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Song J, Li C, Rivailler P, Wang H, Hu M, Zhu Z, Cui A, Mao N, Xu W, Zhang Y. Molecular evolution and genomic characteristics of genotype H1 of measles virus. J Med Virol 2021; 94:521-530. [PMID: 34761827 DOI: 10.1002/jmv.27448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/25/2021] [Accepted: 11/09/2021] [Indexed: 11/10/2022]
Abstract
Measles is one of the most infectious diseases of humans. It is caused by the measles virus (MeV) and can lead to serious illness, lifelong complications, and even death. Whole-genome sequencing (WGS) is now available to study molecular epidemiology and identify MeV transmission pathways. In the present study, WGS of 23 MeV strains of genotype H1, collected in Mainland China between 2006 and 2018, were generated and compared to 31 WGSs from the public domain to analyze genomic characteristics, evolutionary rates and date of emergence of H1 genotype. The noncoding region between M and F protein genes (M/F NCR) was the most variable region throughout the genome. Although the nucleotide substitution rate of H1 WGS was around 0.75 × 10-3 substitution per site per year, the M/F NCR had an evolutionary rate three times higher, with 2.44 × 10-3 substitution per site per year. Phylogenetic analysis identified three distinct genetic groups. The Time of the Most Recent Common Ancestor (TMRCA) of H1 genotype was estimated at approximately 1988, while the first genetic group appeared around 1995 followed by two other genetic groups in 1999-2002. Bayesian skyline plot showed that the genetic diversity of the H1 genotype remained stable even though the number of MeV cases decreased 50 times between 2014 (52 628) and 2020 (993). The current coronavirus disease 2019 (COVID-19) pandemic might have some effect on the measles epidemic and further studies will be necessary to assess the genetic diversity of the H1 genotype in a post-COVID area.
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Affiliation(s)
- Jinhua Song
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases. National Institute for Viral Disease Control and Prevention, China CDC;, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Chongshan Li
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai
| | - Pierre Rivailler
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases. National Institute for Viral Disease Control and Prevention, China CDC;, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Huiling Wang
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases. National Institute for Viral Disease Control and Prevention, China CDC;, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Manli Hu
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases. National Institute for Viral Disease Control and Prevention, China CDC;, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China.,Department of Public Health Laboratory Sciences, School of Public Health, Changsha Medical University, Changsha, Hunan, China
| | - Zhen Zhu
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases. National Institute for Viral Disease Control and Prevention, China CDC;, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Aili Cui
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases. National Institute for Viral Disease Control and Prevention, China CDC;, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Naiying Mao
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases. National Institute for Viral Disease Control and Prevention, China CDC;, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Wenbo Xu
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases. National Institute for Viral Disease Control and Prevention, China CDC;, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases. National Institute for Viral Disease Control and Prevention, China CDC;, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China
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2
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Yang Q, Rivailler P, Zhu S, Yan D, Xie N, Tang H, Zhang Y, Xu W. Detection of multiple viruses potentially infecting humans in sewage water from Xinjiang Uygur Autonomous Region, China. Sci Total Environ 2021; 754:142322. [PMID: 33254887 DOI: 10.1016/j.scitotenv.2020.142322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 06/12/2023]
Abstract
The progress of sequencing technologies has facilitated metagenomics projects on environmental samples like sewage water. The present study concerned the analysis of sewage samples collected from 3 locations in Xinjiang Uygur Autonomous Region in China. The analysis focused on RNA viruses known to infect humans and identified viruses from 10 families. The proportion of human virus species in the sewage samples was relatively stable with an average of 17%. Thirty virus species known to infect humans were identified and they belonged to 6 families: Picornaviridae (12), Astroviridae (11), Reoviridae (3), Caliciviridae (2), Papillomaviridae (1) and Picobirnaviridae (1). A total of 16 full-length genomes were generated from Astroviridae, Picornaviridae (Salivirus and Kobuvirus) and Picobirnaviridae. Astroviruses appeared to be the most present viruses and were detected in all sewage samples. Analyzing the virome of sewage samples should help to monitor any potential risks to public health.
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Affiliation(s)
- Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Pierre Rivailler
- WHO WPRO Regional Reference Measles/Rubella Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Na Xie
- Xinjiang Uygur Autonomous Region Center for Disease Control and Prevention, Jianquanyi Road, Urumqi 830002, China
| | - Haishu Tang
- Xinjiang Uygur Autonomous Region Center for Disease Control and Prevention, Jianquanyi Road, Urumqi 830002, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China; WHO WPRO Regional Reference Measles/Rubella Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
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3
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Mao N, Zhu Z, Rivailler P, Yang J, Li Q, Han G, Yin J, Yu D, Sun L, Jiang H, Zhan Z, Xiang X, Mei H, Wang X, Zhang B, Yu P, Li H, Lei Z, Xu W. Multiple divergent Human mastadenovirus C co-circulating in mainland of China. Infect Genet Evol 2019; 76:104035. [PMID: 31505276 DOI: 10.1016/j.meegid.2019.104035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 01/22/2023]
Abstract
The human mastadenovirus C (HAdV-C) cause respiratory infections in children. Homologous recombination was clearly involved in the molecular evolution of HAdV-A, B, and D, but little is known about the molecular evolution of HAdV-C. From 2000 to 2016, 201 HAdV-C strains were collected from nine provinces covering six administrative regions of mainland of China via 3 existing surveillance programs, namely the febrile respiratory syndrome surveillance, the acute flaccid paralysis surveillance, and the hand, foot, and mouth disease surveillance system. The genes coding for the capsid protein (penton base, hexon, and fiber) of 201 HAdV-C strains were sequenced and compared with representative sequences publicly available. In addition, the whole genome sequence of 24 representative strains of HAdV-C was generated for further recombination analysis. Phylogenetic analysis of the penton base sequences of HAdV-C revealed six genetic groups (labelled as Px1-6), which showed that the penton base had more variation than previously thought. Based on the penton base, hexon, and fiber gene sequences, 16 new genetic patterns of HAdV-C circulating in mainland of China were identified in this study. Whole genome sequence analysis revealed frequent recombination events among HAdV-C genomes. This study is highly beneficial for case classification, tracking the transmission chain, and further epidemiological exploration of HAdV-C-related severe clinical diseases in the near future. Our data demonstrated that multiple newly divergent HAdV-C co-circulated across mainland China during the research period.
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Affiliation(s)
- Naiying Mao
- WHO WPRO Regional Reference Measles, Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Zhen Zhu
- WHO WPRO Regional Reference Measles, Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Pierre Rivailler
- WHO WPRO Regional Reference Measles, Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Jianfang Yang
- Shanxi Provincial Center for Disease Control and Prevention, Taiyuan, China
| | - Qi Li
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Guangyue Han
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, China
| | - Jie Yin
- Yunnan Provincial Center for Disease Control and Prevention, Kunming, China
| | - Deshan Yu
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, China
| | - Liwei Sun
- Changchun Children's Hospital, Changchun, China
| | | | - Zhifei Zhan
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Xingyu Xiang
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Hong Mei
- Xizang Provincial Center for Disease Control and Prevention, Lasa, China
| | - Xianjun Wang
- Shandong Provincial Center for Disease Control and Prevention, Jinan, China
| | - Bo Zhang
- Shandong Provincial Center for Disease Control and Prevention, Jinan, China
| | - Pengbo Yu
- Shaanxi Provincial Center for Disease Control and Prevention, Xian, China
| | - Hong Li
- WHO WPRO Regional Reference Measles, Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China; Anhui University of Science and Technology, Huainan, China
| | - Zhenqiang Lei
- WHO WPRO Regional Reference Measles, Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- WHO WPRO Regional Reference Measles, Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, China.
