1
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Erdelyan CNG, Kandeil A, Signore AV, Jones MEB, Vogel P, Andreev K, Bøe CA, Gjerset B, Alkie TN, Yason C, Hisanaga T, Sullivan D, Lung O, Bourque L, Ayilara I, Pama L, Jeevan T, Franks J, Jones JC, Seiler JP, Miller L, Mubareka S, Webby RJ, Berhane Y. Multiple transatlantic incursions of highly pathogenic avian influenza clade 2.3.4.4b A(H5N5) virus into North America and spillover to mammals. Cell Rep 2024; 43:114479. [PMID: 39003741 DOI: 10.1016/j.celrep.2024.114479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Highly pathogenic avian influenza (HPAI) viruses have spread at an unprecedented scale, leading to mass mortalities in birds and mammals. In 2023, a transatlantic incursion of HPAI A(H5N5) viruses into North America was detected, followed shortly thereafter by a mammalian detection. As these A(H5N5) viruses were similar to contemporary viruses described in Eurasia, the transatlantic spread of A(H5N5) viruses was most likely facilitated by pelagic seabirds. Some of the Canadian A(H5N5) viruses from birds and mammals possessed the PB2-E627K substitution known to facilitate adaptation to mammals. Ferrets inoculated with A(H5N5) viruses showed rapid, severe disease onset, with some evidence of direct contact transmission. However, these viruses have maintained receptor binding traits of avian influenza viruses and were susceptible to oseltamivir and zanamivir. Understanding the factors influencing the virulence and transmission of A(H5N5) in migratory birds and mammals is critical to minimize impacts on wildlife and public health.
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Affiliation(s)
| | - Ahmed Kandeil
- Department of Pathology and Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, 12622, Egypt
| | - Anthony V Signore
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada
| | - Megan E B Jones
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, PEI C1A 4P3, Canada
| | - Peter Vogel
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Konstantin Andreev
- Department of Pathology and Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | | | - Tamiru N Alkie
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada
| | - Carmencita Yason
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada
| | - Tamiko Hisanaga
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada
| | - Daniel Sullivan
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada; Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2M5, Canada
| | - Laura Bourque
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, PEI C1A 4P3, Canada
| | - Ifeoluwa Ayilara
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada
| | - Lemarie Pama
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada
| | - Trushar Jeevan
- Department of Pathology and Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John Franks
- Department of Pathology and Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy C Jones
- Department of Pathology and Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jon P Seiler
- Department of Pathology and Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lance Miller
- Department of Pathology and Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Richard J Webby
- Department of Pathology and Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38105, USA.
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada; Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada.
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2
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Delima GK, Ganti K, Holmes KE, Shartouny JR, Lowen AC. Influenza A virus coinfection dynamics are shaped by distinct virus-virus interactions within and between cells. PLoS Pathog 2023; 19:e1010978. [PMID: 36862762 PMCID: PMC10013887 DOI: 10.1371/journal.ppat.1010978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/14/2023] [Accepted: 02/07/2023] [Indexed: 03/03/2023] Open
Abstract
When multiple viral populations propagate within the same host environment, they often shape each other's dynamics. These interactions can be positive or negative and can occur at multiple scales, from coinfection of a cell to co-circulation at a global population level. For influenza A viruses (IAVs), the delivery of multiple viral genomes to a cell substantially increases burst size. However, despite its relevance for IAV evolution through reassortment, the implications of this positive density dependence for coinfection between distinct IAVs has not been explored. Furthermore, the extent to which these interactions within the cell shape viral dynamics at the level of the host remains unclear. Here we show that, within cells, diverse coinfecting IAVs strongly augment the replication of a focal strain, irrespective of their homology to the focal strain. Coinfecting viruses with a low intrinsic reliance on multiple infection offer the greatest benefit. Nevertheless, virus-virus interactions at the level of the whole host are antagonistic. This antagonism is recapitulated in cell culture when the coinfecting virus is introduced several hours prior to the focal strain or under conditions conducive to multiple rounds of viral replication. Together, these data suggest that beneficial virus-virus interactions within cells are counterbalanced by competition for susceptible cells during viral propagation through a tissue. The integration of virus-virus interactions across scales is critical in defining the outcomes of viral coinfection.
