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Abstract
Through their specific interactions with proteins, cellular glycans play key roles in a wide range of physiological and pathological processes. One of the main goals of research in the areas of glycobiology and glycomedicine is to understand glycan-protein interactions at the molecular level. Over the past two decades, glycan microarrays have become powerful tools for the rapid evaluation of interactions between glycans and proteins. In this review, we briefly describe methods used for the preparation of glycan probes and the construction of glycan microarrays. Next, we highlight applications of glycan microarrays to rapid profiling of glycan-binding patterns of plant, animal and pathogenic lectins, as well as other proteins. Finally, we discuss other important uses of glycan microarrays, including the rapid analysis of substrate specificities of carbohydrate-active enzymes, the quantitative determination of glycan-protein interactions, discovering high-affinity or selective ligands for lectins, and identifying functional glycans within cells. We anticipate that this review will encourage researchers to employ glycan microarrays in diverse glycan-related studies.
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Affiliation(s)
- Yujun Kim
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
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2
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Guo F, Roy A, Wang R, Yang J, Zhang Z, Luo W, Shen X, Chen RA, Irwin DM, Shen Y. Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. Front Microbiol 2021; 12:655228. [PMID: 34194404 PMCID: PMC8236823 DOI: 10.3389/fmicb.2021.655228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Since its first isolation in around 2007, the avian-origin H3N2 canine influenza virus (CIV) has become established and continues to circulate in dog populations. This virus serves as a useful model for deciphering the complex evolutionary process of interspecies transmission of influenza A virus (IAV) from one species to its subsequent circulation in another mammalian host. The present investigation is a comprehensive effort to identify and characterize genetic changes that accumulated in the avian-origin H3N2 CIV during its circulation in the dog. We revealed that H3N2 CIV experiences greater selection pressure with extremely high global non-synonymous to synonymous substitution ratios per codon (dN/dS ratio) for each gene compared to the avian reservoir viruses. A total of 54 amino acid substitutions were observed to have accumulated and become fixed in the H3N2 CIV population based on our comprehensive codon-based frequency diagram analysis. Of these substitutions, 11 sites also display high prevalence in H3N8 CIV, indicating that convergent evolution has occurred on different lineages of CIV. Notably, six substitutions, including HA-G146S, M1-V15I, NS1-E227K, PA-C241Y, PB2-K251R, and PB2-G590S, have been reported to play imperative roles in facilitating the transmission and spillover of IAVs across species barriers. Most of these substitutions were found to have become fixed in around 2015, which might have been a favorable factor that facilitating the spread of these CIV lineages from South Asia to North America and subsequent further circulation in these areas. We also detected 12 sites in six viral genes with evidence for positive selection by comparing the rates of non-synonymous and synonymous substitutions at each site. Besides, our study reports trends of enhanced ongoing adaptation of H3N2 CIV to their respective host cellular systems, based on the codon adaptation index analysis, which points toward increasing fitness for efficient viral replication. In addition, a reduction in the abundance of the CpG motif, as evident from an analysis of relative dinucleotide abundance, may contribute to the successful evasion of host immune recognition. The present study provides key insights into the adaptive changes that have accumulated in the avian-origin H3N2 viral genomes during its establishment and circulation into dog populations.