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4
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Cui A, Rivailler P, Zhu Z, Deng X, Hu Y, Wang Y, Li F, Sun Z, He J, Si Y, Tian X, Zhou S, Lei Y, Zheng H, Rota PA, Xu W. Evolutionary analysis of mumps viruses of genotype F collected in mainland China in 2001-2015. Sci Rep 2017; 7:17144. [PMID: 29215070 PMCID: PMC5719434 DOI: 10.1038/s41598-017-17474-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/26/2017] [Indexed: 01/29/2023] Open
Abstract
Mumps incidence in mainland China remains at a high level. Genotype F has been the predominant genotype of mumps virus (MuV) in the last 20 years in mainland China. To better understand the genetic characteristics of MuV in China, the sequences of the Small Hydrophobic (SH), Hemagglutinin-Neuraminidase (HN) and Fusion (F) genes of MuVs of genotype F collected during 2001-2015 were determined. The evolutionary rates of the HN and F genes were similar (0.5 × 10-3 substitutions/site/year) whereas the SH gene evolutionary rate was three times faster. The most recent common ancestor of genotype F was traced back to 1980. Four lineages were identified within HN and F MuV sequences. A phylogeographic analysis indicated that the genotype F viruses originally spread from the Liaoning and Shandong provinces followed by a spread to the South and East of China. This study provides important genetic baseline data for the development of prevention and control measures of mumps.
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Affiliation(s)
- Aili Cui
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Pierre Rivailler
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road Atlanta, Atlanta, GA, 30329-4027, United States
| | - Zhen Zhu
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Xiuying Deng
- Jiangsu Provincial Centers for Disease Control and Prevention, No. 172, Jiangsu Road, Nanjing, 210009, The People's Republic of China
| | - Ying Hu
- Jiangsu Provincial Centers for Disease Control and Prevention, No. 172, Jiangsu Road, Nanjing, 210009, The People's Republic of China
| | - Yan Wang
- Liaoning Provincial Centers for Disease Control and Prevention, No. 242, Shayang Road, Heping District, Shenyang, 110005, The People's Republic of China
| | - Fangcai Li
- Hunan Provincial Centers for Disease Control and Prevention, No. 450, Furongzhongluyiduan Road, Changsha, 410005, The People's Republic of China
| | - Zhaodan Sun
- Heilongjiang Provincial Centers for Disease Control and Prevention, No. 40, Youfang Road, Xiangfang District, Ha'erbin, 150030, The People's Republic of China
| | - Jilan He
- Sichuan Provincial Centers for Disease Control and Prevention, No. 6, Zhongxue Road, Chengdu, 610041, The People's Republic of China
| | - Yuan Si
- Shannxi Provincial Centers for Disease Control and Prevention, No. 3, Hepingwenwaijiandong Road, Xi'an, 710054, The People's Republic of China
| | - Xiaoling Tian
- Inner Mongolia Autonomous Region Center for Disease Control and Prevention, No. 50, E'erduosida Road, Huhehaote, 010031, The People's Republic of China
| | - Shujie Zhou
- Anhui Provincial Centers for Disease Control and Prevention, No. 12560, Fanhuadadao Road, Hefei, 230601, The People's Republic of China
| | - Yake Lei
- Hubei Provincial Centers for Disease Control and Prevention, No.6, Zhuodaoquanbeilu Road, Hongshan District, Wuhan, 430079, The People's Republic of China
| | - Huanying Zheng
- Guangdong Provincial Centers for Disease Control and Prevention, No. 176, Xingangxi Road, Guangzhou, 510300, The People's Republic of China
| | - Paul A Rota
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road Atlanta, Atlanta, GA, 30329-4027, United States.
| | - Wenbo Xu
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China.
- Medical school, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China.
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5
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Jensen NJ, Rivailler P, Tseng HF, Quinlivan ML, Radford K, Folster J, Harpaz R, LaRussa P, Jacobsen S, Scott Schmid D. Revisiting the genotyping scheme for varicella-zoster viruses based on whole-genome comparisons. J Gen Virol 2017; 98:1434-1438. [PMID: 28613146 DOI: 10.1099/jgv.0.000772] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report whole-genome sequences (WGSs) for four varicella-zoster virus (VZV) samples from a shingles study conducted by Kaiser Permanente of Southern California. Comparative genomics and phylogenetic analysis of all published VZV WGSs revealed that strain KY037798 is in clade IX, which shall henceforth be designated clade 9. Previously published single nucleotide polymorphisms (SNP)-based genotyping schemes fail to discriminate between clades 6 and VIII and employ positions that are not clade-specific. We provide an updated list of clade-specific positions that supersedes the list determined at the 2008 VZV nomenclature meeting. Finally, we propose a new targeted genotyping scheme that will discriminate the circulating VZV clades with at least a twofold redundancy. Genotyping strategies using a limited set of targeted SNPs will continue to provide an efficient 'first pass' method for VZV strain surveillance as vaccination programmes for varicella and zoster influence the dynamics of VZV transmission.
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Affiliation(s)
- Nancy J Jensen
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Pierre Rivailler
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Hung Fu Tseng
- Kaiser Permanente of Southern California, Department of Research and Evaluation, Pasadena, CA, USA
| | - Mark L Quinlivan
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA.,Present address: Labtech International Ltd, Uckfield, East Sussex, UK
| | - Kay Radford
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Jennifer Folster
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Rafael Harpaz
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Philip LaRussa
- Department of Pediatrics, Columbia University, College of Physicians and Surgeons,, New York, NY, USA
| | - Steven Jacobsen
- Kaiser Permanente of Southern California, Department of Research and Evaluation, Pasadena, CA, USA
| | - D Scott Schmid
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
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6
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Rivailler P, Abernathy E, Icenogle J. Genetic diversity of currently circulating rubella viruses: a need to define more precise viral groups. J Gen Virol 2017; 98:396-404. [PMID: 27959771 PMCID: PMC5797949 DOI: 10.1099/jgv.0.000680] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/08/2016] [Indexed: 02/07/2023] Open
Abstract
Recent studies have shown that the currently circulating rubella viruses are mostly members of two genotypes, 1E and 2B. Also, genetically distinct viruses of genotype 1G have been found in East and West Africa. This study used a Mantel test to objectively include both genetic diversity and geographic location in the definition of lineages, and identified statistically justified lineages (n=13) and sub-lineages (n=9) of viruses within genotypes 1G, 1E and 2B. Genotype 2B viruses were widely distributed, while viruses of genotype 1E as well as 1G and 1J were much more geographically restricted. This analysis showed that more precise groupings for rubella viruses are possible, which should improve the ability to track rubella viruses worldwide. A year-by-year analysis revealed gaps in surveillance that need to be resolved in order to support the surveillance needed for enhanced control and elimination goals for rubella.
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Affiliation(s)
- P Rivailler
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - E Abernathy
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - J Icenogle
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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7
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Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream MA, Shirley MW, Wan KL, Berriman M, Tomley FM, Pain A. Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Res 2014; 24:1676-85. [PMID: 25015382 PMCID: PMC4199364 DOI: 10.1101/gr.168955.113] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.
