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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:e0343223. [PMID: 39264196 DOI: 10.1128/spectrum.03432-23] [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: 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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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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Mizukoshi F, Kimura H, Sugimoto S, Kimura R, Nagasawa N, Hayashi Y, Hashimoto K, Hosoya M, Shirato K, Ryo A. Molecular Evolutionary Analyses of the Fusion Genes in Human Parainfluenza Virus Type 4. Microorganisms 2024; 12:1633. [PMID: 39203475 PMCID: PMC11356533 DOI: 10.3390/microorganisms12081633] [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: 07/09/2024] [Revised: 07/31/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
The human parainfluenza virus type 4 (HPIV4) can be classified into two distinct subtypes, 4a and 4b. The full lengths of the fusion gene (F gene) of 48 HPIV4 strains collected during the period of 1966-2022 were analyzed. Based on these gene sequences, the time-scaled evolutionary tree was constructed using Bayesian Markov chain Monte Carlo methods. A phylogenetic tree showed that the first division of the two subtypes occurred around 1823, and the most recent common ancestors of each type, 4a and 4b, existed until about 1940 and 1939, respectively. Although the mean genetic distances of all strains were relatively wide, the distances in each subtype were not wide, indicating that this gene was conserved in each subtype. The evolutionary rates of the genes were relatively low (4.41 × 10-4 substitutions/site/year). Moreover, conformational B-cell epitopes were predicted in the apex of the trimer fusion protein. These results suggest that HPIV4 subtypes diverged 200 years ago and the progenies further diverged and evolved.
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Affiliation(s)
- Fuminori Mizukoshi
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
| | - Hirokazu Kimura
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (Y.H.)
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi 377-0008, Gunma, Japan
- Department of Clinical Engineering, Faculty of Medical Technology, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan
| | - Satoko Sugimoto
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
- Research Center for Biosafety, Laboratory Animal and Pathogen Bank, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan
| | - Ryusuke Kimura
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi 371-8511, Gunma, Japan;
| | - Norika Nagasawa
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (Y.H.)
| | - Yuriko Hayashi
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (Y.H.)
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima-shi 960-1295, Fukushima, Japan;
| | - Mitsuaki Hosoya
- Department of Perinatology and Pediatrics for Regional Medical Support, Fukushima Medical University, Fukushima-shi 960-1295, Fukushima, Japan;
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
| | - Akihide Ryo
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
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Trifonova I, Korsun N, Madzharova I, Alexiev I, Ivanov I, Levterova V, Grigorova L, Stoikov I, Donchev D, Christova I. Epidemiological and Genetic Characteristics of Respiratory Viral Coinfections with Different Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Viruses 2024; 16:958. [PMID: 38932250 PMCID: PMC11209099 DOI: 10.3390/v16060958] [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: 05/21/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
This study aimed to determine the incidence and etiological, seasonal, and genetic characteristics of respiratory viral coinfections involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between October 2020 and January 2024, nasopharyngeal samples were collected from 2277 SARS-CoV-2-positive patients. Two multiplex approaches were used to detect and sequence SARS-CoV-2, influenza A/B viruses, and other seasonal respiratory viruses: multiplex real-time polymerase chain reaction (PCR) and multiplex next-generation sequencing. Coinfections of SARS-CoV-2 with other respiratory viruses were detected in 164 (7.2%) patients. The most common co-infecting virus was respiratory syncytial virus (RSV) (38 cases, 1.7%), followed by bocavirus (BoV) (1.2%) and rhinovirus (RV) (1.1%). Patients ≤ 16 years of age had the highest rate (15%) of mixed infections. Whole-genome sequencing produced 19 complete genomes of seasonal respiratory viral co-pathogens, which were subjected to phylogenetic and amino acid analyses. The detected influenza viruses were classified into the genetic groups 6B.1A.5a.2a and 6B.1A.5a.2a.1 for A(H1N1)pdm09, 3C.2a1b.2a.2a.1 and 3C.2a.2b for A(H3N2), and V1A.3a.2 for the B/Victoria lineage. The RSV-B sequences belonged to the genetic group GB5.0.5a, with HAdV-C belonging to type 1, BoV to genotype VP1, and PIV3 to lineage 1a(i). Multiple amino acid substitutions were identified, including at the antibody-binding sites. This study provides insights into respiratory viral coinfections involving SARS-CoV-2 and reinforces the importance of genetic characterization of co-pathogens in the development of therapeutic and preventive strategies.