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Affiliation(s)
- Fucheng Guo
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Phagwara, India
| | - Ruichen Wang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinjin Yang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhipeng Zhang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wen Luo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuejuan Shen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - Rui-Ai Chen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, Canada
| | - Yongyi Shen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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3
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Saha P, Biswas M, Gupta R, Majumdar A, Mitra S, Banerjee A, Mukherjee A, Dutta S, Chawla-Sarkar M. Molecular characterization of Influenza A pandemic H1N1 viruses circulating in eastern India during 2017-19: Antigenic diversity in comparison to the vaccine strains. INFECTION GENETICS AND EVOLUTION 2020; 81:104270. [PMID: 32142936 DOI: 10.1016/j.meegid.2020.104270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/08/2020] [Accepted: 03/02/2020] [Indexed: 11/27/2022]
Abstract
In the endemic settings of India, high CFR (3.6-7.02%) was observed in the consecutive 2009, 2015 and 2017 A/H1N1pdm09 outbreaks, though in eastern India CFR varied between 0 and 5.5% during same period. Recurrent outbreaks of pandemic Influenza A/H1N1pdm09, fragmented nationwide incidence data, lack of national policy for Influenza vaccination in India underscores the necessity for generating regional level data. Thus, during 2017-19, 4106 referred samples from patients hospitalized with severe acute respiratory illness (SARI) in eastern India were tested for A/H1N1pdm09 infection. Among which 16.5% (n = 677/4106) were found A/H1N1pdm09 positive. Individuals <20 years and middle-aged persons (40-60 years) were most susceptible to A/H1N1pdm09 infection. The vaccine strain (A/human/California/07/2009) which was globally used before 2017, clustered in a different lineage away from the representative eastern Indian strains in the phylogenetic dendrogram. The vaccine strain (A/human/Michigan/45/2015) used in India during the study period and the WHO recommended strain (A/human/Brisbane/02/2018) for 2019-20 flu season for the northern hemisphere, clustered with the circulating isolates in the same lineage-6b. Dissimilarities in the amino acids encompassing the antigenic epitopes were seen to be highest with the vaccine strain- A/human/California/07/2009. The significant amino acid variations in the circulating strains with the current WHO recommended vaccine strain, implies the exigency of continuous pandemic A/H1N1pdm09 surveillance studies in this epidemiological setting. The absence of any Oseltamivir resistant mutation (H275Y) in the neuraminidase gene of the current isolates suggests continuing use of Tamiflu® as an antiviral therapy in suspected subjects in this region.
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Affiliation(s)
- Priyanka Saha
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Madhumonti Biswas
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Rudrak Gupta
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Agniva Majumdar
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Anindita Banerjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Shanta Dutta
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.
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4
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Luo T, Liu L, Shen X, Irwin DM, Liao M, Shen Y. The evolutionary dynamics of H1N1/pdm2009 in India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 65:276-282. [PMID: 30118873 DOI: 10.1016/j.meegid.2018.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 02/05/2023]
Abstract
After the 2009 pandemic H1N1 outbreak, this new reassortant virus replaced the previous seasonal H1N1 and established itself in human populations. In 2014-2015, the H1N1/pdm2009 pandemic strain caused the worst influenza outbreak in India in recent years. It is still unclear whether this outbreak was due to a genetic change in the H1N1/pdm2009 virus. Here, we collected all available data from India, and used data from other South and Southeast Asian countries (Bangladesh, Myanmar, Nepal, Singapore, and Vietnam) that are geographically nearby India for comparison, to examine the evolutionary dynamics of this influenza virus. We detected signals of population expansion in both HA and NA in the 2014/2015 season in India, which coincided with the outbreak in India of 2015. Signals of positive selection in HA in the 2012/2013 and 2013/2014 seasons, and in NA in the 2012/2013 and 2014/2015 seasons were also found. These selective patterns were different from those seen in other South and Southeast Asian countries. However, none of the eight positively selected sites are endemic to India. The rapid circulation of H1N1/pdm2009 between these South and Southeast Asian countries may explain this result. Further studies are still needed to identify the genetic basis of the great 2015 outbreak in India.
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Affiliation(s)
- Tingting Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Lu Liu
- Shantou University Medical College, Shantou 515041, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada; Banting and Best Diabetes Centre, University of Toronto, Toronto M5S 1A8, Canada
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China.
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China.
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5
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Hashem AM, Azhar EI, Shalhoub S, Abujamel TS, Othman NA, Al Zahrani AB, Abdullah HM, Al-Alawi MM, Sindi AA. Genetic characterization and diversity of circulating influenza A/H1N1pdm09 viruses isolated in Jeddah, Saudi Arabia between 2014 and 2015. Arch Virol 2018; 163:1219-1230. [PMID: 29396684 DOI: 10.1007/s00705-018-3732-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 12/19/2017] [Indexed: 12/28/2022]
Abstract
The emerged influenza A/H1N1pdm09 viruses have replaced the previously circulating seasonal H1N1 viruses. The close antigenic properties of these viruses to the 1918 H1N1 pandemic viruses and their post-pandemic evolution pattern could further enhance their adaptation and pathogenicity in humans representing a major public health threat. Given that data on the dynamics and evolution of these viruses in Saudi Arabia is sparse we investigated the genetic diversity of circulating influenza A/H1N1pdm09 viruses from Jeddah, Saudi Arabia, by analyzing 39 full genomes from isolates obtained between 2014-2015, from patients with varying symptoms. Phylogenetic analysis of all gene segments and concatenated genomes showed similar topologies and co-circulation of clades 6b, 6b.1 and 6b.2, with clade 6b.1 being the most predominate since 2015. Most viruses were more closely related to the vaccine strain (Michigan/45/2015) recommended for the 2017/2018 season, than to the California/07/2009 strain. Low sequence variability was observed in the haemagglutinin protein compared to the neuraminidase protein. Resistance to neuraminidase inhibitors was limited as only one isolate had the H275Y substitution. Interestingly, two isolates had short PA-X proteins of 206 amino acids compared to the 232 amino acid protein found in most influenza A/H1N1pdm09 viruses. Together, the co-circulation of several clades and the predominance of clade 6b.1, despite its low circulation in Asia in 2015, suggests multiple introductions most probably during the mass gathering events of Hajj and Umrah. Jeddah represents the main port of entry to the holy cities of Makkah and Al-Madinah, emphasizing the need for vigilant surveillance in the kingdom.