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Affiliation(s)
- Gabrielle K. Delima
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Katie E. Holmes
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Jessica R. Shartouny
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
- * E-mail:
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3
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Gass JD, Dusek RJ, Hall JS, Hallgrimsson GT, Halldórsson HP, Vignisson SR, Ragnarsdottir SB, Jónsson JE, Krauss S, Wong SS, Wan XF, Akter S, Sreevatsan S, Trovão NS, Nutter FB, Runstadler JA, Hill NJ. Global dissemination of influenza A virus is driven by wild bird migration through arctic and subarctic zones. Mol Ecol 2023; 32:198-213. [PMID: 36239465 PMCID: PMC9797457 DOI: 10.1111/mec.16738] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/31/2022]
Abstract
Influenza A viruses (IAV) circulate endemically among many wild aquatic bird populations that seasonally migrate between wintering grounds in southern latitudes to breeding ranges along the perimeter of the circumpolar arctic. Arctic and subarctic zones are hypothesized to serve as ecologic drivers of the intercontinental movement and reassortment of IAVs due to high densities of disparate populations of long distance migratory and native bird species present during breeding seasons. Iceland is a staging ground that connects the East Atlantic and North Atlantic American flyways, providing a unique study system for characterizing viral flow between eastern and western hemispheres. Using Bayesian phylodynamic analyses, we sought to evaluate the viral connectivity of Iceland to proximal regions and how inter-species transmission and reassortment dynamics in this region influence the geographic spread of low and highly pathogenic IAVs. Findings demonstrate that IAV movement in the arctic and subarctic reflects wild bird migration around the perimeter of the circumpolar north, favouring short-distance flights between proximal regions rather than long distance flights over the polar interior. Iceland connects virus movement between mainland Europe and North America, consistent with the westward migration of wild birds from mainland Europe to Northeastern Canada and Greenland. Though virus diffusion rates were similar among avian taxonomic groups in Iceland, gulls play an outsized role as sinks of IAVs from other avian hosts prior to onward migration. These data identify patterns of virus movement in northern latitudes and inform future surveillance strategies related to seasonal and emergent IAVs with potential public health concern.
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Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | | | | | | | | | - Solvi Runar Vignisson
- University of Iceland’s Research Centre in Suðurnes
- Suðurnes Science and Learning Center
| | | | | | - Scott Krauss
- Department of Infectious Diseases, St. Jude Children’s Research Hospital
| | - Sook-San Wong
- Department of Infectious Diseases, St. Jude Children’s Research Hospital
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia
- Bond Life Sciences Center, University of Missouri, Columbia
- Department of Electronic Engineering and Computer Science, University of Missouri, Columbia
| | - Sadia Akter
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia
- Bond Life Sciences Center, University of Missouri, Columbia
- Department of Electronic Engineering and Computer Science, University of Missouri, Columbia
| | | | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | - Nichola J. Hill
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
- Department of Biology, University of Massachusetts, Boston
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4
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Ganti K, Bagga A, Carnaccini S, Ferreri LM, Geiger G, Joaquin Caceres C, Seibert B, Li Y, Wang L, Kwon T, Li Y, Morozov I, Ma W, Richt JA, Perez DR, Koelle K, Lowen AC. Influenza A virus reassortment in mammals gives rise to genetically distinct within-host subpopulations. Nat Commun 2022; 13:6846. [PMID: 36369504 PMCID: PMC9652339 DOI: 10.1038/s41467-022-34611-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Influenza A virus (IAV) genetic exchange through reassortment has the potential to accelerate viral evolution and has played a critical role in the generation of multiple pandemic strains. For reassortment to occur, distinct viruses must co-infect the same cell. The spatio-temporal dynamics of viral dissemination within an infected host therefore define opportunity for reassortment. Here, we used wild type and synonymously barcoded variant viruses of a pandemic H1N1 strain to examine the within-host viral dynamics that govern reassortment in guinea pigs, ferrets and swine. The first two species are well-established models of human influenza, while swine are a natural host and a frequent conduit for cross-species transmission and reassortment. Our results show reassortment to be pervasive in all three hosts but less frequent in swine than in ferrets and guinea pigs. In ferrets, tissue-specific differences in the opportunity for reassortment are also evident, with more reassortants detected in the nasal tract than the lower respiratory tract. While temporal trends in viral diversity are limited, spatial patterns are clear, with heterogeneity in the viral genotypes detected at distinct anatomical sites revealing extensive compartmentalization of reassortment and replication. Our data indicate that the dynamics of viral replication in mammals allow diversification through reassortment but that the spatial compartmentalization of variants likely shapes their evolution and onward transmission.
