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Liu Y, Han Z, Kang C, Cui A, Zhang Y, Liu L, Chen Y, Deng L, Zhao H, Zhou J, Li F, Zhou S, Feng D, Tian X, Feng Y, Cui X, Lei Y, Wang Y, Yuan F, Fan L, Tang X, Chen M, Peng X, Guo Y, Gao H, Wang S, Li L, Zhang T, Deng X, Chen H, Wang S, Ma Y, Zhu Z, Xu W. Importation and circulation of rubella virus lineages 1E-L2 and 2B-L2c between 2018 and 2021 in China: Virus evolution and spatial-temporal transmission characteristics. Virus Evol 2022; 8:veac083. [PMID: 36533147 PMCID: PMC9752544 DOI: 10.1093/ve/veac083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/26/2022] [Accepted: 09/03/2022] [Indexed: 11/19/2023] Open
Abstract
To better understand the importation and circulation patterns of rubella virus lineages 1E-L2 and 2B-L2c circulating in China since 2018, 3,312 viral strains collected from 27 out of 31 provinces in China between 2018 and 2021 were sequenced and analyzed with the representative international strains of lineages 1E-L2 and 2B-L2c based on genotyping region. Time-scale phylogenetic analysis revealed that the global lineages 1E-L2 and 2B-L2c presented distinct evolutionary patterns. Lineage 1E-L2 circulated in relatively limited geographical areas (mainly Asia) and showed geographical and temporal clustering, while lineage 2B-L2c strains circulated widely throughout the world and exhibited a complicated topology with several independently evolved branches. Furthermore, both lineages showed extensive international transmission activities, and phylogeographic inference provided evidence that lineage 1E-L2 strains circulating in China possibly originated from Japan, while the source of lineage 2B-L2c isolated since 2018 is still unclear. After importation into China in 2018, the spread of lineage 1E-L2 presented a three-stage transmission pattern from southern to northern China, whereas lineage 2B-L2c spread from a single point in western China to all the other four regions. These two transmission patterns allowed both imported lineages to spread rapidly across China during the 2018-9 rubella epidemic and eventually established endemic circulations. This study provides critical scientific data for rubella control and elimination in China and worldwide.
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Affiliation(s)
- Ying Liu
- WHO WPRO Regional Reference Measles/Rubella Laboratory, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China
| | - Zhenzhi Han
- WHO WPRO Regional Reference Measles/Rubella Laboratory, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Chuyun Kang
- Department of Maternal and Child Health, School of Public Health, Peking University, Beijing, China
| | - Aili Cui
- WHO WPRO Regional Reference Measles/Rubella Laboratory, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China
| | - Yan Zhang
- WHO WPRO Regional Reference Measles/Rubella Laboratory, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China
| | - Li Liu
- Institute of Microbiology, Sichuan Provincial Center for Disease Control and Prevention, Chengdu City, Sichuan Province China
| | - Ying Chen
- Department of Immunization Program, Gansu Provincial Center for Disease Control and Prevention, Lanzhou City, Gansu Province China
| | - Lili Deng
- Department of Expanded Programme on Immunization, Guangxi Provincial Center for Disease Control and Prevention, Nanning City, Guangxi Province, China
| | - Hua Zhao
- Department of Microbiological Testing, Chongqing Provincial Center for Disease Control and Prevention, Chongqing, China
| | - Jun Zhou
- Institute of Virology, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang City, Jiangxi Province, China
| | - Fangcai Li
- Department of Microbiological Testing, Hunan Provincial Center for Disease Control and Prevention, Changsha City, Hunan Province, China
| | - Shujie Zhou
- Department of Expanded Programme on Immunization, Anhui Provincial Center for Disease Control and Prevention, Hefei City, Anhui Province, China
| | - Daxing Feng
- Department of Expanded Programme on Immunization, Henan Provincial Center for Disease Control and Prevention, Zhengzhou City, Henan Province, China
| | - Xiaoling Tian
- Department of Immunization Program, Neimeng Provincial Center for Disease Control and Prevention, Huhehaote City, Neimeng Province, China
| | - Yan Feng
- Department of Immunization Program, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou City, Zhejiang Province, China
| | - Xiaoxian Cui
- Division of Microbiology, Shanghai Provincial Center for Disease Control and Prevention, Shanghai, China
| | - Yue Lei