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Affiliation(s)
- Ivelina Trifonova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Neli Korsun
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Iveta Madzharova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivailo Alexiev
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivan Ivanov
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Viktoria Levterova
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Lyubomira Grigorova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivan Stoikov
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Dean Donchev
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Iva Christova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
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Lee K, Park K, Sung H, Kim MN. Phylogenetic lineage dynamics of global parainfluenza virus type 3 post-COVID-19 pandemic. mSphere 2024; 9:e0062423. [PMID: 38501829 PMCID: PMC11036794 DOI: 10.1128/msphere.00624-23] [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: 10/24/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, outbreaks of parainfluenza virus type 3 (PIV-3) decreased due to infection control measures. However, a post-pandemic resurgence of PIV-3 has recently been observed. Nonetheless, the role of viral genetic epidemiology, possibly influenced by a genetic bottleneck effect, remains unexplored. We investigated the phylogenetic structure of the publicly available PIV-3 whole-genome and hemagglutinin-neuraminidase (HN) gene sequences spanning the last 65 years, including the COVID-19 pandemic. Sequences were retrieved from the nucleotide database of the National Center for Biotechnology Information using the search term "Human respirovirus 3." Sequence subsets covering all six genes of PIV-3 or the HN gene were designated as the whole-genome and HN surveillance data sets, respectively. Using these data sets, we constructed maximum-likelihood phylogenetic trees and performed a time-scaled analysis using a Bayesian SkyGrid coalescent prior. A total of 455 whole-genome and 1,139 HN gene sequences were extracted, revealing 10 and 11 distinct lineages, respectively, with >98% concurrence in lineage assignments. During the 2020 COVID-19 pandemic, only three single-lineage clusters were identified in Japan, Korea, and the USA. The inferred year of origin for PIV-3 was 1938 (1903-1963) for the whole-genome data set and 1955 (1930-1963) for the HN gene data set. Our study suggests that PIV-3 epidemics in the post-COVID era are likely influenced by a pandemic-driven bottleneck phenomenon and supports previous hypotheses suggesting s that PIV-3 originated during the early half of the 20th century.IMPORTANCEUsing publicly available parainfluenza virus type 3 (PIV-3) whole-genome sequences, we estimated that PIV-3 originated during the 1930s, consistent with previous hypotheses. Lineage typing and time-scaled phylogenetic analysis revealed that PIV-3 experienced a bottleneck phenomenon in Korea and the USA during the coronavirus disease 2019 pandemic. We identified the conservative hemagglutinin-neuraminidase gene as a viable alternative marker in long-term epidemiological studies of PIV-3 when whole-genome analysis is limited.
