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Chen X, Wang H, Li Q, Qi Y, Li F, He W, Wang Q, Jin F, Guo Y, Hei M, Xie Z. A fatal case of neonatal viral sepsis caused by human parainfluenza virus type 3. Virol J 2023; 20:248. [PMID: 37891594 PMCID: PMC10612315 DOI: 10.1186/s12985-023-02141-9] [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: 05/16/2023] [Accepted: 07/25/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Sepsis is a systemic inflammatory response syndrome caused by severe infection in children, but cases of sepsis associated with human parainfluenza virus (HPIV) have been rarely reported in newborns. CASE PRESENTATION We report a case of HPIV-3 positive full-term newborn admitted to the Neonatal Intensive Care Unit of Beijing Children's Hospital due to hematuria, gloomy spirit, inactivity and loss of appetite for 6 h. He had septic shock when he arrived the Accident & Emergency Department requiring immediate intubation and mechanical ventilation. Intravenous antibiotics were started. He had completely negative response to all anti-shock treatments including fluid resuscitation and vasopressor supports, and died 14 h later. Viral nucleic acid detection and metagenomic next-generation sequencing (mNGS) analyses of nasopharyngeal aspirate and blood specimens verified an HPIV-3 infection, with negative bacterial culture results. The HPIV-3 strain detected in this patient was subtyped as HPIV C3a, and two unreported amino acid mutations were found in the HN protein region. CONCLUSION The patient had a severe infection associated with HPIV-3, which was the cause of sepsis and septic shock. This study showed the diagnostic value of mNGS in etiological diagnosis, especially in severe neonatal case.
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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, Laboratory of Infection and Virology, Beijing Children's Hospital, Chinese Academy of Medical Sciences, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, No. 56 Nan-li-shi Road, Xicheng District, Beijing, 2019RU016, 100045, China
| | - Hong Wang
- Department of Neonatology, Neonatal Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Qi Li
- 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, Laboratory of Infection and Virology, Beijing Children's Hospital, Chinese Academy of Medical Sciences, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, No. 56 Nan-li-shi Road, Xicheng District, Beijing, 2019RU016, 100045, China
| | - Yujie Qi
- Department of Neonatology, Neonatal Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Fei Li
- 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, Laboratory of Infection and Virology, Beijing Children's Hospital, Chinese Academy of Medical Sciences, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, No. 56 Nan-li-shi Road, Xicheng District, Beijing, 2019RU016, 100045, China
| | - Wenwen He
- Department of Neonatology, Neonatal Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Qiushi Wang
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd, Tianjin, 301700, China
| | - Fei Jin
- Department of Neonatology, Neonatal Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Yanqing Guo
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd, Tianjin, 301700, China
| | - Mingyan Hei
- Department of Neonatology, Neonatal Center, 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, Laboratory of Infection and Virology, Beijing Children's Hospital, Chinese Academy of Medical Sciences, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, No. 56 Nan-li-shi Road, Xicheng District, Beijing, 2019RU016, 100045, China.