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Affiliation(s)
- Adam J Reid
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Damer P Blake
- Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom
| | - Hifzur R Ansari
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Karen Billington
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom
| | - Hilary P Browne
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Josephine Bryant
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Matt Dunn
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Stacy S Hung
- Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Fumiya Kawahara
- Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan
| | - Diego Miranda-Saavedra
- Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Tareq B Malas
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Hardeep Naghra
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Mridul Nair
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Neil D Rawlings
- European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Pierre Rivailler
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Chandra Subramaniam
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom
| | - Yea-Ling Tay
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia; Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Yong Woo
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Xikun Wu
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Amgen Limited, Uxbridge UB8 1DH, United Kingdom
| | - Bart Barrell
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Paul H Dear
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Christian Doerig
- Department of Microbiology, Monash University, Clayton VIC 3800, Australia
| | - Arthur Gruber
- Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Alasdair C Ivens
- Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - John Parkinson
- Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Marie-Adèle Rajandream
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Martin W Shirley
- The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF, United Kingdom
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia; Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Fiona M Tomley
- Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;
| | - Arnab Pain
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia;
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8
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Xu S, Zhang Y, Rivailler P, Wang H, Ji Y, Zhen Z, Mao N, Li C, Bellini WJ, Xu W, Rota PA. Evolutionary genetics of genotype H1 measles viruses in China from 1993 to 2012. J Gen Virol 2014; 95:1892-1899. [PMID: 24914068 PMCID: PMC4135087 DOI: 10.1099/vir.0.066746-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Virologic surveillance is a critical component of measles management. One of the criteria for verification of elimination of endemic measles is genetic analysis of wild-type viruses to demonstrate lack of an indigenous genotype. Measles is yet to be eliminated in China, and genotype H1 has been detected continuously since virologic surveillance was initiated in 1993. Virologic surveillance has been very active in China, providing a unique opportunity to conduct a detailed study of the evolution of a single, endemic genotype over a timespan of nearly two decades. Phylogenetic analysis performed on the 450 nt coding sequence for the C-terminal 150 amino acids of the nucleoprotein (N-450), fusion (F) gene and haemagglutinin (H) gene confirmed the continued circulation of genotype H1 viruses for 19 years. No evidence of selective pressure for the H protein was found. The substitution rates ranged from 0.75×10(-3) substitutions site(-1) year(-1) for H to 1.65×10(-3) substitutions site(-1) year(-1) for N-450. The time of most recent common ancestor (TMRCA) for genotype H1 was estimated as approximately 1985 (95 % highest probability density, 1979-1989). Finally, the overall diversity of measles sequences from China decreased from 2005 to 2012, coincident with a substantial decrease in measles cases. The results suggest that detailed evolutionary analyses should facilitate the documentation of eventual measles elimination in China. Moreover, the molecular approaches used in this study can be applied in other countries approaching measles elimination.
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Affiliation(s)
- Songtao Xu
- WHO Regional Reference Laboratory for Measles for the Western Pacific Region, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yan Zhang
- WHO Regional Reference Laboratory for Measles for the Western Pacific Region, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Pierre Rivailler
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Huiling Wang
- WHO Regional Reference Laboratory for Measles for the Western Pacific Region, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yixin Ji
- WHO Regional Reference Laboratory for Measles for the Western Pacific Region, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Zhu Zhen
- WHO Regional Reference Laboratory for Measles for the Western Pacific Region, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Naiying Mao
- WHO Regional Reference Laboratory for Measles for the Western Pacific Region, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Chongshan Li
- Shanghai Center for Disease Control and Prevention, Shanghai City, PR China
| | - William J Bellini
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Wenbo Xu
- WHO Regional Reference Laboratory for Measles for the Western Pacific Region, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Paul A Rota
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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9
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Namuwulya P, Abernathy E, Bukenya H, Bwogi J, Tushabe P, Birungi M, Seguya R, Kabaliisa T, Alibu VP, Kayondo JK, Rivailler P, Icenogle J, Bakamutumaho B. Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012. J Med Virol 2014; 86:2107-13. [PMID: 24700073 DOI: 10.1002/jmv.23935] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2014] [Indexed: 11/07/2022]
Abstract
Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confirm measles and rubella, but molecular epidemiologic aspects of rubella circulation have so far not been documented in Uganda. Twenty throat swab or oral fluid samples collected from 12 districts during routine rash and fever surveillance between 2003 and 2012 were identified as rubella virus RNA positive and PCR products encompassing the region used for genotyping were sequenced. Phylogenetic analysis of the 20 sequences identified 19 genotype 1G viruses and 1 genotype 1E virus. Genotype-specific trees showed that the Uganda viruses belonged to specific clusters for both genotypes 1G and 1E and grouped with similar sequences from neighboring countries. Genotype 1G was predominant in Uganda. More epidemiological and molecular epidemiological data are required to determine if genotype 1E is also endemic in Uganda. The information obtained in this study will assist the immunization program in monitoring changes in circulating genotypes.
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10
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Tseng HF, Schmid DS, Harpaz R, LaRussa P, Jensen NJ, Rivailler P, Radford K, Folster J, Jacobsen SJ. Herpes zoster caused by vaccine-strain varicella zoster virus in an immunocompetent recipient of zoster vaccine. Clin Infect Dis 2014; 58:1125-8. [PMID: 24470276 DOI: 10.1093/cid/ciu058] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report the first laboratory-documented case of herpes zoster caused by the attenuated varicella zoster virus (VZV) contained in Zostavax in a 68-year-old immunocompetent adult with strong evidence of prior wild-type VZV infection. The complete genome sequence of the isolate revealed that the strain carried 15 of 42 (36%) recognized varicella vaccine-associated single-nucleotide polymorphisms, including all 5 of the fixed vaccine markers present in nearly all of the strains in the vaccine. The case of herpes zoster was relatively mild and resolved without complications.
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Affiliation(s)
- Hung Fu Tseng
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena
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11
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Shepard SS, Davis CT, Bahl J, Rivailler P, York IA, Donis RO. LABEL: fast and accurate lineage assignment with assessment of H5N1 and H9N2 influenza A hemagglutinins. PLoS One 2014; 9:e86921. [PMID: 24466291 PMCID: PMC3900692 DOI: 10.1371/journal.pone.0086921] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/16/2013] [Indexed: 11/30/2022] Open
Abstract
The evolutionary classification of influenza genes into lineages is a first step in understanding their molecular epidemiology and can inform the subsequent implementation of control measures. We introduce a novel approach called Lineage Assignment By Extended Learning (LABEL) to rapidly determine cladistic information for any number of genes without the need for time-consuming sequence alignment, phylogenetic tree construction, or manual annotation. Instead, LABEL relies on hidden Markov model profiles and support vector machine training to hierarchically classify gene sequences by their similarity to pre-defined lineages. We assessed LABEL by analyzing the annotated hemagglutinin genes of highly pathogenic (H5N1) and low pathogenicity (H9N2) avian influenza A viruses. Using the WHO/FAO/OIE H5N1 evolution working group nomenclature, the LABEL pipeline quickly and accurately identified the H5 lineages of uncharacterized sequences. Moreover, we developed an updated clade nomenclature for the H9 hemagglutinin gene and show a similarly fast and reliable phylogenetic assessment with LABEL. While this study was focused on hemagglutinin sequences, LABEL could be applied to the analysis of any gene and shows great potential to guide molecular epidemiology activities, accelerate database annotation, and provide a data sorting tool for other large-scale bioinformatic studies.
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MESH Headings
- Animals
- Bayes Theorem
- Cell Lineage
- Chickens
- Evolution, Molecular
- Hemagglutinin Glycoproteins, Influenza Virus/analysis
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Influenza A Virus, H5N1 Subtype/classification
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza A Virus, H9N2 Subtype/classification
- Influenza A Virus, H9N2 Subtype/genetics
- Influenza A Virus, H9N2 Subtype/pathogenicity
- Influenza in Birds/genetics
- Influenza in Birds/virology
- Phylogeny
- Poultry Diseases/virology
- Sequence Analysis, DNA
- Software
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Affiliation(s)
- Samuel S. Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - C. Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Justin Bahl
- Laboratory of Virus Evolution in Program of Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, Texas, United States of America
| | - Pierre Rivailler
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ian A. York
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ruben O. Donis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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12
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Ariza ME, Rivailler P, Glaser R, Chen M, Williams MV. Epstein-Barr virus encoded dUTPase containing exosomes modulate innate and adaptive immune responses in human dendritic cells and peripheral blood mononuclear cells. PLoS One 2013; 8:e69827. [PMID: 23894549 PMCID: PMC3718799 DOI: 10.1371/journal.pone.0069827] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/15/2013] [Indexed: 12/11/2022] Open
Abstract
We have recently demonstrated that Epstein-Barr virus (EBV)-encoded deoxyuridine triphosphate nucleotidohydrolase (dUTPase) modulates innate immunity in human primary monocyte-derived macrophages through toll-like receptor (TLR) 2 leading to NF-κB activation and the production of pro-inflammatory cytokines. Our previous depletion studies indicated that dendritic cells (DCs) may also be a target of the EBV-encoded dUTPase. However, the role of EBV-encoded dUTPase in DC activation/function and its potential contribution to the inflammatory cellular milieu characteristic of EBV-associated diseases remains poorly understood. In the present study, we demonstrate that EBV-encoded dUTPase significantly altered the expression of genes involved in oncogenesis, inflammation and viral defense mechanisms in human primary DCs by microarray analysis. Proteome array studies revealed that EBV-encoded dUTPase modulates DC immune responses by inducing the secretion of pro-inflammatory TH1/TH17 cytokines. More importantly, we demonstrate that EBV-encoded dUTPase is secreted in exosomes from chemically induced Raji cells at sufficient levels to induce NF-κB activation and cytokine secretion in primary DCs and peripheral blood mononuclear cells (PBMCs). Interestingly, the production of pro-inflammatory cytokines in DCs and PBMCs was TLR2-dependent. Together these findings suggest that the EBV-encoded dUTPase may act as an intercellular signaling molecule capable of modulating the cellular microenvironment and thus, it may be important in the pathophysiology of EBV related diseases.
