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Huang J, Li Y, Chen H, Liu H, Li W, Isiaka ID, Du H, Noman M, Rizwan MA, Du Q, Li Y, Lin Y, Liu Y, Lu X, Liu D, Yan Y. Epidemiological, Clinical, and Genomic Traits of PIV in Hospitalized Children After the COVID-19 Pandemic in Wuhan, China. J Med Virol 2024; 96:e70117. [PMID: 39673291 PMCID: PMC11645542 DOI: 10.1002/jmv.70117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Revised: 10/25/2024] [Accepted: 11/26/2024] [Indexed: 12/16/2024]
Abstract
Human parainfluenza virus (PIV) is a main cause of acute lower respiratory tract infections (ALRTIs), which contributes to childrens' mortality worldwide; however, the epidemiology of PIVs following the SARS-CoV-2 pandemic is still not clarified, and poses risks of potential outbreaks. Herein, we conducted a retrospective observational study from September 26, 2020 to September 30, 2023 to assess PIV epidemiology in Wuhan, China, as well as the clinical characteristics of PIV infections. In total, 14,065 inpatients with ALRTIs were enrolled, of which 936 were identified to have PIV infection. We also obtained 69 PIV3 RNA to reveal its molecular traits. An alteration in PIV season pattern away from spring and summer prevalence was noted, as well as a progressive rise in its detection rate. PIV-related ALRTIs were more prevalent in male patients. PIV3 was the dominant PIV type in recent years. In comparison with the phase before the cancellation of Dynamic Zero-COVID Policy in December 2022, symptoms after its repeal were milder. All Wuhan strains were classified with C3f lineage and possibly evolved from native strains in China. Additionally, some mutations, such as Q499P in protein hemagglutinin-neuraminidase, should be given further attention. In summary, our study demonstrates the clinical characteristics of PIVs and genomic traits of PIV3 in Wuhan, China, thus holds importance for the diagnosis and control of PIV infections in the post-pandemic era.
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Grants
- This study was supported by the Natural Science Foundation of Hubei Province (2023AFB221, 2021CFA012), the Funding for Scientific Research Projects from Wuhan Children's Hospital (2024FEBSJJ007), Medical Research Project of Wuhan Health Commission (S202401120097), the Knowledge Innovation Program of Wuhan-Basic Research (2022020801010569), and the Health Commission of Hubei Province (WJ2021M262).
- This study was supported by the Natural Science Foundation of Hubei Province (2023AFB221, 2021CFA012), the Funding for Scientific Research Projects from Wuhan Children's Hospital (2024FEBSJJ007), Medical Research Project of Wuhan Health Commission (S202401120097), the Knowledge Innovation Program of Wuhan‐Basic Research (2022020801010569), and the Health Commission of Hubei Province (WJ2021M262).
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Affiliation(s)
- Jiaming Huang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega‐Science, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Key Laboratory of Virology and Biosafety, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Computational Virology Group, Etiology Research Center, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ying Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega‐Science, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Key Laboratory of Virology and Biosafety, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Computational Virology Group, Etiology Research Center, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Hebin Chen
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Haizhou Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega‐Science, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Key Laboratory of Virology and Biosafety, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Computational Virology Group, Etiology Research Center, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
| | - Wenqing Li
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Ismaila Damilare Isiaka
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega‐Science, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Key Laboratory of Virology and Biosafety, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Computational Virology Group, Etiology Research Center, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hui Du
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Muhammad Noman
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega‐Science, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Key Laboratory of Virology and Biosafety, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Computational Virology Group, Etiology Research Center, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Muhammad Arif Rizwan
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega‐Science, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Key Laboratory of Virology and Biosafety, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Computational Virology Group, Etiology Research Center, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qing Du
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yang Li
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yaxin Lin
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yuehu Liu
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiaoxia Lu
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega‐Science, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Key Laboratory of Virology and Biosafety, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- Computational Virology Group, Etiology Research Center, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Yan
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Pediatric Respiratory Disease Laboratory, Institute of Maternal and Child Health, Wuhan Children's Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Tramuto F, Maida CM, Randazzo G, Guzzetta V, Santino A, Li Muli R, Costantino C, Graziano G, Amodio E, Mazzucco W, Vitale F. Whole-Genome Sequencing and Genetic Diversity of Human Respiratory Syncytial Virus in Patients with Influenza-like Illness in Sicily (Italy) from 2017 to 2023. Viruses 2024; 16:851. [PMID: 38932144 PMCID: PMC11209242 DOI: 10.3390/v16060851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Monitoring the genetic variability of human respiratory syncytial virus (hRSV) is of paramount importance, especially for the potential implication of key antigenic mutations on the emergence of immune escape variants. Thus, to describe the genetic diversity and evolutionary dynamics of hRSV circulating in Sicily (Italy), a total of 153 hRSV whole-genome sequences collected from 770 hRSV-positive subjects between 2017 and 2023, before the introduction of expanded immunization programs into the population, were investigated. The phylogenetic analyses indicated that the genotypes GA.2.3.5 (ON1) for hRSV-A and GB.5.0.5a (BA9) for hRSV-B co-circulated in our region. Amino acid (AA) substitutions in the surface and internal proteins were evaluated, including the F protein antigenic sites, as the major targets of immunoprophylactic monoclonal antibodies and vaccines. Overall, the proportion of AA changes ranged between 1.5% and 22.6% among hRSV-A, whereas hRSV-B varied in the range 0.8-16.9%; the latter was more polymorphic than hRSV-A within the key antigenic sites. No AA substitutions were found at site III of both subgroups. Although several non-synonymous mutations were found, none of the polymorphisms known to potentially affect the efficacy of current preventive measures were documented. These findings provide new insights into the global hRSV molecular epidemiology and highlight the importance of defining a baseline genomic picture to monitor for future changes that might be induced by the selective pressures of immunological preventive measures, which will soon become widely available.
