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Zhu Y, Sun Y, Li C, Lu G, Jin R, Xu B, Shang Y, Ai J, Wang R, Duan Y, Chen X, Xie Z. Genetic characteristics of human parainfluenza viruses 1-4 associated with acute lower respiratory tract infection in Chinese children, during 2015-2021. Microbiol Spectr 2024; 12:e0343223. [PMID: 39264196 PMCID: PMC11448424 DOI: 10.1128/spectrum.03432-23] [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: 09/21/2023] [Accepted: 08/09/2024] [Indexed: 09/13/2024] Open
Abstract
Human parainfluenza viruses (HPIVs) are a significant cause of acute lower respiratory tract infections (ALRTIs) among young children and elderly individuals worldwide. The four types of HPIVs (HPIV1-4) can cause recurrent infections and pose a significant economic burden on health care systems globally. However, owing to the limited availability of complete genome sequences, the genetic evolution of these viruses and the development of vaccines and antiviral treatments are hampered. To address this issue, this study utilized next-generation sequencing to obtain 156 complete genome sequences of HPIV1-4, which were isolated from hospitalized children with ALRTIs in six regions of China between 2015 and 2021. This study revealed multiple clades, lineages, or sublineages of HPIVs circulating in mainland China, with a novel clade D of HPIV1 identified as geographically restricted to China. Moreover, this study identified the endemic dominant genotype of HPIV3, lineage C3, which has widely spread and continuously circulated in China. Bioinformatic analysis of the genome sequences revealed that the proteins of HPIV3 possessed the most variable sites, with the P protein showing more diversity than the other proteins among all types of HPIVs. The HN proteins of HPIV1-3 are all under negative/purifying selection, and two amino acid substitutions in the HN proteins correspond to known mAb neutralizing sites in the two HPIV3 strains. These findings provide crucial insights into the genetic diversity and evolutionary dynamics of HPIVs circulating among children in China and may facilitate research on the molecular diagnosis, vaccine development, and surveillance of HPIVs.IMPORTANCEPhylogenetic analysis revealed the prevalence of multiple clades, lineages, or sublineages of human parainfluenza viruses (HPIVs) circulating in mainland China. Notably, a unique evolutionary branch of HPIV1 containing only Chinese strains was identified and designated clade D. Furthermore, in 2023, HPIV3 strains from Pakistan and Russia formed a new lineage within clade C, named C6. The first HPIV4b sequence obtained in this study from China belongs to lineage C2. Evolutionary rate assessments revealed that both the HN and whole-genome sequences of HPIV3 presented the lowest evolutionary rates compared with those of the other HPIV types, with rates of 6.98E-04 substitutions/site/year (95% HPD: 5.87E-04 to 8.25E-03) and 5.85E-04 substitutions/site/year (95% HPD: 5.12E-04 to 6.62E-04), respectively. Recombination analysis revealed a potential recombination event in the F gene of an HPIV1 strain in this study. Additionally, all the newly obtained HPIV1-3 strains exhibited negative selection pressure, and two mutations were identified in the HN protein of two HPIV3 strains at monoclonal antibody-binding sites.
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MESH Headings
- Humans
- China/epidemiology
- Respiratory Tract Infections/virology
- Respiratory Tract Infections/epidemiology
- Phylogeny
- Child, Preschool
- Genome, Viral/genetics
- Child
- Male
- Genotype
- Female
- Infant
- Parainfluenza Virus 1, Human/genetics
- Parainfluenza Virus 1, Human/isolation & purification
- Parainfluenza Virus 1, Human/classification
- Parainfluenza Virus 4, Human/genetics
- Parainfluenza Virus 4, Human/classification
- Parainfluenza Virus 4, Human/isolation & purification
- Parainfluenza Virus 3, Human/genetics
- Parainfluenza Virus 3, Human/classification
- Parainfluenza Virus 3, Human/isolation & purification
- High-Throughput Nucleotide Sequencing
- Whole Genome Sequencing
- Genetic Variation
- Respirovirus Infections/virology
- Respirovirus Infections/epidemiology
- Respirovirus/genetics
- Respirovirus/classification
- Respirovirus/isolation & purification
- Parainfluenza Virus 2, Human/genetics
- Parainfluenza Virus 2, Human/classification
- Parainfluenza Virus 2, Human/isolation & purification
- East Asian People
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Affiliation(s)
- Yun Zhu
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Yun Sun
- The Division of General Pediatrics, Yinchuan Women and Children Healthcare Hospital, Yinchuan, China
| | - Changchong Li
- Department of Pediatric of Pulmonology, The 2nd Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Gen Lu
- The Respiratory Department, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Rong Jin
- The Respiratory Department, Guizhou Maternal and Child Health Care Hospital, Guiyang Children’s Hospital, Guiyang, China
| | - Baoping Xu
- Department of Respiratory Diseases I, Beijing Children’s Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
| | - Yunxiao Shang
- The Division of Pediatric Respiratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Junhong Ai
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Ran Wang
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Yali Duan
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangpeng Chen
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhengde Xie
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
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Current view on novel vaccine technologies to combat human infectious diseases. Appl Microbiol Biotechnol 2022; 106:25-56. [PMID: 34889981 PMCID: PMC8661323 DOI: 10.1007/s00253-021-11713-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 02/06/2023]
Abstract
Inactivated and live attenuated vaccines have improved human life and significantly reduced morbidity and mortality of several human infectious diseases. However, these vaccines have faults, such as reactivity or suboptimal efficacy and expensive and time-consuming development and production. Additionally, despite the enormous efforts to develop vaccines against some infectious diseases, the traditional technologies have not been successful in achieving this. At the same time, the concerns about emerging and re-emerging diseases urge the need to develop technologies that can be rapidly applied to combat the new challenges. Within the last two decades, the research of vaccine technologies has taken several directions to achieve safe, efficient, and economic platforms or technologies for novel vaccines. This review will give a brief overview of the current state of the novel vaccine technologies, new vaccine candidates in clinical trial phases 1-3 (listed by European Medicines Agency (EMA) and Food and Drug Administration (FDA)), and vaccines based on the novel technologies which have already been commercially available (approved by EMA and FDA) with the special reference to pandemic COVID-19 vaccines. KEY POINTS: • Vaccines of the new generation follow the minimalist strategy. • Some infectious diseases remain a challenge for the vaccine development. • The number of new vaccine candidates in the late phase clinical trials remains low.