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Affiliation(s)
- Maria Eugenia Ariza
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA.
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13
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Younan M, Poh MK, Elassal E, Davis T, Rivailler P, Balish AL, Simpson N, Jones J, Deyde V, Loughlin R, Perry I, Gubareva L, ElBadry MA, Truelove S, Gaynor AM, Mohareb E, Amin M, Cornelius C, Pimentel G, Earhart K, Naguib A, Abdelghani AS, Refaey S, Klimov AI, Donis RO, Kandeel A. Microevolution of highly pathogenic avian influenza A(H5N1) viruses isolated from humans, Egypt, 2007-2011. Emerg Infect Dis 2013; 19:43-50. [PMID: 23260983 PMCID: PMC3563221 DOI: 10.3201/eid1901.121080] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We analyzed highly pathogenic avian influenza A(H5N1) viruses isolated from humans infected in Egypt during 2007-2011. All analyzed viruses evolved from the lineage of subtype H5N1 viruses introduced into Egypt in 2006; we found minimal evidence of reassortment and no exotic introductions. The hemagglutinin genes of the viruses from 2011 formed a monophyletic group within clade 2.2.1 that also included human viruses from 2009 and 2010 and contemporary viruses from poultry; this finding is consistent with zoonotic transmission. Although molecular markers suggestive of decreased susceptibility to antiviral drugs were detected sporadically in the neuraminidase and matrix 2 proteins, functional neuraminidase inhibition assays did not identify resistant viruses. No other mutations suggesting a change in the threat to public health were detected in the viral proteomes. However, a comparison of representative subtype H5N1 viruses from 2011 with older subtype H5N1 viruses from Egypt revealed substantial antigenic drift.
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Affiliation(s)
- Mary Younan
- US Naval Medical Research Unit No.3, Cairo, Egypt
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14
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Xu J, Davis CT, Christman MC, Rivailler P, Zhong H, Donis RO, Lu G. Evolutionary history and phylodynamics of influenza A and B neuraminidase (NA) genes inferred from large-scale sequence analyses. PLoS One 2012; 7:e38665. [PMID: 22808012 PMCID: PMC3394769 DOI: 10.1371/journal.pone.0038665] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 05/10/2012] [Indexed: 12/22/2022] Open
Abstract
Background Influenza neuraminidase (NA) is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamics, although critical for the prevention and control of influenza epidemics and pandemics, remains lacking. Methodology/Principal findings Evolutionary and phylogenetic analyses of influenza NA sequences using Maximum Likelihood and Bayesian MCMC methods demonstrated that the divergence of influenza viruses into types A and B occurred earlier than the divergence of influenza A NA subtypes. Twenty-three lineages were identified within influenza A, two lineages were classified within influenza B, and most lineages were specific to host, subtype or geographical location. Interestingly, evolutionary rates vary not only among lineages but also among branches within lineages. The estimated tMRCAs of influenza lineages suggest that the viruses of different lineages emerge several months or even years before their initial detection. The dN/dS ratios ranged from 0.062 to 0.313 for influenza A lineages, and 0.257 to 0.259 for influenza B lineages. Structural analyses revealed that all positively selected sites are at the surface of the NA protein, with a number of sites found to be important for host antibody and drug binding. Conclusions/Significance The divergence into influenza type A and B from a putative ancestral NA was followed by the divergence of type A into nine NA subtypes, of which 23 lineages subsequently diverged. This study provides a better understanding of influenza NA lineages and their evolutionary dynamics, which may facilitate early detection of newly emerging influenza viruses and thus improve influenza surveillance.
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Affiliation(s)
- Jianpeng Xu
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
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15
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Chen LM, Rivailler P, Hossain J, Carney P, Balish A, Perry I, Davis CT, Garten R, Shu B, Xu X, Klimov A, Paulson JC, Cox NJ, Swenson S, Stevens J, Vincent A, Gramer M, Donis RO. Receptor specificity of subtype H1 influenza A viruses isolated from swine and humans in the United States. Virology 2011; 412:401-10. [PMID: 21333316 DOI: 10.1016/j.virol.2011.01.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 12/21/2010] [Accepted: 01/13/2011] [Indexed: 12/31/2022]
Abstract
The evolution of classical swine influenza viruses receptor specificity preceding the emergence of the 2009 H1N1 pandemic virus was analyzed in glycan microarrays. Classical swine influenza viruses from the α, β, and γ antigenic clusters isolated between 1945 and 2009 revealed a binding profile very similar to that of 2009 pandemic H1N1 viruses, with selectivity for α2-6-linked sialosides and very limited binding to α2-3 sialosides. Despite considerable genetic divergence, the 'human-like' H1N1 viruses circulating in swine retained strong binding preference for α2-6 sialylated glycans. Interspecies transmission of H1N1 influenza viruses from swine to humans or from humans to swine has not driven selection of viruses with distinct novel receptor binding specificities. Classical swine and human seasonal H1N1 influenza viruses have conserved specificity for similar α2-6-sialoside receptors in spite of long term circulation in separate hosts, suggesting that humans and swine impose analogous selection pressures on the evolution of receptor binding function.
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Affiliation(s)
- Li-Mei Chen
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
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16
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Robertson JS, Nicolson C, Harvey R, Johnson R, Major D, Guilfoyle K, Roseby S, Newman R, Collin R, Wallis C, Engelhardt OG, Wood JM, Le J, Manojkumar R, Pokorny BA, Silverman J, Devis R, Bucher D, Verity E, Agius C, Camuglia S, Ong C, Rockman S, Curtis A, Schoofs P, Zoueva O, Xie H, Li X, Lin Z, Ye Z, Chen LM, O'Neill E, Balish A, Lipatov AS, Guo Z, Isakova I, Davis CT, Rivailler P, Gustin KM, Belser JA, Maines TR, Tumpey TM, Xu X, Katz JM, Klimov A, Cox NJ, Donis RO. The development of vaccine viruses against pandemic A(H1N1) influenza. Vaccine 2011; 29:1836-43. [PMID: 21199698 DOI: 10.1016/j.vaccine.2010.12.044] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 11/26/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
Abstract
Wild type human influenza viruses do not usually grow well in embryonated hens' eggs, the substrate of choice for the production of inactivated influenza vaccine, and vaccine viruses need to be developed specifically for this purpose. In the event of a pandemic of influenza, vaccine viruses need to be created with utmost speed. At the onset of the current A(H1N1) pandemic in April 2009, a network of laboratories began a race against time to develop suitable candidate vaccine viruses. Two approaches were followed, the classical reassortment approach and the more recent reverse genetics approach. This report describes the development and the characteristics of current pandemic H1N1 candidate vaccine viruses.