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Feng Y, Zhu Z, Xu J, Sun L, Zhang H, Xu H, Zhang F, Wang W, Han G, Jiang J, Liu Y, Zhou S, Zhang Y, Ji Y, Mao N, Xu W. Molecular Evolution of Human Parainfluenza Virus Type 2 Based on Hemagglutinin-Neuraminidase Gene. Microbiol Spectr 2023; 11:e0453722. [PMID: 37039701 PMCID: PMC10269610 DOI: 10.1128/spectrum.04537-22] [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: 11/08/2022] [Accepted: 03/06/2023] [Indexed: 04/12/2023] Open
Abstract
To understand the molecular evolution of human parainfluenza virus type 2 (HPIV2), 21 Hemagglutinin-Neuraminidase (HN) gene sequences covering seven Chinese provinces in 2011 and 2017 to 2021 were combined with 90 published HN sequences worldwide for phylogenetic analysis. The result showed that global HPIV2 could be classified into two distinct clusters (I and II), five lineages (IA to IIE), and four sublineages (IB1 and 2, and IIE1 and 2). The minimum genetic distances between different clusters and lineages were 0.049 and 0.014, respectively. In the last decade, one lineage (IID) and three sublineages (IB1, IB2, and IIE1) have been cocirculating in China, with the sublineages IB2 and IIE1 dominating, while sublineages IB1 and IIE1 are dominant globally. In addition, the spread of HPIV2 had relative spatial clustering, and sublineage IB2 has only been detected in China thus far. The overall evolution rate of HPIV2 was relatively low, on the order of 10-4 substitutions/site/year, except for sublineage IB2 at 10-3 substitutions/site/year. Furthermore, human-animal transmission was observed, suggesting that the HPIV2 might have jumped out of animal reservoirs in approximately 1922, the predicted time of a common ancestor. The entire HN protein was under purifying/negative selection, and the specific amino acid changes and two novel N-glycosylation sites (N316 and N517) in sublineages IB1, IB2, and IIE1 were mostly located in the globular head region of the HN protein. In this study, preliminary evolutionary characteristics of HPIV2 based on the HN gene were obtained, increasing the recognition of the evolution and adaptation of HPIV2. IMPORTANCE The phylogenetic analysis showed that global HPIV2 could be classified into two distinct clusters (I and II) and five lineages (IA to IIE) with at least 0.049 and 0.014 genetic distances between clusters and lineages, respectively. Furthermore, lineages IB and IIE could be further divided into two sublineages (IB1-2 and IIE1-2). All China sequences belong to one lineage and three sublineages (IB1, IB2, IID, and IIE1), among which sublineages IB2 and IIE1 are predominant and cocirculating in China, while sublineages IB1 and IIE1 are dominant globally. The overall evolution rate of HPIV2 is on the order of 10-4 substitutions/site/year, with the highest rate of 2.18 × 10-3 for sublineage IB2. The entire HN protein is under purifying/negative selection, and the specific amino acid substitutions and two novel N-glycosylation sites (N316 and N517) in sublineages IB1, IB2, and IIE1 are mostly located in the globular head region of the HN protein.
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Affiliation(s)
- Yi Feng
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhen Zhu
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jin Xu
- Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Liwei Sun
- Changchun Children's Hospital, Changchun, China
| | - Hui Zhang
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, China
| | - Hongmei Xu
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Feng Zhang
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Wenyang Wang
- Department of Immunology, School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Guangyue Han
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Jie Jiang
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Liu
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shanshan Zhou
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yan Zhang
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yixin Ji
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Naiying Mao
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Kim HN, Yoon SY, Lim CS, Lee CK, Yoon J. Phylogenetic analysis of human parainfluenza type 3 virus strains responsible for the outbreak during the COVID-19 pandemic in Seoul, South Korea. J Clin Virol 2022; 153:105213. [DOI: 10.1016/j.jcv.2022.105213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