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Aso J, Kimura H, Ishii H, Saraya T, Kurai D, Nagasawa K, Matsushima Y, Ryo A, Takizawa H. Molecular evolution of the hemagglutinin-neuraminidase (HN) gene in human respirovirus 3. Virus Res 2019; 277:197824. [PMID: 31783038 DOI: 10.1016/j.virusres.2019.197824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/08/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022]
Abstract
Human respirovirus 3 (HRV3) is a major causative agent of acute respiratory infections in humans. HRV3 can manifest as a recurrent infection, although exactly how is not known. In the present study, we conducted detailed molecular evolutionary analyses of the major antigen-coding hemagglutinin-neuraminidase (HN) gene of this virus detected/isolated in various countries. We performed analyses of time-scaled evolution, similarity, selective pressure, phylodynamics, and conformational epitope prediction by mapping to HN protein models. In this way, we estimated that a common ancestor of the HN gene of HRV3 and bovine respirovirus 3 diverged around 1815 and formed many lineages in the phylogenetic tree. The evolutionary rates of the HN gene were 1.1 × 10-3 substitutions/site/year, although the majority of these substitutions were synonymous. Some positive and many negative selection sites were predicted in the HN protein. Phylodynamic fluctuations of the gene were observed, and these were different in each lineage. Furthermore, most of the predicted B cell epitopes did not correspond to the neutralization-related mouse monoclonal antibody binding sites. The lack of a link between the conformational epitopes and neutralization sites may explain the naturally occurring HRV3 reinfection.
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Affiliation(s)
- Jumpei Aso
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School of Health Science, Gunma, Japan; Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan.
| | - Haruyuki Ishii
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Takeshi Saraya
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Daisuke Kurai
- Department of General Medicine, Division of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan
| | - Koo Nagasawa
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kanagawa, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan
| | - Hajime Takizawa
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
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Monette A, Mouland AJ. T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 342:175-263. [PMID: 30635091 PMCID: PMC7104940 DOI: 10.1016/bs.ircmb.2018.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Continuous epidemiological surveillance of existing and emerging viruses and their associated disorders is gaining importance in light of their abilities to cause unpredictable outbreaks as a result of increased travel and vaccination choices by steadily growing and aging populations. Close surveillance of outbreaks and herd immunity are also at the forefront, even in industrialized countries, where previously eradicated viruses are now at risk of re-emergence due to instances of strain recombination, contractions in viral vector geographies, and from their potential use as agents of bioterrorism. There is a great need for the rational design of current and future vaccines targeting viruses, with a strong focus on vaccine targeting of adaptive immune effector memory T cells as the gold standard of immunity conferring long-lived protection against a wide variety of pathogens and malignancies. Here, we review viruses that have historically caused large outbreaks and severe lethal disorders, including respiratory, gastric, skin, hepatic, neurologic, and hemorrhagic fevers. To observe trends in vaccinology against these viral disorders, we describe viral genetic, replication, transmission, and tropism, host-immune evasion strategies, and the epidemiology and health risks of their associated syndromes. We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates.
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Russell CJ, Hurwitz JL. Sendai virus as a backbone for vaccines against RSV and other human paramyxoviruses. Expert Rev Vaccines 2015; 15:189-200. [PMID: 26648515 DOI: 10.1586/14760584.2016.1114418] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human paramyxoviruses are the etiological agents for life-threatening respiratory virus infections of infants and young children. These viruses, including respiratory syncytial virus (RSV), the human parainfluenza viruses (hPIV1-4) and human metapneumovirus (hMPV), are responsible for millions of serious lower respiratory tract infections each year worldwide. There are currently no standard treatments and no licensed vaccines for any of these pathogens. Here we review research with which Sendai virus, a mouse parainfluenza virus type 1, is being advanced as a Jennerian vaccine for hPIV1 and as a backbone for RSV, hMPV and other hPIV vaccines for children.