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Affiliation(s)
- James S Robertson
- Division of Virology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar EN6 3QG, UK.
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17
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Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RAM, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox NJ. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009; 325:197-201. [PMID: 19465683 PMCID: PMC3250984 DOI: 10.1126/science.1176225] [Citation(s) in RCA: 1771] [Impact Index Per Article: 118.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Since its identification in April 2009, an A(H1N1) virus containing a unique combination of gene segments from both North American and Eurasian swine lineages has continued to circulate in humans. The lack of similarity between the 2009 A(H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Its low genetic diversity suggests that the introduction into humans was a single event or multiple events of similar viruses. Molecular markers predictive of adaptation to humans are not currently present in 2009 A(H1N1) viruses, suggesting that previously unrecognized molecular determinants could be responsible for the transmission among humans. Antigenically the viruses are homogeneous and similar to North American swine A(H1N1) viruses but distinct from seasonal human A(H1N1).
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MESH Headings
- Animals
- Antibodies, Viral/immunology
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Disease Outbreaks
- Evolution, Molecular
- Genes, Viral
- Genetic Variation
- Genome, Viral
- Hemagglutination Inhibition Tests
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A virus/genetics
- Influenza, Human/epidemiology
- Influenza, Human/immunology
- Influenza, Human/virology
- Mutation
- Neuraminidase/genetics
- Orthomyxoviridae Infections/veterinary
- Orthomyxoviridae Infections/virology
- Phylogeny
- Reassortant Viruses/genetics
- Swine
- Swine Diseases/virology
- Viral Matrix Proteins/genetics
- Viral Nonstructural Proteins/genetics
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Affiliation(s)
- Rebecca J Garten
- WHO Collaborating Center for Influenza, Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA
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18
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Hughes AL, Friedman R, Rivailler P, French JO. Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. Mol Biol Evol 2008; 25:2199-209. [PMID: 18667439 PMCID: PMC2734133 DOI: 10.1093/molbev/msn166] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2008] [Indexed: 11/14/2022] Open
Abstract
Comparison of the ratio of nonsynonymous to synonymous polymorphisms within species with the ratio of nonsynonymous to synonymous substitutions between species has been widely used as a supposed indicator of positive Darwinian selection, with the ratio of these 2 ratios being designated as a neutrality index (NI). Comparison of genome-wide polymorphism within 12 species of bacteria with divergence from an outgroup species showed substantial differences in NI among taxa. A low level of nonsynonymous polymorphism at a locus was the best predictor of NI < 1, rather than a high level of nonsynonymous substitution between species. Moreover, genes with NI < 1 showed a strong tendency toward the occurrence of rare nonsynonymous polymorphisms, as expected under the action of ongoing purifying selection. Thus, our results are more consistent with the hypothesis that a high relative rate of between-species nonsynonymous substitution reflects mainly the action of purifying selection within species to eliminate slightly deleterious mutations rather than positive selection between species. This conclusion is consistent with previous results highlighting an important role of slightly deleterious variants in bacterial evolution and suggests caution in the use of the McDonald-Kreitman test and related statistics as tests of positive selection.
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Affiliation(s)
- Austin L Hughes
- Department of Biological Sciences, University of South Carolina, USA
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19
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Hughes AL, Rivailler P. Phylogeny and recombination history of gallid herpesvirus 2 (Marek's disease virus) genomes. Virus Res 2007; 130:28-33. [PMID: 17566585 PMCID: PMC2756229 DOI: 10.1016/j.virusres.2007.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 05/08/2007] [Accepted: 05/08/2007] [Indexed: 01/25/2023]
Abstract
Phylogenetic analyses based on concatenated amino acid sequences from orthologous loci from eight genomes of alpha herpesviruses infecting birds provided strong support for the following hypotheses: (1) gallid HV3 is a sister taxon to gallid HV2 but gallid HV1 is not closely related to the other two chicken herpesviruses; (2) meleagrid HV1 is closer to both gallid HV2 and gallid HV3 than is gallid HV1; (3) within gallid HV2, the virulent GA genome forms an outgroup to both the avirulent CVI988 genome and the highly virulent Md5 and Md11 genomes. Analysis of the pattern of synonymous nucleotide substitution between orthologous genes shared by four complete genomes of gallid HV2 showed strong evidence of past events of homologous recombination that homogenized certain loci between genomes. Eight of these loci represented cases of loci homogenized between the CVI988, on the one hand, and the Md5 and Md11 genomes, on the other hand. Two others represented loci where the GA genome was homogenized with those of Md5 and Md11. The two loci (UL49.5 and RLORF12) that were homogenized among the virulent genomes GA, Md5, and Md11 are candidates for contributing to viral virulence.
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MESH Headings
- Animals
- Birds
- Genome, Viral/genetics
- Herpesvirus 1, Gallid/classification
- Herpesvirus 1, Gallid/genetics
- Herpesvirus 1, Gallid/isolation & purification
- Herpesvirus 2, Gallid/classification
- Herpesvirus 2, Gallid/genetics
- Herpesvirus 2, Gallid/isolation & purification
- Herpesvirus 3, Gallid/classification
- Herpesvirus 3, Gallid/genetics
- Herpesvirus 3, Gallid/isolation & purification
- Marek Disease/virology
- Phylogeny
- Recombination, Genetic
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Affiliation(s)
- Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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20
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Ling KH, Rajandream MA, Rivailler P, Ivens A, Yap SJ, Madeira AM, Mungall K, Billington K, Yee WY, Bankier AT, Carroll F, Durham AM, Peters N, Loo SS, Mat Isa MN, Novaes J, Quail M, Rosli R, Nor Shamsudin M, Sobreira TJ, Tivey AR, Wai SF, White S, Wu X, Kerhornou A, Blake D, Mohamed R, Shirley M, Gruber A, Berriman M, Tomley F, Dear PH, Wan KL. Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization. Genome Res 2007; 17:311-9. [PMID: 17284678 PMCID: PMC1800922 DOI: 10.1101/gr.5823007] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Eimeria tenella is an intracellular protozoan parasite that infects the intestinal tracts of domestic fowl and causes coccidiosis, a serious and sometimes lethal enteritis. Eimeria falls in the same phylum (Apicomplexa) as several human and animal parasites such as Cryptosporidium, Toxoplasma, and the malaria parasite, Plasmodium. Here we report the sequencing and analysis of the first chromosome of E. tenella, a chromosome believed to carry loci associated with drug resistance and known to differ between virulent and attenuated strains of the parasite. The chromosome--which appears to be representative of the genome--is gene-dense and rich in simple-sequence repeats, many of which appear to give rise to repetitive amino acid tracts in the predicted proteins. Most striking is the segmentation of the chromosome into repeat-rich regions peppered with transposon-like elements and telomere-like repeats, alternating with repeat-free regions. Predicted genes differ in character between the two types of segment, and the repeat-rich regions appear to be associated with strain-to-strain variation.
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Affiliation(s)
- King-Hwa Ling
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- Molecular Genetics Laboratory, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Marie-Adele Rajandream
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Pierre Rivailler
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Alasdair Ivens
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Soon-Joo Yap
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Alda M.B.N. Madeira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Karen Mungall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Karen Billington
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Wai-Yan Yee
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Alan T. Bankier
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
| | - Fionnadh Carroll
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Alan M. Durham
- Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Nicholas Peters
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Shu-San Loo
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Jeniffer Novaes
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Michael Quail
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Rozita Rosli
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- Molecular Genetics Laboratory, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Mariana Nor Shamsudin
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Tiago J.P. Sobreira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Adrian R. Tivey
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Siew-Fun Wai
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Sarah White
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Xikun Wu
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Arnaud Kerhornou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Damer Blake
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Rahmah Mohamed
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Martin Shirley
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Arthur Gruber
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo SP, 05508-000, Brazil
| | - Matthew Berriman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Fiona Tomley
- Division of Microbiology, Institute for Animal Health, Compton Laboratory, Compton, Near Newbury, Berkshire, RG20 7NN, United Kingdom
| | - Paul H. Dear
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
- Corresponding author.E-mail ; fax 44-1-223-412-178
| | - Kiew-Lian Wan
- Malaysia Genome Institute, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- Corresponding author.E-mail ; fax 44-1-223-412-178
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Abstract
A pathogenic isolate of rhesus cytomegalovirus (rhCMV 180.92) was cloned, sequenced, and annotated. Comparisons with the published rhCMV 68.1 genome revealed 8 open reading frames (ORFs) in isolate 180.92 that are absent in 68.1, 10 ORFs in 68.1 that are absent in 180.92, and 34 additional ORFs that were not previously annotated. Most of the differences appear to be due to genetic rearrangements in both isolates from a region that is frequently altered in human CMV (hCMV) during in vitro passage. These results indicate that the rhCMV ORF repertoire is larger than previously recognized. Like hCMV, understanding of the complete coding capacity of rhCMV is complicated by genomic instability and may require comparisons with additional isolates in vitro and in vivo.