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Affiliation(s)
- Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anish Bagga
- Emory College of Arts and Sciences, Atlanta, GA, USA
| | - Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Lucas M Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - C Joaquin Caceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Yonghai Li
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Liping Wang
- Department of Veterinary Pathobiology, and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Taeyong Kwon
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yuhao Li
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Igor Morozov
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Wenjun Ma
- Department of Veterinary Pathobiology, and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
- St. Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, TN, USA
| | - Juergen A Richt
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
- St. Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, TN, USA
| | - Daniel R Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- The Center for Research on Influenza Pathogenesis and Transmission (CRIPT CEIRR), New York, NY, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, GA, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, GA, USA.
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5
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Cavany SM, Barbera C, Carpenter M, Rodgers C, Sherman T, Stenglein M, Mayo C, Perkins TA. Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges. Virus Evol 2022; 8:veac094. [PMID: 36381232 PMCID: PMC9662319 DOI: 10.1093/ve/veac094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 10/10/2023] Open
Abstract
When related segmented RNA viruses co-infect a single cell, viral reassortment can occur, potentially leading to new strains with pandemic potential. One virus capable of reassortment is bluetongue virus (BTV), which causes substantial health impacts in ruminants and is transmitted via Culicoides midges. Because midges can become co-infected by feeding on multiple different host species and remain infected for their entire life span, there is a high potential for reassortment to occur. Once a midge is co-infected, additional barriers must be crossed for a reassortant virus to emerge, such as cellular co-infection and dissemination of reassortant viruses to the salivary glands. We developed three mathematical models of within-midge BTV dynamics of increasing complexity, allowing us to explore the conditions leading to the emergence of reassortant viruses. In confronting the simplest model with published data, we estimate that the average life span of a bluetongue virion in the midge midgut is about 6 h, a key determinant of establishing a successful infection. Examination of the full model, which permits cellular co-infection and reassortment, shows that small differences in fitness of the two infecting strains can have a large impact on the frequency with which reassortant virions are observed. This is consistent with experimental co-infection studies with BTV strains with different relative fitnesses that did not produce reassortant progeny. Our models also highlight several gaps in existing data that would allow us to elucidate these dynamics in more detail, in particular the times it takes the virus to disseminate to different tissues, and measurements of viral load and reassortant frequency at different temperatures.
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Affiliation(s)
- Sean M Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Carly Barbera
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Molly Carpenter
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Case Rodgers
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Tyler Sherman
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Mark Stenglein
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - Christie Mayo
- Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO 80523, USA
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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6
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Sun Y, Zhang Y, Zhang X. Complementary Effects of Virus Population Are Required for Efficient Virus Infection. Front Microbiol 2022; 13:877702. [PMID: 35633682 PMCID: PMC9137883 DOI: 10.3389/fmicb.2022.877702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
It is believed that the virions of a virus infecting a host may share the identical viral genome and characteristics. However, the role of genomic heterogeneity of the virions of a virus in virus infection has not been extensively explored. To address this issue, white spot syndrome virus (WSSV), a DNA virus infecting crustaceans, was characterized in the current study. In WSSV, differences in two nucleotides of the viral genome generated two types of WSSV, forming a virus population that consisted of Type A WSSV (encoding WSSV lncRNA-24) and Type B WSSV (encoding the wsv195 gene) at a ratio of 1:3. The virus populations in all virus-infected cells and tissues of different hosts exhibited a stable 1:3 structure. WSSV lncRNA-24 in Type A WSSV promoted virus infection by binding to shrimp and WSSV miRNAs, while the wsv195 gene in Type B WSSV played an essential role in virus infection. Loss of Type A WSSV or Type B WSSV in the WSSV population led to a 100-fold decrease in viral copy number in shrimp. Simultaneous loss of both types of WSSV prevented virus infection. These results indicated that the virus infection process was completed by two types of WSSV encoding different functional genes, revealing the complementary effects of WSSV population. Therefore, our study highlights the importance of the complementarity of virus population components in virus infection.
