRSV‐positive patients who were monitored due to acute lower respiratory tract illness. There were no significant differences in the clinical diagnosis, hospitalization rates, laboratory findings and treatment observed between the HRSVA and HRSVB groups, and co‐infections in this study. The major population afflicted by HRSV infections included infants and children between 13 and 24 months of age. We detected that the CB1, GB5, and THB strains clustered in the same branch with a bootstrap value of 100%. CB‐B and BA12 strains clustered in the same branch with a bootstrap value of 65%. The BA11 genotype was clustered in the BA9 genotype in our study. The present study may contribute on the molecular epidemiology of HRSV in Turkey and provide data for HRSV strains circulating in local communities and other regions worldwide.
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Affiliation(s)
- Fatma Bayrakdar
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Can Naci Kocabas
- Pediatric Immunology and Allergy Unit, Faculty of Medicine, Mugla Sitki Koçman Universty, Muğla, Turkey
| | - Ayse Basak Altas
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - H Gokhan Kavuncuoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Yasemin Cosgun
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Emine Dibek Mısırlıoglu
- Department of Pediatric Allergy and Immunology, Ankara Children's Hematology Oncology Training and Research Hospital, Ankara, Turkey
| | - Ihsan Durmaz
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Gulay Korukluoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Aykut Ozkul
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey
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A Virological and Phylogenetic Analysis of the Emergence of New Clades of Respiratory Syncytial Virus. Sci Rep 2017; 7:12232. [PMID: 28947776 PMCID: PMC5612963 DOI: 10.1038/s41598-017-12001-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/30/2017] [Indexed: 12/14/2022] Open
Abstract
The significant burden of Respiratory Syncytial Virus (RSV) in pediatric and elderly populations is well recognized. However, questions remain about transmission and evolution of RSV in the community, between seasons, and the role played by viral genetics in viral replication. Therefore, we integrated next generation sequencing, patient viral load, and viral replication analysis with surveillance of RSV to initiate a better understanding of viral adaptation in communities. RSV type-A and B infections were most closely related to RSV sequences from the USA and Asia, respectfully. The sample titres between RSV types-A and B were not significantly different. However, when the patient sample titre was compared to the phylogenetics of RSV, emergent clades were identified that we termed High Titre (HiT) clades of RSV. In conclusion, the correlation between patient viral load and replication kinetics of RSV patient isolates in culture indicated that viral genetics may determine virus replicative ability within patients. There was evolution or introduction of high-titre RSV type-A and B infections that seeded HiT clades in the subsequent year. Therefore, virological analysis of RSV isolates in conjunction with RSV phylogenetics may be a tool for predicting new clades of RSV in impending seasons.
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Kimura H, Nagasawa K, Kimura R, Tsukagoshi H, Matsushima Y, Fujita K, Hirano E, Ishiwada N, Misaki T, Oishi K, Kuroda M, Ryo A. Molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B. INFECTION GENETICS AND EVOLUTION 2017; 52:1-9. [PMID: 28414106 DOI: 10.1016/j.meegid.2017.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/09/2017] [Accepted: 04/12/2017] [Indexed: 11/19/2022]
Abstract
In this study, we examined the molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B (HRSV-B). First, we performed time-scale evolution analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. Next, we performed genetic distance, linear B-cell epitope prediction, N-glycosylation, positive/negative selection site, and Bayesian skyline plot analyses. We also constructed a structural model of the F protein and mapped the amino acid substitutions and the predicted B-cell epitopes. The MCMC-constructed phylogenetic tree indicated that the HRSV F gene diverged from the bovine respiratory syncytial virus gene approximately 580years ago and had a relatively low evolutionary rate (7.14×10-4substitutions/site/year). Furthermore, a common ancestor of HRSV-A and -B diverged approximately 290years ago, while HRSV-B diverged into three clusters for approximately 60years. The genetic similarity of the present strains was very high. Although a maximum of 11 amino acid substitutions were observed in the structural model of the F protein, only one strain possessed an amino acid substitution located within the palivizumab epitope. Four epitopes were predicted, although these did not correspond to the neutralization sites of the F protein including the palivizumab epitope. In addition, five N-glycosylation sites of the present HRSV-B strains were inferred. No positive selection sites were identified; however, many sites were found to be under negative selection. The effective population size of the gene has remained almost constant. On the basis of these results, it can be concluded that the HRSV-B F gene is highly conserved, as is the F protein of HRSV-A. Moreover, our prediction of B-cell epitopes does not show that the palivizumab reaction site may be recognized as an epitope during naturally occurring infections.
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Affiliation(s)
- Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan; Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan.
| | - Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Ryusuke Kimura
- Faculty of Pharmacy, Takasaki University of Health and Welfare, 37-1 Nakaoruimachi, Takasaki-shi, Gunma 370-0033, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Yuki Matsushima
- Kawasaki City Institute for Public Health, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan
| | - Kiyotaka Fujita
- School of Medical Technology, Faculty of Health Science, Gumma Paz College, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan
| | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science, 39-4 Harame-cho, Fukui-shi, Fukui 910-8851, Japan
| | - Naruhiko Ishiwada
- Division of Infection Control and Prevention, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan
| | - Takako Misaki
- Kawasaki City Institute for Public Health, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan
| | - Kazunori Oishi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
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Genomic Loads and Genotypes of Respiratory Syncytial Virus: Viral Factors during Lower Respiratory Tract Infection in Chilean Hospitalized Infants. Int J Mol Sci 2017; 18:ijms18030654. [PMID: 28335547 PMCID: PMC5372666 DOI: 10.3390/ijms18030654] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/02/2017] [Accepted: 03/13/2017] [Indexed: 11/17/2022] Open
Abstract
The clinical impact of viral factors (types and viral loads) during respiratory syncytial virus (RSV) infection is still controversial, especially regarding newly described genotypes. In this study, infants with RSV bronchiolitis were recruited to describe the association of these viral factors with severity of infection. RSV antigenic types, genotypes, and viral loads were determined from hospitalized patients at Hospital Roberto del Río, Santiago, Chile. Cases were characterized by demographic and clinical information, including days of lower respiratory symptoms and severity. A total of 86 patients were included: 49 moderate and 37 severe cases. During 2013, RSV-A was dominant (86%). RSV-B predominated in 2014 (92%). Phylogenetic analyses revealed circulation of GA2, Buenos Aires (BA), and Ontario (ON) genotypes. No association was observed between severity of infection and RSV group (p = 0.69) or genotype (p = 0.87). After a clinical categorization of duration of illness, higher RSV genomic loads were detected in infants evaluated earlier in their disease (p < 0.001) and also in infants evaluated later, but coursing a more severe infection (p = 0.04). Although types and genotypes did not associate with severity in our children, higher RSV genomic loads and delayed viral clearance in severe patients define a group that might benefit from new antiviral therapies.
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