- Department of Pathogenic Microbiology, Tianjin Provincial Center for Disease Control and Prevention, Tianjin, China
| | - Yan Wang
- Department of Immunization Program, Liaoning Provincial Center for Disease Control and Prevention, Shenyang City, Liaoning Province, China
| | - Fang Yuan
- Department of Virology, Ningxia Provincial Center for Disease Control and Prevention, Yinchuan City, Ningxia Province, China
| | - Lixia Fan
- Inspection and Testing Center, Qinghai Provincial Center for Disease Control and Prevention, Xining City, Qinghai Province, China
| | - Xiaomin Tang
- Department of Virology, Guizhou Provincial Center for Disease Control and Prevention, Guiyang City, Guizhou Province, China
| | - Meng Chen
- Immunization Prevention Institute, Beijing Provincial Center for Disease Control and Prevention, Beijing, China
| | - Xiaofang Peng
- Institute of Immunization, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou City, Guangdong Province, China
| | - Yu Guo
- Institute of Immunization, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang City, Hebei Province, China
| | - Hui Gao
- Department of Disease Inspection, Shanxi Provincial Center for Disease Control and Prevention, Taiyuan City, Shanxi Province, China
| | - Suting Wang
- Department of Expanded Programme on Immunization, Shandong Provincial Center for Disease Control and Prevention, Jinan City, Shandong Province, China
| | - Liqun Li
- Department of Immunization Program, Yunnan Provincial Center for Disease Control and Prevention, Kunming City, Yunnan Province, China
| | - Ting Zhang
- Virus Detection Department, Institute of Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan City, Hubei Province, China
| | - Xiuying Deng
- Department of Expanded Programme on Immunization, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing City, Jiangsu Province, China
| | - Haiyun Chen
- Microbiological Laboratory, Testing and Inspection Institute, Hainan Provincial Center for Disease Control and Prevention, Haikou City, Hainan Province, China
| | - Shuang Wang
- Department of Viral Disease Control and Prevention, Jilin Provincial Center for Disease Control and Prevention, Changchun City, Jilin Province, China
| | - Yu Ma
- Immunization Planning Institute, Shaanxi Provincial Center for Disease Control and Prevention, Xi’an City, Shaanxi Province, China
| | - Zhen Zhu
- WHO WPRO Regional Reference Measles/Rubella Laboratory, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China
| | - Wenbo Xu
- WHO WPRO Regional Reference Measles/Rubella Laboratory, NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China
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Ou Z, Ouzounis C, Wang D, Sun W, Li J, Chen W, Marlière P, Danchin A. A Path toward SARS-CoV-2 Attenuation: Metabolic Pressure on CTP Synthesis Rules the Virus Evolution. Genome Biol Evol 2020; 12:2467-2485. [PMID: 33125064 PMCID: PMC7665462 DOI: 10.1093/gbe/evaa229] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
In the context of the COVID-19 pandemic, we describe here the singular metabolic background that constrains enveloped RNA viruses to evolve toward likely attenuation in the long term, possibly after a step of increased pathogenicity. Cytidine triphosphate (CTP) is at the crossroad of the processes allowing SARS-CoV-2 to multiply, because CTP is in demand for four essential metabolic steps. It is a building block of the virus genome, it is required for synthesis of the cytosine-based liponucleotide precursors of the viral envelope, it is a critical building block of the host transfer RNAs synthesis and it is required for synthesis of dolichol-phosphate, a precursor of viral protein glycosylation. The CCA 3'-end of all the transfer RNAs required to translate the RNA genome and further transcripts into the proteins used to build active virus copies is not coded in the human genome. It must be synthesized de novo from CTP and ATP. Furthermore, intermediary metabolism is built on compulsory steps of synthesis and salvage of cytosine-based metabolites via uridine triphosphate that keep limiting CTP availability. As a consequence, accidental replication errors tend to replace cytosine by uracil in the genome, unless recombination events allow the sequence to return to its ancestral sequences. We document some of the consequences of this situation in the function of viral proteins. This unique metabolic setup allowed us to highlight and provide a raison d'être to viperin, an enzyme of innate antiviral immunity, which synthesizes 3'-deoxy-3',4'-didehydro-CTP as an extremely efficient antiviral nucleotide.