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Affiliation(s)
- Fabio Tramuto
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Carmelo Massimo Maida
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Giulia Randazzo
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Valeria Guzzetta
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Arianna Santino
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Rita Li Muli
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Claudio Costantino
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Giorgio Graziano
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Emanuele Amodio
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
| | - Walter Mazzucco
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Francesco Vitale
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
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Guo CY, Zhang Y, Zhang YY, Zhao W, Peng XL, Zheng YP, Fu YH, Yu JM, He JS. Comparative analysis of human respiratory syncytial virus evolutionary patterns during the COVID-19 pandemic and pre-pandemic periods. Front Microbiol 2023; 14:1298026. [PMID: 38111642 PMCID: PMC10725919 DOI: 10.3389/fmicb.2023.1298026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023] Open
Abstract
The COVID-19 pandemic has resulted in the implementation of strict mitigation measures that have impacted the transmission dynamics of human respiratory syncytial virus (HRSV). The measures also have the potential to influence the evolutionary patterns of the virus. In this study, we conducted a comprehensive analysis comparing genomic variations and evolving characteristics of its neutralizing antigens, specifically F and G proteins, before and during the COVID-19 pandemic. Our findings showed that both HRSV A and B exhibited an overall chronological evolutionary pattern. For the sequences obtained during the pandemic period (2019-2022), we observed that the HRSV A distributed in A23 genotype, but formed into three subclusters; whereas the HRSV B sequences were relatively concentrated within genotype B6. Additionally, multiple positively selected sites were detected on F and G proteins but none were located at neutralizing antigenic sites of the F protein. Notably, amino acids within antigenic site III, IV, and V of F protein remained strictly conserved, while some substitutions occurred over time on antigenic site Ø, I, II and VIII; substitution S389P on antigenic site I of HRSV B occurred during the pandemic period with nearly 50% frequency. However, further analysis revealed no substitutions have altered the structural conformations of the antigenic sites, the vial antigenicity has not been changed. We inferred that the intensive public health interventions during the COVID-19 pandemic did not affect the evolutionary mode of HRSV.
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Affiliation(s)
| | | | | | | | | | | | | | - Jie-mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jin-sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
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Wan L, Li L, Zhang H, Liu C, Li R, Wu X, Chen J. The changing pattern of common respiratory viruses among children from 2018 to 2021 in Wuhan, China. Arch Virol 2023; 168:291. [PMID: 37962775 PMCID: PMC10645662 DOI: 10.1007/s00705-023-05891-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/18/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Acute respiratory infections in children are a global public health challenge. Owing to the coronavirus disease (COVID-19) pandemic, non-pharmaceutical interventions, including patient isolation, social distancing, hand washing, and mask wearing, have been widely implemented, impacting the transmission of common respiratory viruses. The aim of this study was to clarify the epidemiological features of respiratory viruses in children less than 14 years of age in Wuhan before and after COVID-19. METHODS Respiratory specimens were collected from patients aged < 14 years at two hospitals in Wuhan, China, from January 2018 to December 2021. Seven respiratory viruses were identified using an immunofluorescence assay. Pathogen profiles and seasonality were analysed. RESULTS The number of visits and virus detection rate decreased dramatically after February 2020. The respiratory virus detection rate peaked in January and December and decreased dramatically in February and August. The detection rate was lower in 2021 than in 2018 and 2019. Respiratory syncytial virus (RSV) was identified as the leading pathogen in children aged < 1 year and 1-4 years before and after the COVID-19 pandemic. In children aged 5-14 years, influenza virus was detected at the highest rate before, and RSV after, the COVID-19 pandemic. RSV was the most common virus in coinfections. CONCLUSIONS This study revealed the epidemiological patterns of common respiratory viruses from 2018 to 2021. The spectrum of pathogens involved in paediatric respiratory infections had partly changed. Non-pharmaceutical interventions resulted in fewer opportunities for the spread of common viruses but also in an "immunity debt" that could have negative consequences when the pandemic is under control in Wuhan.
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Affiliation(s)
- Lu Wan
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Liangyu Li
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haiyue Zhang
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Chan Liu
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ruiyun Li
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaojun Wu
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| | - Jianjun Chen
- CAS Key Laboratory of Special Pathogens, Center for Biosafety Mega Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
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