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Affiliation(s)
- Charles J Russell
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA.,b Department of Microbiology, Immunology and Biochemistry , University of Tennessee Health Science Center , Memphis , TN , USA
| | - Julia L Hurwitz
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA.,b Department of Microbiology, Immunology and Biochemistry , University of Tennessee Health Science Center , Memphis , TN , USA
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Henrickson KJ, Savatski LL. Two distinct human parainfluenza virus type 1 genotypes detected during the 1991 Milwaukee epidemic. J Clin Microbiol 1996; 34:695-700. [PMID: 8904440 PMCID: PMC228872 DOI: 10.1128/jcm.34.3.695-700.1996] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The extent of genetic and antigenic variation found in a population of human parainfluenza virus type 1 (HPIV-1) during a single local epidemic was investigated. Fifteen HPIV-1 strains isolated from children in 1991 were analyzed. Nucleotide sequence variation in the hemagglutinin-neuraminidase protein (HN) gene demonstrated two distinct genotypes (genotypes C and D). Unique patterns were identified involving 62 nucleotide and 10 amino acid positions. These patterns represented 40% of all mutations within the HN gene. The remaining mutations were randomly distributed, and 74% involved only one (55%) or two isolates. Genotypes were statistically different from each other at both the nucleotide (P = 0.001) and amino acid (P = 0.001) levels and demonstrated unique potential N-linked glycosylation patterns. Thirty-eight monoclonal antibodies (MAbs) made to four different viral proteins (22 HN, 2 fusion [F], 1 phosphoprotein, and 13 nucleoprotein) (originating from two different genotypes [genotypes A and D]) were compared for their ability to bind to the clinical isolates in enzyme-linked immunosorbent assays (ELISAs) and hemagglutinin-inhibition (HI) assays. Twenty-one MAbs bound well to all clinical isolates in ELISAs and HI assays. The remaining 17 MAbs showed variation in all four structural proteins. Three HN MAbs demonstrated genotype C- and D-specific antigenic and neutralization differences. Evolutionary analysis using parsimony methods confirmed the differences between the two genotypes. No differences in either clinical presentation or disease severity between the two genotypes were found. Geographically localized HPIV-1 epidemics can be caused by at least two distinct genotypes with minor but specific antigenic changes. The clinical and immunologic roles of HPIV-1 genotypes have not been determined.
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Affiliation(s)
- K J Henrickson
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, USA
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Estaquier J, Boutillon C, Gras-Masse H, Ameisen JC, Capron A, Tartar A, Auriault C. Comprehensive delineation of antigenic and immunogenic properties of peptides derived from the nef HIV-1 regulatory protein. Vaccine 1993; 11:1083-92. [PMID: 8249426 DOI: 10.1016/0264-410x(93)90066-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Human Immunodeficiency Virus (HIV-1) nef regulatory protein, a protein involved in AIDS pathology, was used as a model to investigate and analyze B- and T-cell epitopes. In this paper, we describe the potential structural basis of antigenic and immunogenic reactivity of synthetic peptides derived from the macromolecular antigen. The relationship between B- and T-cell determinants in the context of regulatory mechanisms involved in immune recognition, while integrating recent data concerning MHC presentation. As a result of the recent progress in the field of peptide recognition and presentation, the potential of the peptide approach for constructing successful synthetic vaccines needs to be continuously re-evaluated.
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Affiliation(s)
- J Estaquier
- Centre d'Immunologie des Maladies Transmissibles et Allergiques, Unité mixte Inserm U 167-CNRS 624, Institut Pasteur, Lille, France
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Orten DJ, Xue W, van Drunen Littel-van den hurk S, Abdelmagid OY, Reddy DN, Campos M, Babiuk LA, Blecha F, Minocha HC. Comparison of bovine immune responses to affinity-purified bovine herpesvirus-1 antiidiotypes and glycoproteins. Viral Immunol 1993; 6:109-17. [PMID: 8216712 DOI: 10.1089/vim.1993.6.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Bovine immune responses to rabbit antiidiotypic antibodies (anti-Id) against neutralizing monoclonal antibodies to bovine herpesvirus-1 (BHV-1) envelope glycoproteins and to BHV-1 glycoproteins were compared. Glycoprotein-immunized animals produced high titers of anti-BHV-1 antibodies and were protected against BHV-1 challenge. Recombinant bovine interleukin-2 (rIL-2)-treated, anti-Id-immunized animals showed a slight reduction in clinical disease, and one calf produced BHV-1-neutralizing antibodies. Treatment with rIL-2 augmented non-BHV-1-specific immune responses. However, even with rIL-2 as an adjuvant, the mixture of polyclonal anti-Id did not elicit a consistent, protective BHV-1-specific immune response in calves.
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Affiliation(s)
- D J Orten
- Department of Pathology and Microbiology, Kansas State University, Manhattan
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