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Affiliation(s)
- Pierre Rivailler
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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22
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Rivailler P, Carville A, Kaur A, Rao P, Quink C, Kutok JL, Westmoreland S, Klumpp S, Simon M, Aster JC, Wang F. Experimental rhesus lymphocryptovirus infection in immunosuppressed macaques: an animal model for Epstein-Barr virus pathogenesis in the immunosuppressed host. Blood 2004; 104:1482-9. [PMID: 15150077 DOI: 10.1182/blood-2004-01-0342] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To develop a model for Epstein-Barr virus (EBV) pathogenesis in immunosuppressed hosts, we studied experimental infections of immunocompetent versus SHIV 89.6P-infected, immunosuppressed rhesus macaques with the EBV-related rhesus lymphocryptovirus (LCV). Primary LCV infection after oral inoculation of 4 immunocompetent animals was characterized by an acute viremia and seroconversion followed by asymptomatic LCV persistence. Four immunosuppressed macaques infected orally with LCV failed to develop an LCV-specific humoral response and viremia was more pronounced, but there was no evidence of LCV-induced lymphoproliferative disease. A more aggressive primary challenge was administered by intravenous inoculation of 10(8) autologous, LCV-immortalized B cells in 4 additional immunosuppressed animals. Two animals with modest immunosuppression remained asymptomatic, and 1 of 2 severely immunosuppressed animals developed an aggressive, monoclonal LCV-positive lymphoma. These studies demonstrate the potential for lymphomagenesis in an experimental model system for EBV infection and underscore the strength and depth of immune control in limiting LCV-induced lymphoproliferative disease.
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Affiliation(s)
- Pierre Rivailler
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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23
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Rivailler P, Cho YG, Wang F. Complete genomic sequence of an Epstein-Barr virus-related herpesvirus naturally infecting a new world primate: a defining point in the evolution of oncogenic lymphocryptoviruses. J Virol 2002; 76:12055-68. [PMID: 12414947 PMCID: PMC136909 DOI: 10.1128/jvi.76.23.12055-12068.2002] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Callitrichine herpesvirus 3 (CalHV-3) was isolated from a B-cell lymphoma arising spontaneously in the New World primate Callithrix jacchus, the common marmoset. Partial genomic sequence analysis definitively identified CalHV-3 as a member of the Epstein-Barr virus (EBV)-related lymphocryptovirus (LCV) genus and extended the known host range of LCVs beyond humans and Old World nonhuman primates. We have now completed the first genomic sequence of an LCV infecting a New World primate by describing the unique short region, the major internal repeat, and a portion of the unique long region. This portion of the genome contains the putative latent origin of replication and 13 additional open reading frames (ORFs), 5 of which show no homology to any viral or cell genes. One of the novel genes, C5, is a positional homologue for the transformation-essential EBV gene EBNA-2. The marmoset LCV genome is also notable for the absence of viral interleukin-10 and small nonpolyadenylated RNA homologues. Marmoset LCV transcripts encoding putative latent infection nuclear proteins have a common leader sequence that is spliced from the major internal repeat in a manner similar to that of the EBV EBNA-LP, suggesting strong conservation of a common promoter and splicing of these latent infection mRNAs. An EBV LMP2A-like spliced transcript crossing the terminal repeats encodes a unique ORF, C7, with multiple transmembrane domains and tyrosine kinase phosphorylation sites functionally reminiscent of EBV LMP2A. However, the carboxy-terminal location of the candidate phosphotyrosine residues is more reminiscent of the Kaposi's sarcoma-associated herpesvirus K15 gene and provides potential evidence of an evolutionary transition from rhadinoviruses to lymphocryptoviruses. The unusual gene repertoire of the marmoset LCV differentiates ancestral viral genes likely present in an LCV progenitor from viral genes acquired later as primates and LCV coevolved, providing a defining point in the evolution of oncogenic LCVs.
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Affiliation(s)
- Pierre Rivailler
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
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24
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Marie JC, Astier AL, Rivailler P, Rabourdin-Combe C, Wild TF, Horvat B. Linking innate and acquired immunity: divergent role of CD46 cytoplasmic domains in T cell induced inflammation. Nat Immunol 2002; 3:659-66. [PMID: 12055630 DOI: 10.1038/ni810] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
CD46 is a widely expressed transmembrane protein that was initially identified as binding and inactivating C3b and C4b complement products. We used mice that were transgenic for one of two human CD46 isoforms that differ in their cytoplasmic domains (termed CD46-1 and CD46-2) to analyze the effect of CD46 stimulation on the immune response. We show here that CD46 can regulate inflammatory responses, either by inhibiting (CD46-1) or increasing (CD46-2) the contact hypersensitivity reaction. We found that engagement of CD46-1 or CD46-2 differentially affected CD8(+) T cell cytotoxicity, CD4(+) T cell proliferation, interleukin 2 (IL-2) and IL-10 production as well as tyrosine phosphorylation of Vav in T lymphocytes. These results indicate that CD46 plays a role in regulating the T cell induced inflammatory reaction and in fine-tuning the cellular immune response by bridging innate and acquired immunity.
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MESH Headings
- Animals
- Antigens, CD/genetics
- Antigens, CD/immunology
- Binding Sites
- CD4-Positive T-Lymphocytes/cytology
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- Cell Division
- Cytoplasm
- Cytotoxicity, Immunologic/immunology
- Dermatitis, Contact/immunology
- Dinitrofluorobenzene/adverse effects
- Disease Models, Animal
- Immunity, Active/immunology
- Immunity, Innate/immunology
- Interleukin-10/biosynthesis
- Interleukin-2/biosynthesis
- Membrane Cofactor Protein
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/immunology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Transgenic
- Protein Isoforms/immunology
- Signal Transduction/immunology
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Affiliation(s)
- Julien C Marie
- INSERM U404, Immunité et Vaccination, CERVI, 21 avenue Tony Garnier, 69365 Lyon, cedex 07, France
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25
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Rivailler P, Jiang H, Cho YG, Quink C, Wang F. Complete nucleotide sequence of the rhesus lymphocryptovirus: genetic validation for an Epstein-Barr virus animal model. J Virol 2002; 76:421-6. [PMID: 11739708 PMCID: PMC135707 DOI: 10.1128/jvi.76.1.421-426.2002] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We sequenced the rhesus lymphocryptovirus (LCV) genome in order to determine its genetic similarity to Epstein-Barr virus (EBV). The rhesus LCV encodes a repertoire identical to that of EBV, with 80 open reading frames, including cellular interleukin-10, bcl-2, and colony-stimulating factor 1 receptor homologues and an equivalent set of viral glycoproteins. The highly conserved rhesus LCV gene repertoire provides a unique animal model for the study of EBV pathogenesis.