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Affiliation(s)
| | - Kuenyoul Park
- Department of Laboratory Medicine, Sanggye Paik Hospital, School of Medicine, Inje University, Seoul, South Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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Lee H, Kim SH, Cho SJ, Lee YU, Lee K, Lee YP, Seo J, Chung YS. Genetic Analysis of HPIV3 That Emerged during the SARS-CoV-2 Pandemic in Gwangju, South Korea. Viruses 2022; 14:v14071446. [PMID: 35891425 PMCID: PMC9317768 DOI: 10.3390/v14071446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022] Open
Abstract
Community mitigation measures taken owing to the COVID-19 pandemic have caused a decrease in the number of respiratory viruses, including the human parainfluenza virus type 3 (HPIV3), and a delay in their occurrence. HPIV3 was rarely detected as a consequence of monitoring respiratory viral pathogens in Gwangju, Korea, in 2020; however, it resurfaced as a delayed outbreak and peaked in September–October 2021. To understand the genetic characteristics of the reemerging virus, antigenic gene sequences and evolutionary analyses of the hemagglutinin-neuraminidase (HN) and fusion (F) genes were performed for 129 HPIV3 pathogens prevalent in Gwangju from 2018 to 2021. Unlike the prevalence of various HPIV3 strains in 2018-2019, the prevalence of HPIV3 by strains with reduced diversity was confirmed in 2021. It could be inferred that this decrease in genetic diversity was due to the restriction of inflow from other regions at home and abroad following the community mitigation measures and the spread within the region. The HPIV3 that emerged in 2021 consisted of HN coding regions that were 100% consistent with the sequence identified in Saitama, Japan, in 2018, and F coding regions exhibiting 99.6% homology to a sequence identified in India in 2017, among the ranks reported to the National Center for Biotechnology Information. The emergence of a new lineage in a community can lead to a mass outbreak by collapsing the collective immunity of the existing acquired area; therefore, continuous monitoring is necessary.
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Affiliation(s)
- Hongsu Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Sun-Hee Kim
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
- Correspondence: (S.-H.K.); (Y.-S.C.)
| | - Sun-Ju Cho
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Yeong-Un Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Kwangho Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Yong-Pyo Lee
- Division of Infectious Disease Diagnosis Control, Honam Regional Center for Disease Control and Prevention, Korea Diseases Control and Prevention Agency, Gwangju 61947, Korea;
| | - Jinjong Seo
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Korea; (H.L.); (S.-J.C.); (Y.-U.L.); (K.L.); (J.S.)
| | - Yoon-Seok Chung
- Division of Infectious Disease Diagnosis Control, Honam Regional Center for Disease Control and Prevention, Korea Diseases Control and Prevention Agency, Gwangju 61947, Korea;
- Correspondence: (S.-H.K.); (Y.-S.C.)
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Elusah J, Bulimo WD, Opanda SM, Symekher SL, Wamunyokoli F. Genetic diversity and evolutionary analysis of human respirovirus type 3 strains isolated in Kenya using complete hemagglutinin-neuraminidase (HN) gene. PLoS One 2020; 15:e0229355. [PMID: 32155160 PMCID: PMC7064169 DOI: 10.1371/journal.pone.0229355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/04/2020] [Indexed: 12/16/2022] Open
Abstract
Human respirovirus type 3 (HRV3) is a leading etiology of lower respiratory tract infections in young children and ranks only second to the human respiratory syncytial virus (HRSV). Despite the public health importance of HRV3, there is limited information about the genetic characteristics and diversity of these viruses in Kenya. To begin to address this gap, we analyzed 35 complete hemagglutinin-neuraminidase (HN) sequences of HRV3 strains isolated in Kenya between 2010 and 2013. Viral RNA was extracted from the isolates, and the entire HN gene amplified by RT-PCR followed by nucleotide sequencing. Phylogenetic analyses of the sequences revealed that all the Kenyan isolates grouped into genetic Cluster C; sub-clusters C1a, C2, and C3a. The majority (54%) of isolates belonged to sub-cluster C3a, followed by C2 (43%) and C1a (2.9%). Sequence analysis revealed high identities between the Kenyan isolates and the HRV3 prototype strain both at the amino acid (96.5-97.9%) and nucleotide (94.3-95.6%) levels. No amino acid variations affecting the catalytic/active sites of the HN glycoprotein were observed among the Kenyan isolates. Selection pressure analyses showed that the HN glycoprotein was evolving under positive selection. Evolutionary analyses revealed that the mean TMRCA for the HN sequence dataset was 1942 (95% HPD: 1928-1957), while the mean evolutionary rate was 4.65x10-4 nucleotide substitutions/site/year (95% HPD: 2.99x10-4 to 6.35x10-4). Overall, our results demonstrate the co-circulation of strains of cluster C HRV3 variants in Kenya during the study period. This is the first study to describe the genetic and molecular evolutionary aspects of HRV3 in Kenya using the complete HN gene.