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Affiliation(s)
| | | | - Xiaobo Zhang
- College of Life Sciences and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, China
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7
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Kopanke J, Carpenter M, Lee J, Reed K, Rodgers C, Burton M, Lovett K, Westrich JA, McNulty E, McDermott E, Barbera C, Cavany S, Rohr JR, Perkins TA, Mathiason CK, Stenglein M, Mayo C. Bluetongue Research at a Crossroads: Modern Genomics Tools Can Pave the Way to New Insights. Annu Rev Anim Biosci 2022; 10:303-324. [PMID: 35167317 DOI: 10.1146/annurev-animal-051721-023724] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bluetongue virus (BTV) is an arthropod-borne, segmented double-stranded RNA virus that can cause severe disease in both wild and domestic ruminants. BTV evolves via several key mechanisms, including the accumulation of mutations over time and the reassortment of genome segments.Additionally, BTV must maintain fitness in two disparate hosts, the insect vector and the ruminant. The specific features of viral adaptation in each host that permit host-switching are poorly characterized. Limited field studies and experimental work have alluded to the presence of these phenomena at work, but our understanding of the factors that drive or constrain BTV's genetic diversification remains incomplete. Current research leveraging novel approaches and whole genome sequencing applications promises to improve our understanding of BTV's evolution, ultimately contributing to the development of better predictive models and management strategies to reduce future impacts of bluetongue epizootics.
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Affiliation(s)
- Jennifer Kopanke
- Office of the Campus Veterinarian, Washington State University, Spokane, Washington, USA;
| | - Molly Carpenter
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Justin Lee
- Genomic Sequencing Laboratory, Centers for Disease Control and Prevention, Atlanta, Georgia, USA;
| | - Kirsten Reed
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Case Rodgers
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Mollie Burton
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Kierra Lovett
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Joseph A Westrich
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Erin McNulty
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Emily McDermott
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, Arkansas, USA;
| | - Carly Barbera
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Sean Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Jason R Rohr
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Candace K Mathiason
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Mark Stenglein
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Christie Mayo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
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8
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Bono LM, Mao S, Done RE, Okamoto KW, Chan BK, Turner PE. Advancing phage therapy through the lens of virus host-breadth and emergence potential. Adv Virus Res 2021; 111:63-110. [PMID: 34663499 DOI: 10.1016/bs.aivir.2021.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Phages are viruses that specifically infect bacteria, and their biodiversity contributes to historical and current development of phage therapy to treat myriad bacterial infections. Phage therapy holds promise as an alternative to failing chemical antibiotics, but there are benefits and costs of this technology. Here, we review the rich history of phage therapy, highlighting reasons (often political) why it was widely rejected by Western medicine until recently. One longstanding idea involves mixing different phages together in cocktails, to increase the probability of killing target pathogenic bacteria without pre-screening for phage susceptibility. By challenging 30 lytic phages to infect 14 strains of the bacteria Pseudomonas aeruginosa, we showed that some phages were "generalists" with broad host-ranges, emphasizing that extreme host-specificity of phages was not necessarily a liability. Using a "greedy algorithm" analysis, we identified the best cocktail mixture of phages to achieve broad bacteria killing. Additionally, we review how virus host-range can evolve and connect lessons learned from virus emergence-including contributions of elevated virus mutation rates in promoting emergence and virus evolutionary transitions from specialized to generalized host-use-as cautionary tales for avoiding risk of "off-target" phage emergence on commensal bacteria in microbiomes. Throughout, we highlight how fundamental understanding of virus ecology and evolution is vital for developing phage therapy; heeding these principles should help in designing therapeutic strategies that do not recapitulate consequences of virus selection to emerge on novel hosts.
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Affiliation(s)
- Lisa M Bono
- Department of Biology, Emory University, Atlanta, GA, United States.