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Affiliation(s)
- Pierre Rivailler
- Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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26
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Evlashev A, Valentin H, Rivailler P, Azocar O, Rabourdin-Combe C, Horvat B. Differential permissivity to measles virus infection of human and CD46-transgenic murine lymphocytes. J Gen Virol 2001; 82:2125-2129. [PMID: 11514721 DOI: 10.1099/0022-1317-82-9-2125] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of measles virus (MV) pathogenesis requires the development of an adequate small animal model of MV infection. In this study, permissivity to MV infection was compared in human and transgenic murine T lymphocytes, expressing different levels of the human MV receptor, CD46. Whereas MV binding and entry correlated with CD46 expression, higher levels of MV replication were always observed in human T lymphocytes. This suggests the existence of intracellular factors, acting posterior to virus entry, that could limit MV replication in murine lymphocytes and should be considered when creating new animal models of MV infection.
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Affiliation(s)
- Alexey Evlashev
- INSERM U503, Immunobiologie Fondamentale et Clinique1 and INSERM U404, Immunité et Vaccination, CERVI2, 21 Av. Tony Garnier, 69365 Lyon, France
| | - Hélène Valentin
- INSERM U503, Immunobiologie Fondamentale et Clinique1 and INSERM U404, Immunité et Vaccination, CERVI2, 21 Av. Tony Garnier, 69365 Lyon, France
| | - Pierre Rivailler
- INSERM U503, Immunobiologie Fondamentale et Clinique1 and INSERM U404, Immunité et Vaccination, CERVI2, 21 Av. Tony Garnier, 69365 Lyon, France
| | - Olga Azocar
- INSERM U503, Immunobiologie Fondamentale et Clinique1 and INSERM U404, Immunité et Vaccination, CERVI2, 21 Av. Tony Garnier, 69365 Lyon, France
| | - Chantal Rabourdin-Combe
- INSERM U503, Immunobiologie Fondamentale et Clinique1 and INSERM U404, Immunité et Vaccination, CERVI2, 21 Av. Tony Garnier, 69365 Lyon, France
| | - Branka Horvat
- INSERM U503, Immunobiologie Fondamentale et Clinique1 and INSERM U404, Immunité et Vaccination, CERVI2, 21 Av. Tony Garnier, 69365 Lyon, France
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27
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Abstract
Gamma-herpesviruses closely related to the Epstein-Barr virus (EBV) are known to naturally infect Old World non-human primates and are classified in the same lymphocryptovirus (LCV) genera. LCV infecting humans and Old World primates share similar biology, and recent studies have demonstrated that these viruses share a similar repertoire of viral genes. Surprisingly, the latent infection genes associated with cell growth transformation demonstrate the most striking sequence divergence, but the functional mechanisms for these genes are generally well conserved. The recent discovery of LCVs naturally infecting New World primates has rewritten the old paradigm of LCV host range restriction to humans and Old World non-human primates, so that these viruses are more widespread than previously believed. However, the New World LCV genome has significant and interesting differences from EBV and other Old World LCVs despite similar biological properties. Thus, the simian homologues of EBV can provide an important animal model for studying LCV pathogenesis, and the similarities and differences that have evolved among these related viruses can provide a unique perspective towards a better understanding of EBV.
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Affiliation(s)
- F Wang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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28
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Abstract
Epstein-Barr virus (EBV) is implicated in the development of human B cell lymphomas and carcinomas. Although related oncogenic herpesviruses were believed to be endemic only in Old World primate species, we now find these viruses to be endemic in New World primates. We have isolated a transforming, EBV-related virus from spontaneous B cell lymphomas of common marmosets (Callithrix jacchus). Sequencing of two-thirds of the genome reveals considerable divergence from the genomes of EBV and Old World primate EBV-related viruses, including differences in genes important for virus-induced cell growth transformation and pathogenesis. DNA related to the C. jacchus herpesvirus is frequently detected in squirrel monkey peripheral blood lymphocytes, indicating that persistent infection with EBV-related viruses is prevalent in both New World primate families. Understanding how these more divergent EBV-related viruses achieve similar biologic outcomes in their natural host is likely to provide important insights into EBV infection, B cell growth transformation, and oncogenesis.
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MESH Headings
- Amino Acid Sequence
- Animals
- Callithrix
- Cloning, Molecular
- DNA, Viral/genetics
- Gammaherpesvirinae/classification
- Gammaherpesvirinae/genetics
- Gammaherpesvirinae/isolation & purification
- Genetic Variation
- Genome, Viral
- Glutathione Transferase/genetics
- Herpesvirus 4, Human/classification
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/isolation & purification
- Herpesvirus 8, Human/genetics
- Humans
- Lymphoma, B-Cell/veterinary
- Lymphoma, B-Cell/virology
- Molecular Sequence Data
- Open Reading Frames
- Phylogeny
- Primate Diseases/virology
- Saimiri
- Sequence Alignment
- Sequence Homology, Amino Acid
- Transfection
- Tumor Cells, Cultured
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Affiliation(s)
- Y Cho
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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29
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Abstract
Latent membrane protein 2B (LMP2B) is expressed during latent Epstein-Barr virus (EBV) infection, but little is known about its role. The goal of this study was to determine whether an LMP2B homologue is conserved in the rhesus monkey lymphocryptovirus (LCV). Both rhesus LCV LMP2A and LMP2B genes were cloned and sequenced. The rhesus LCV LMP2B gene is positionally conserved, and the EBNA-2 responsiveness and the bidirectional nature of the LMP1-LMP2B promoter have also been functionally conserved. However, this region of the genome encoding the LMP1, LMP1-LMP2B promoter, and LMP2B first exon demonstrates the most dramatic nucleotide sequence divergence between human and nonhuman LCV observed to date. Evolution of the rhesus LCV LMP2B promoter and transcript despite the dynamic nature of this genomic region reflects strong selective pressure for a yet-to-be-identified LMP2B function.
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Affiliation(s)
- P Rivailler
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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30
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Rivailler P, Trescol-Biémont MC, Gimenez C, Rabourdin-Combe C, Horvat B. Enhanced MHC class II-restricted presentation of measles virus (MV) hemagglutinin in transgenic mice expressing human MV receptor CD46. Eur J Immunol 1998; 28:1301-14. [PMID: 9565370 DOI: 10.1002/(sici)1521-4141(199804)28:04<1301::aid-immu1301>3.0.co;2-s] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This study analyzes the role of the measles virus (MV) receptor, i.e. the human CD46 molecule, in the MHC class II-restricted presentation of MV hemagglutinin (H). We generated transgenic mice ubiquitously expressing CD46, with a similar level of transgene expression on the surface of antigen-presenting cells (APC), i.e. B cells, dendritic cells (DC) and macrophages. APC isolated from transgenic mice and nontransgenic controls were tested for their ability to present MV H to H-specific CD4+ I-Ed-restricted T cell hybridomas. All three populations of APC were capable of presenting MV to T cell hybridomas, DC being the most efficient. Expression of CD46 on B lymphocytes increased MHC class II-dependent presentation of MV H up to 100-fold, while CD46-transgenic DC stimulated H-specific T cell hybridomas up to 10-fold better than nontransgenic DC. Interestingly, expression of CD46 did not change the presentation efficiency of transgenic macrophages, indicating that CD46-dependent enhancement of antigen presentation depends on the nature of the APC. Furthermore, a single injection of UV-inactivated MV particles into CD46-transgenic mice, but not nontransgenic controls, induced generation of MV-specific T lymphocytes and production of anti-H antibodies, suggesting a role for CD46 in the efficient capture of MV in vivo. These results show for the first time that one ubiquitously expressed cell surface receptor, like CD46, could function in receptor-mediated antigen presentation both in vitro and in vivo and its performance depends on the type of APC which expresses it.