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Affiliation(s)
- Juliet Elusah
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Wallace Dimbuson Bulimo
- Department of Emerging infections, US Army Medical Directorate–Africa, Nairobi, Kenya
- Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya
- * E-mail:
| | | | | | - Fred Wamunyokoli
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
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Kamau E, Oketch JW, de Laurent ZR, Phan MVT, Agoti CN, Nokes DJ, Cotten M. Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia. BMC Genomics 2020; 21:5. [PMID: 31898474 PMCID: PMC6941262 DOI: 10.1186/s12864-019-6400-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/15/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences. RESULTS We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes. CONCLUSION This is the first genomic characterization of HMPV genomes from African patients.
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Affiliation(s)
- Everlyn Kamau
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - John W Oketch
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - My V T Phan
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute, University of Warwick, Coventry, UK
| | - Matthew Cotten
- MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Bose ME, Shrivastava S, He J, Nelson MI, Bera J, Fedorova N, Halpin R, Town CD, Lorenzi HA, Amedeo P, Gupta N, Noyola DE, Videla C, Kok T, Buys A, Venter M, Vabret A, Cordey S, Henrickson KJ. Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes. PLoS One 2019; 14:e0220057. [PMID: 31318956 PMCID: PMC6638977 DOI: 10.1371/journal.pone.0220057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/08/2019] [Indexed: 12/16/2022] Open
Abstract
Human Parainfluenza viruses (HPIV) type 1 and 3 are important causes of respiratory tract infections in young children globally. HPIV infections do not confer complete protective immunity so reinfections occur throughout life. Since no effective vaccine is available for the two virus subtypes, comprehensive understanding of HPIV-1 and HPIV-3 genetic and epidemic features is important for diagnosis, prevention, and treatment of HPIV-1 and HPIV-3 infections. Relatively few whole genome sequences are available for both HPIV-1 and HPIV-3 viruses, so our study sought to provide whole genome sequences from multiple countries to further the understanding of the global diversity of HPIV at a whole-genome level. We collected HPIV-1 and HPIV-3 samples and isolates from Argentina, Australia, France, Mexico, South Africa, Switzerland, and USA from the years 2003-2011 and sequenced the genomes of 40 HPIV-1 and 75 HPIV-3 viruses with Sanger and next-generation sequencing with the Ion Torrent, Illumina, and 454 platforms. Phylogenetic analysis showed that the HPIV-1 genome is evolving at an estimated rate of 4.97 × 10-4 mutations/site/year (95% highest posterior density 4.55 × 10-4 to 5.38 × 10-4) and the HPIV-3 genome is evolving at a similar rate (3.59 × 10-4 mutations/site/year, 95% highest posterior density 3.26 × 10-4 to 3.94 × 10-4). There were multiple genetically distinct lineages of both HPIV-1 and 3 circulating on a global scale. Further surveillance and whole-genome sequencing are greatly needed to better understand the spatial dynamics of these important respiratory viruses in humans.