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Affiliation(s)
- Zhihua Ou
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Christos Ouzounis
- Biological Computation and Process Laboratory, Centre for Research and Technology Hellas, Chemical Process and Energy Resources Institute, Thessalonica, Greece
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Wanying Sun
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Weijun Chen
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China.,BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, Paris, France
| | - Antoine Danchin
- Kodikos Labs, Institut Cochin, Paris, France.,School of Biomedical Sciences, Li KaShing Faculty of Medicine, Hong Kong University, Pokfulam, Hong Kong
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Perelygina L, Chen MH, Suppiah S, Adebayo A, Abernathy E, Dorsey M, Bercovitch L, Paris K, White KP, Krol A, Dhossche J, Torshin IY, Saini N, Klimczak LJ, Gordenin DA, Zharkikh A, Plotkin S, Sullivan KE, Icenogle J. Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies. PLoS Pathog 2019; 15:e1008080. [PMID: 31658304 PMCID: PMC6837625 DOI: 10.1371/journal.ppat.1008080] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 11/07/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022] Open
Abstract
Rubella viruses (RV) have been found in an association with granulomas in children with primary immune deficiencies (PID). Here, we report the recovery and characterization of infectious immunodeficiency-related vaccine-derived rubella viruses (iVDRV) from diagnostic skin biopsies of four patients. Sequence evolution within PID hosts was studied by comparison of the complete genomic sequences of the iVDRVs with the genome of the vaccine virus RA27/3. The degree of divergence of each iVDRV correlated with the duration of persistence indicating continuous intrahost evolution. The evolution rates for synonymous and nonsynonymous substitutions were estimated to be 5.7 x 10-3 subs/site/year and 8.9 x 10-4 subs/site/year, respectively. Mutational spectra and signatures indicated a major role for APOBEC cytidine deaminases and a secondary role for ADAR adenosine deaminases in generating diversity of iVDRVs. The distributions of mutations across the genes and 3D hotspots for amino acid substitutions in the E1 glycoprotein identified regions that may be under positive selective pressure. Quasispecies diversity was higher in granulomas than in recovered infectious iVDRVs. Growth properties of iVDRVs were assessed in WI-38 fibroblast cultures. None of the iVDRV isolates showed complete reversion to wild type phenotype but the replicative and persistence characteristics of iVDRVs were different from those of the RA27/3 vaccine strain, making predictions of iVDRV transmissibility and teratogenicity difficult. However, detection of iVDRV RNA in nasopharyngeal specimen and poor neutralization of some iVDRV strains by sera from vaccinated persons suggests possible public health risks associated with iVDRV carriers. Detection of IgM antibody to RV in sera of two out of three patients may be a marker of virus persistence, potentially useful for identifying patients with iVDRV before development of lesions. Studies of the evolutionary dynamics of iVDRV during persistence will contribute to development of infection control strategies and antiviral therapies.
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Affiliation(s)
- Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Min-hsin Chen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Suganthi Suppiah
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Adebola Adebayo
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Emily Abernathy
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Morna Dorsey
- Department of Pediatrics, University of California, San Francisco, San Francisco, California, United States of America
| | - Lionel Bercovitch
- Department of Dermatology, Hasbro Children's Hospital and Warren Alpert Medical School of Brown University, Providence, Rhode Island, United States of America
| | - Kenneth Paris
- Division of Allergy and Immunology, Children's Hospital New Orleans, New Orleans, Louisiana, United States of America
| | - Kevin P. White
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Alfons Krol
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Julie Dhossche
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Ivan Y. Torshin
- Institute of Pharmacoinformatics, Federal Research Center “Computer Science and Control” of Russian Academy of Sciences, Dorodnicyn Computing Center, Moscow, Russian Federation
| | - Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Andrey Zharkikh
- Myriad Genetics, Inc., Salt Lake City, Utah, United States of America
| | - Stanley Plotkin
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Kathleen E. Sullivan
- Division of Allergy and Immunology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Joseph Icenogle
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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