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Divergent Viruses Discovered in Swine Alter the Understanding of Evolutionary History and Genetic Diversity of the Respirovirus Genus and Related Porcine Parainfluenza Viruses. Microbiol Spectr 2022; 10:e0024222. [PMID: 35647875 PMCID: PMC9241844 DOI: 10.1128/spectrum.00242-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Paramyxoviridae is a rapidly growing family of viruses, whose potential for cross-species transmission makes it difficult to predict the harm of newly emerging viruses to humans and animals. To better understand their diversity, evolutionary history, and co-evolution with their hosts, we analyzed a collection of porcine parainfluenza virus (PPIV) genomes to reconstruct the species classification basis and evolutionary history of the Respirovirus genus. We sequenced 17 complete genomes of porcine respirovirus 1 (also known as porcine parainfluenza virus 1; PPIV-1), thereby nearly tripling the number of currently available PPIV-1 genomes. We found that PPIV-1 was widely prevalent in China with two divergent lineages, PPIV-1a and PPIV-1b. We further provided evidence that a new species, porcine parainfluenza virus 2 (PPIV-2), had recently emerged in China. Our results pointed to a need for revising the current species demarcation criteria of the Respirovirus genus. In addition, we used PPIV-1 as an example to explore recombination and diversity of the Respirovirus genus. Interestingly, we only detected heterosubtypic recombination events between PPIV-1a and PPIV-1b with no intrasubtypic recombination events. The recombination hotspots highlighted a diverse geography-dependent genome structure of paramyxovirus infecting swine in China. Furthermore, we found no evidence of co-evolution between respirovirus and its host, indicating frequent cross-species transmission. In summary, our analyses showed that swine can be infected with a broad range of respiroviruses and recombination may serve as an important evolutionary mechanism for the Respirovirus genus’ greater diversity in genome structure than previously anticipated. IMPORTANCE Livestock have emerged as critically underrecognized sources of paramyxovirus diversity, including pigs serving as the source of Nipah virus (NiV) and swine parainfluenza virus type 3, and goats and bovines harboring highly divergent viral lineages. Here, we identified a new species of Respirovirus genus named PPIV-2 in swine and proposed to revise the species demarcation criteria of the Respirovirus genus. We found heterosubtypic recombination events and high genetic diversity in PPIV-1. Further, we showed that genetic recombination may have occurred in the Respirovirus genus which may be associated with host range expansion. The continued expansion of Respirovirus genus diversity in livestock with relatively high human contact rates requires enhanced surveillance and ongoing evaluation of emerging cross-species transmission threats.
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Shao N, Liu B, Xiao Y, Wang X, Ren L, Dong J, Sun L, Zhu Y, Zhang T, Yang F. Genetic Characteristics of Human Parainfluenza Virus Types 1-4 From Patients With Clinical Respiratory Tract Infection in China. Front Microbiol 2021; 12:679246. [PMID: 34335501 PMCID: PMC8320325 DOI: 10.3389/fmicb.2021.679246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/17/2021] [Indexed: 11/27/2022] Open
Abstract
Human parainfluenza viruses (HPIV1–4) cause acute respiratory tract infections, thereby impacting human health worldwide. However, there are no current effective antivirals or licensed vaccines for infection prevention. Moreover, sequence information for human parainfluenza viruses (HPIVs) circulating in China is inadequate. Therefore, to shed light on viral genetic diversity and evolution, we collected samples from patients infected with HPIV1–4 in China from 2012 to 2018 to sequence the viruses. We obtained 24 consensus sequences, comprising 1 for HPIV1, 2 for HPIV2, 19 for HPIV3, and 2 for HPIV4A. Phylogenetic analyses classified the 1 HPIV1 into clade 2, and the 2 HPIV4 sequences into cluster 4A. Based on the hemagglutinin-neuraminidase (HN) gene, a new sub-cluster was identified in one of the HPIV2, namely G1c, and the 19 HPIV3 sequences were classified into the genetic lineages of C3f and C3a. The results indicated that HPIV1–4 were co-circulated in China. Further, the lineages of sub-cluster C3 of HPIV3 were co-circulated in China. A recombination analysis indicated that a putative recombination event may have occurred in the HN gene of HPIV3. In the obtained sequences of HPIV3, we found that two amino acid substitution sites (R73K in the F protein of PUMCH14028/2014 and A281V in the HN protein of PUMCH13961/2014) and a negative selection site (amino acid position 398 in the F protein) corresponded to the previously reported neutralization-related sites. Moreover, amino acid substitution site (K108E) corresponded to the negative selection site (amino acid position 108) in the 10 F proteins of HPIV3. However, no amino acid substitution site corresponded to the glycosylation site in the obtained HPIV3 sequences. These results might help in studying virus evolution, developing vaccines, and monitoring HPIV-related respiratory diseases.
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Affiliation(s)
- Nan Shao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Xiao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinming Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lilian Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yafang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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