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Affiliation(s)
- Michael E. Bose
- Midwest Respiratory Virus Program, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | | | - Jie He
- Midwest Respiratory Virus Program, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Martha I. Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Jayati Bera
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Nadia Fedorova
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Rebecca Halpin
- J. Craig Venter Institute, Rockville, MD, United States of America
| | | | | | - Paolo Amedeo
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Neha Gupta
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Daniel E. Noyola
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Cristina Videla
- Clinical Virology Laboratory, Centro de Educación Médica e Investigaciones Clínicas (CEMIC) University Hospital, Buenos Aires, Argentina
| | - Tuckweng Kok
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Sandringham, South Africa
| | - Marietjie Venter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Sandringham, South Africa
- Zoonotic, arbo and respiratory virus program, Department Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Astrid Vabret
- Normandie Université, Caen, France
- Groupe de Recherche sur l'Adaptation Microbienne (GRAM), Université de Caen, Caen, France
- Laboratoire de Virologie, Centre Hospitalier Universitaire de Caen, Caen, France
| | - Samuel Cordey
- Division of Infectious Diseases and Laboratory of Virology, University of Geneva Hospitals, Geneva, Switzerland
| | - Kelly J. Henrickson
- Midwest Respiratory Virus Program, Medical College of Wisconsin, Milwaukee, WI, United States of America
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9
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Smielewska A, Pearson C, Popay A, Roddick I, Reacher M, Emmott E, He J, Thaxter R, Chenery C, Goodfellow I, Burke A, Jalal H. Unrecognised Outbreak: Human parainfluenza virus infections in a pediatric oncology unit. A new diagnostic PCR and virus monitoring system may allow early detection of future outbreaks. Wellcome Open Res 2018; 3:119. [PMID: 30687791 PMCID: PMC6338131 DOI: 10.12688/wellcomeopenres.14732.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 12/15/2022] Open
Abstract
Background: Human parainfluenza viruses (HPIVs) are significant causes of both upper and lower respiratory tract infections with type 3 (HPIV3) causing the most severe disease in the immunocompromised cohorts. The objective of this study was to analyse the epidemiological nature of a cluster of cases of HPIV3 in a pediatric oncology unit of a major teaching hospital. Methods: In order to determine whether the activity observed represented a deviation from the norm, seasonal trends of HPIV3 in the surrounding geographical area as well as on the ward in question were analysed. The genetic link between cases was established by the phylogenetic analysis of the non-coding hypervariable region between the M (Matrix) and F (fusion) genes of HPIV3. The 15 cases involved and 15 unrelated cases were sequenced. Transmission routes were subsequently inferred and visualized using Konstanz Information Miner (KNIME) 3.3.2. Results: Of the 15 cases identified, 14 were attributed to a point source outbreak. Two out of 14 outbreak cases were found to differ by a single mutation A182C. The outbreak strain was also seen in 1 out of 15 unrelated cases, indicating that it was introduced from the community. Transmission modeling was not able to link all the cases and establish a conclusive chain of transmission. No staff were tested during the outbreak period. No deaths occurred as a result of the outbreak. Conclusion: A point source outbreak of HPIV3 was recognized post factum on an oncology pediatric unit in a major teaching hospital. This raised concern about the possibility of a future more serious outbreak. Weaknesses in existing systems were identified and a new dedicated respiratory virus monitoring system introduced. Pediatric oncology units require sophisticated systems for early identification of potentially life-threatening viral outbreaks.
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Affiliation(s)
- Anna Smielewska
- Division of Virology, Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB2 0QQ, UK
- Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Public Health England, Cambridge, Cambridgeshire, CB2 0QQ, UK
| | - Callum Pearson
- Field Epidemiology Service East of England, Public Health England, Cambridge, Cambridgeshire, CB20SR, UK
| | - Ashley Popay
- Field Epidemiology Service East of England, Public Health England, Cambridge, Cambridgeshire, CB20SR, UK
| | - Iain Roddick
- Field Epidemiology Service East of England, Public Health England, Cambridge, Cambridgeshire, CB20SR, UK
| | - Mark Reacher
- Field Epidemiology Service East of England, Public Health England, Cambridge, Cambridgeshire, CB20SR, UK
| | - Edward Emmott
- Division of Virology, Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB2 0QQ, UK
- Department of Bioengineering, Northeastern University, Boston, MA, 02115-5000, USA
| | - Jenny He
- Infection Control, Cambridge University Hospitals, NHS Foundation Trust, Cambridge, Cambridgeshire, CB2 0QQ, UK
| | - Rachel Thaxter
- Infection Control, Cambridge University Hospitals, NHS Foundation Trust, Cambridge, Cambridgeshire, CB2 0QQ, UK
| | - Carol Chenery
- Infection Control, Cambridge University Hospitals, NHS Foundation Trust, Cambridge, Cambridgeshire, CB2 0QQ, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, Cambridgeshire, CB2 0QQ, UK
| | - Amos Burke
- Department of Paediatric Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, CB2 0QQ, UK
| | - Hamid Jalal
- Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Public Health England, Cambridge, Cambridgeshire, CB2 0QQ, UK
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