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MESH Headings
- Amino Acid Substitution
- Female
- Genetic Variation
- Genome, Viral
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/transmission
- Influenza, Human/virology
- Male
- Nasopharynx/virology
- Neuraminidase/genetics
- Phylogeny
- RNA, Viral/genetics
- Saudi Arabia/epidemiology
- Seasons
- Sequence Analysis, DNA
- Viral Proteins/genetics
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Affiliation(s)
- Anwar M Hashem
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Esam I Azhar
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Sarah Shalhoub
- Division of Infectious Diseases, Department of Medicine, King Fahd Armed Forces Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Turki S Abujamel
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Norah A Othman
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abdulwahab B Al Zahrani
- Molecular Diagnostics Laboratory, King Fahd Armed Forces Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Hanan M Abdullah
- Students' Research and Innovation Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Maha M Al-Alawi
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Infection Control and Environmental Health Unit, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Anees A Sindi
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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6
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A singular mutation in the hemagglutinin of the 1918 pandemic virus. Arch Biochem Biophys 2017; 625-626:13-16. [DOI: 10.1016/j.abb.2017.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/19/2017] [Accepted: 05/24/2017] [Indexed: 11/20/2022]
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7
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Moncla LH, Zhong G, Nelson CW, Dinis JM, Mutschler J, Hughes AL, Watanabe T, Kawaoka Y, Friedrich TC. Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus. Cell Host Microbe 2016; 19:169-80. [PMID: 26867176 PMCID: PMC4761429 DOI: 10.1016/j.chom.2016.01.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/26/2015] [Accepted: 01/25/2016] [Indexed: 01/14/2023]
Abstract
Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses.
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Affiliation(s)
- Louise H Moncla
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Gongxun Zhong
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA
| | - Chase W Nelson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Jorge M Dinis
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - James Mutschler
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Tokiko Watanabe
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA.
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Romero-Beltran L, Baker SF, Puerto-Solís M, González-Losa R, Conde-Ferraez L, Alvarez-Sánchez LC, Martínez-Sobrido L, Ayora-Talavera G. Mutations at highly conserved residues in influenza A(H1N1)pdm09 virus affect neuraminidase activity. Virus Res 2016; 225:1-9. [PMID: 27596738 DOI: 10.1016/j.virusres.2016.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/17/2016] [Accepted: 09/02/2016] [Indexed: 01/16/2023]
Abstract
Influenza virus neuraminidase (NA) plays a pivotal role during viral growth since its sialidase activity allows the efficient release of nascent virions from infected cells. Consequently, mutations in the NA catalytic site affecting sialic acid (SA) cleavage may influence the biological properties of influenza viruses. This study reports two amino acid substitutions (N386K and P431S) in the NA of the influenza A(H1N1)pdm09 virus that emerged in 2009 in Mexico. The NA sialidase activity to cleave SA-like substrates, and viral growth were examined and the mutant viruses had various deficiencies. NA mutations N386K and P431S together or separately, and in the presence or absence of H275Y were further evaluated using recombinant influenza A/California/04/2009 (pH1N1) viruses containing single, double, or triple mutations. Viral growth was reduced in the presence of mutation P431S alone or combined with N386K and/or H275Y. Substrates hydrolysis was reduced when recombinant pH1N1 viruses were analyzed by NA inhibitory assays. Moreover, elution assays with guinea pig red blood cells indicated an unbalanced hemagglutinin (HA):NA functionality. Altogether, our data underline the functional significance of mutations at highly conserved sites in influenza virus NA glycoprotein and the occurrence of permissive mutations to compensate virus viability in vitro.