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Affiliation(s)
- P Rivailler
- Laboratoire d'Immunobiologie Moléculaire, Ecole Normale Supérieure de Lyon, UMR 49, CNRS, France
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31
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Fugier-Vivier I, Servet-Delprat C, Rivailler P, Rissoan MC, Liu YJ, Rabourdin-Combe C. Measles virus suppresses cell-mediated immunity by interfering with the survival and functions of dendritic and T cells. J Exp Med 1997; 186:813-23. [PMID: 9294136 PMCID: PMC2199042 DOI: 10.1084/jem.186.6.813] [Citation(s) in RCA: 334] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/1997] [Revised: 07/11/1997] [Indexed: 02/05/2023] Open
Abstract
Secondary infections due to a marked immunosuppression have long been recognized as a major cause of the high morbidity and mortality rate associated with acute measles. The mechanisms underlying the inhibition of cell-mediated immunity are not clearly understood but dysfunctions of monocytes as antigen-presenting cells (APC) are implicated. In this report, we demonstrate that measles virus (MV) replicates weakly in the resting dendritic cells (DC) as in lipopolysaccharide-activated monocytes, but intensively in CD40-activated DC. The interaction of MV-infected DC with T cells not only induces syncytia formation where MV undergoes massive replication, but also leads to an impairment of DC and T cell function and cell death. CD40-activated DC decrease their capacity to produce interleukin (IL) 12, and T cells are unable to proliferate in response to MV-infected DC stimulation. A massive apoptosis of both DC and T cells is observed in the MV pulsed DC-T cell cocultures. This study suggests that DC represent a major target of MV. The enhanced MV replication during DC-T cell interaction, leading to an IL-12 production decrease and the deletion of DC and T cells, may be the essential mechanism of immunosuppression induced by MV.
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Affiliation(s)
- I Fugier-Vivier
- Laboratory for Immunological Research, Schering-Plough, Dardilly, France
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32
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Horvat B, Rivailler P, Trescol-Biémont M, Gimenez C, Rabourdin-Combe C. Role of CD46 in the class II restricted presentation of measles virus antigens. Immunol Lett 1997. [DOI: 10.1016/s0165-2478(97)86079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Thorley BR, Milland J, Christiansen D, Lanteri MB, McInnes B, Moeller I, Rivailler P, Horvat B, Rabourdin-Combe C, Gerlier D, McKenzie IF, Loveland BE. Transgenic expression of a CD46 (membrane cofactor protein) minigene: studies of xenotransplantation and measles virus infection. Eur J Immunol 1997; 27:726-34. [PMID: 9079815 DOI: 10.1002/eji.1830270322] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
CD46 (membrane cofactor protein) is a human cell-surface regulator of activated complement and a receptor for the measles virus. A CD46 transgenic mouse line with an expression pattern similar to that of human tissues has been produced, to develop an animal model of (i) the control of complement activation by complement regulators in hyperacute rejection of xenografts, and (ii) measles virus infection. The mouse line was made using a CD46 minigene that includes promoter sequence and the first two introns of genomic CD46, which was coinjected into mouse ova with chicken lysozyme matrix attachment region DNA. A high level of CD46 expression in homozygotic transgenic mice was obtained with spleen cells having approximately 75% of the level found on human peripheral blood mononuclear cells. CD46 was detected in all tissues examined by immunohistochemistry, radioimmunoassay and Western blotting, showing that these mice were suitable for transplantation and measles virus infection studies. It also indicated that the transgene included the important regulatory elements of the CD46 promoter. Transgenic spleen cells were significantly protected in vitro from human complement activated by either the classical or alternative pathways and from alternative pathway rat complement. Furthermore, transgenic mouse hearts transplanted to rats regulated complement deposition in an in vivo model of antibody-dependent hyperacute xenograft rejection. Similar to human lymphocytes, transgenic lymphoblasts could be infected in vitro with measles virus; infected cells expressed viral proteins and produced infectious viral particles. The data demonstrate the suitability of this minigene for obtaining high-level CD46 expression sufficient for enhanced resistance of transgenic cells to complement attack and for obtaining wide tissue distribution of CD46, analogous to human tissues and, therefore, useful for comparative studies.
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Affiliation(s)
- B R Thorley
- The Austin Research Institute, Heidelberg, Australia
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Horvat B, Rivailler P, Varior-Krishnan G, Cardoso A, Gerlier D, Rabourdin-Combe C. Transgenic mice expressing human measles virus (MV) receptor CD46 provide cells exhibiting different permissivities to MV infections. J Virol 1996; 70:6673-81. [PMID: 8794303 PMCID: PMC190709 DOI: 10.1128/jvi.70.10.6673-6681.1996] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have generated transgenic mice ubiquitously expressing the human receptor for measles virus (MV), CD46 (membrane cofactor protein). Various cell types were isolated from these transgenic mice and analyzed for their ability to support MV replication in vitro. Although MV could enter into all CD46-expressing cells, differential susceptibilities to MV infection were detected depending on the cell type. Cell cultures obtained from transgenic lungs and kidneys were found to be permissive of MV infection, since RNA specific for MV genes was detected and viral particles were released, although at a low level. Similarly to human lymphocytes, activated T and B lymphocytes isolated from transgenic mice could support MV replication; virus could enter, transcribe viral RNA, and produce new infectious particles. When expressing viral proteins, lymphocytes down-regulated CD46 from the surface. Interestingly, while activated T lymphocytes from nontransgenic mice did not support MV infection, activated nontransgenic murine B lymphocytes replicated MV as well as transgenic B lymphocytes, suggesting the use of an alternative virus receptor for entry. In contrast to the previous cell types, murine peritoneal and bone marrow-derived macrophages, regardless of whether they were activated, could not support MV replication. Furthermore, although MV entered into macrophages and virus-specific RNA transcription occurred, no virus protein or infectious virus particles could be detected. These results show the importance of the particular cell-type-specific host factors for MV replication in murine cells which may be responsible for the differential permissivity of MV infection.
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Affiliation(s)
- B Horvat
- Laboratoire d'Immunobiologie Moléculaire, Ecole Normale Supérieure deLyon, UMR 49, CNRS, France
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Abstract
In Spisula solidissima oocytes, serotonin (5-hydroxytryptamine, 5-HT)-dependent meiosis reinitiation is mediated via specific 5-HT membrane binding sites. This oocyte response is inhibited by the phorbol ester TPA. To assess whether the inhibitory effect of TPA was due to alteration of oocyte membrane binding sites, we studied their characteristics after TPA treatment. [3H]-5HT binding assays revealed that TPA decreased the affinity and, after prolonged treatment, increased the number of oocyte binding sites. Moreover, inhibitory actions of TPA on 5-HT-induced meiosis reinitiation paralleled its inhibitory effects on 5-HT binding site affinity. The inhibitory actions in biological assays were restricted to TPA (an inactive analog of TPA, TPA-met was inefficient) and were completely reversed by staurosporine. Our data thus suggest an inhibitory role for protein kinase C on oocyte 5-HT binding sites under physiological conditions.
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Affiliation(s)
- P Rivailler
- Ecole Normale Supérieure, Laboratoire de Biologie Moléculaire et Cellulaire, Lyon, France
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Abdelmajid H, Rivailler P, Krantic S, Guerrier P. Differences in tyrosine phosphorylation of oocyte key proteins during 5HT-induced meiosis reinitiation in two bivalve species. Exp Cell Res 1994; 212:422-5. [PMID: 7514540 DOI: 10.1006/excr.1994.1163] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The neurohormone serotonin (5HT) triggers meiosis reinitiation in oocytes of the pelecypod molluscs Spisula solidissima and Ruditapes philippinarum. However, while Spisula oocytes complete maturation, Ruditapes oocytes arrest in metaphase I. Anti-phosphotyrosine antibody revealed that serotonin triggered an early tyrosine phosphorylation of p42mapk which was transient in Spisula, but persisted in Ruditapes. Moreover, dephosphorylation of tyrosine residues of p34cdc2 was only observed in Spisula oocytes, simultaneously with germinal vesicle breakdown. The possibility is discussed that such differences may account for maintenance of the metaphase I block.
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Affiliation(s)
- H Abdelmajid
- UMR 49, Ecole Normale Supérieure de Lyon, France
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