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Affiliation(s)
| | - Steven F Baker
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
| | | | | | | | - Leidi C Alvarez-Sánchez
- Laboratorio de Virología, Universidad Autonoma de Yucatan, Mexico; Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
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9
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Lewis NS, Russell CA, Langat P, Anderson TK, Berger K, Bielejec F, Burke DF, Dudas G, Fonville JM, Fouchier RA, Kellam P, Koel BF, Lemey P, Nguyen T, Nuansrichy B, Peiris JM, Saito T, Simon G, Skepner E, Takemae N, Webby RJ, Van Reeth K, Brookes SM, Larsen L, Watson SJ, Brown IH, Vincent AL. The global antigenic diversity of swine influenza A viruses. eLife 2016; 5:e12217. [PMID: 27113719 PMCID: PMC4846380 DOI: 10.7554/elife.12217] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 03/23/2016] [Indexed: 12/11/2022] Open
Abstract
Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. There is considerable diversity in both H1 and H3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Much of this diversity is characterized genetically but the antigenic diversity of these viruses is poorly understood. Critically, the antigenic diversity shapes the risk profile of swine influenza viruses in terms of their epizootic and pandemic potential. Here, using the most comprehensive set of swine influenza virus antigenic data compiled to date, we quantify the antigenic diversity of swine influenza viruses on a multi-continental scale. The substantial antigenic diversity of recently circulating viruses in different parts of the world adds complexity to the risk profiles for the movement of swine and the potential for swine-derived infections in humans. DOI:http://dx.doi.org/10.7554/eLife.12217.001 Influenza viruses, commonly called flu, infect millions of people and animals every year and occasionally causes pandemics in humans. The immune system can neutralise flu viruses by recognising the proteins on the virus surface, generically referred to as antigens. These antigens change as flu viruses evolve to escape detection by the immune system. These changes tend to be relatively small such that exposure to one flu virus generates immunity that is still effective against other related flu viruses. However, over time, the accumulation of these small changes can result in larger differences such that prior infections no longer provide protection against the new virus. Influenza A viruses infect a wide variety of birds and mammals. Viruses can also transmit from one species to another, which may result in the introduction of viruses with antigens that are new to the recipient species and which have the potential to cause substantial outbreaks. Pig flu viruses have long been considered to be a potential risk for human pandemic viruses and were the source of the 2009 pandemic H1N1 virus. Importantly, humans often transmit flu viruses to pigs. Understanding the dynamics and consequences of this two-way transmission is important for designing effective strategies to detect and respond to new strains of flu. Influenza A viruses of the H1 and H3 subtypes circulate widely in pigs. However, it was poorly understood how closely related swine and human viruses circulating in different regions were to one another and how much the antigens varied between the different viruses. Lewis, Russell et al. have now analysed the antigenic variation of hundreds of H1 and H3 viruses from pigs on multiple continents. The antigenic diversity of recent swine flu viruses resembles the diversity of H1 and H3 viruses observed in humans over the last 40 years. A key factor driving the diversity of the H1 and H3 viruses in pigs is the frequent introduction of human viruses to pigs. In contrast, only one flu virus from a bird had contributed to the observed antigenic diversity in pigs in a substantial way. Once in pigs, human-derived flu viruses continue to evolve their antigens. This results in a tremendous diversity of flu viruses that can be transmitted to other pigs and also to humans. These flu viruses could pose a serious risk to public health because they are no longer similar to the current human flu strains. These findings have important implications not only for developing flu vaccines for pigs but also for informing the development of more-effective surveillance and disease-control strategies to prevent the spread of new flu variants. DOI:http://dx.doi.org/10.7554/eLife.12217.002
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Affiliation(s)
- Nicola S Lewis
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Colin A Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Pinky Langat
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, United States
| | - Kathryn Berger
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Filip Bielejec
- Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - David F Burke
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Judith M Fonville
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Ron Am Fouchier
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Bjorn F Koel
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Philippe Lemey
- Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Tung Nguyen
- Department of Animal Health, National Centre for Veterinary Diagnostics, Hanoi, Vietnam
| | | | - Js Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | - Gaelle Simon
- Swine Virology Immunology Unit, Anses, Ploufragan-Plouzané Laboratory, Ploufragan, France
| | - Eugene Skepner
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Richard J Webby
- St Jude Children's Research Hospital, Memphis, United States
| | - Kristien Van Reeth
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | | | - Lars Larsen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Simon J Watson
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Ian H Brown
- Animal Health and Plant Agency, Weybridge, United Kingdom
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, United States
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