| | - Stephanie Mao
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rachel E Done
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA, United States; Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Kenichi W Okamoto
- Department of Biology, University of St. Thomas, St. Paul, MN, United States
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States; Microbiology Program, Yale School of Medicine, New Haven, CT, United States
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9
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Palinski R, Pauszek SJ, Humphreys JM, Peters DP, McVey DS, Pelzel‐McCluskey AM, Derner JD, Burruss ND, Arzt J, Rodriguez LL. Evolution and expansion dynamics of a vector‐borne virus: 2004–2006 vesicular stomatitis outbreak in the western USA. Ecosphere 2021. [DOI: 10.1002/ecs2.3793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Rachel Palinski
- US Department of Agriculture, Agricultural Research Service Plum Island Animal Disease Center Orient Point New York 11957 USA
- Veterinary Diagnostic Laboratory College of Veterinary Medicine Kansas State University 2005 Research Park Manhattan Kansas 66502 USA
| | - Steven J. Pauszek
- US Department of Agriculture, Agricultural Research Service Plum Island Animal Disease Center Orient Point New York 11957 USA
| | - John M. Humphreys
- US Department of Agriculture Agricultural Research Service Jornada Experimental Range Unit Las Cruces New Mexico 88003 USA
| | - Debra P.C. Peters
- US Department of Agriculture Agricultural Research Service Jornada Experimental Range Unit Las Cruces New Mexico 88003 USA
- Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico 88003 USA
| | - D. Scott McVey
- US Department of Agriculture Agricultural Research Service Center for Grain and Animal Health Research Arthropod‐Borne Animal Diseases Research Unit Manhattan Kansas 66506 USA
- School of Veterinary Medicine and Biomedical Sciences University of Nebraska Lincoln Lincoln Nebraska 68583 USA
| | - Angela M. Pelzel‐McCluskey
- US Department of Agriculture, Animal and Plant Health Inspection Service Veterinary Services Fort Collins Colorado 80526 USA
| | - Justin D. Derner
- US Department of Agriculture Agricultural Research Service Rangeland Resources and Systems Research Unit 8408 Hildreth Road Cheyenne Wyoming 82009 USA
| | - N. Dylan Burruss
- US Department of Agriculture Agricultural Research Service Jornada Experimental Range Unit Las Cruces New Mexico 88003 USA
- Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico 88003 USA
| | - Jonathan Arzt
- US Department of Agriculture, Agricultural Research Service Plum Island Animal Disease Center Orient Point New York 11957 USA
| | - Luis L. Rodriguez
- US Department of Agriculture, Agricultural Research Service Plum Island Animal Disease Center Orient Point New York 11957 USA
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10
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Price TRV, Barua SK. Identifying vulnerable populations and transmission pathways by geographic correlation of the environment to human health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146426. [PMID: 33744571 PMCID: PMC8612100 DOI: 10.1016/j.scitotenv.2021.146426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/20/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The social determinants of individuals' health (e.g., socio-economic, demographic, and genetic conditions) play a major role in the health of an entire population. However, in comparison to environmental data, global data on the social determinants of health is spatially coarse, infrequently updated, and costly to measure. From global mapping efforts of the recent COVID-19 pandemic it is clear that social data is not meeting the fine spatial quality needed for mapping vulnerable populations and transmission pathways. Most maps produced generalized to larger administrative units (such as counties, states), and have not identified distinct areas of vulnerable populations apart from the surrounding environment where no population resides. We present a framework that uses environmental determinants of health, instead of social ones. Other studies that link the environment to human health have done so by analyzing one ecosystem service (such as clean air) to the health of the population. Instead of relating one ecosystem service to the health of the population, this framework breaks the environmental features that produce the ecosystem service into parts (forest, temperature, precipitation). Each feature is then related to human health. With the amount of data available it is feasible to include change in monitored features over time, and create predictors for the impact of the change of monitored features on the health of populations. This framework generalizes ecosystem services and disservices into one value that an environmental feature provides. This helps to manage uncertainty of how an individual ecosystem service affects health. Application of this framework will allow for fine scale monitoring of vulnerable populations and transmission pathways of various infectious diseases. This framework is particularly relevant to newly emerging infectious diseases, such as COVID19, whose socially determinant risk factors are unknown (or data scarce) and to which we have to respond in a rapid manner.
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11
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Ganti K, Bagga A, DaSilva J, Shepard SS, Barnes JR, Shriner S, Koelle K, Lowen AC. Avian Influenza A Viruses Reassort and Diversify Differently in Mallards and Mammals. Viruses 2021; 13:v13030509. [PMID: 33808674 PMCID: PMC8003500 DOI: 10.3390/v13030509] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/18/2022] Open
Abstract
Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a coinfected host are likely to be shaped by several factors, including viral load, the extent of viral mixing within the host and the stringency of selection. These factors in turn are expected to vary among the diverse host species that IAV infects. To investigate host differences in IAV reassortment, here we examined reassortment of two distinct avian IAVs within their natural host (mallards) and a mammalian model system (guinea pigs). Animals were co-inoculated with A/wildbird/California/187718-36/2008 (H3N8) and A/mallard/Colorado/P66F1-5/2008 (H4N6) viruses. Longitudinal samples were collected from the cloaca of mallards or the nasal tract of guinea pigs and viral genetic exchange was monitored by genotyping clonal isolates from these samples. Relative to those in guinea pigs, viral populations in mallards showed higher frequencies of reassortant genotypes and were characterized by higher genotype richness and diversity. In line with these observations, analysis of pairwise segment combinations revealed lower linkage disequilibrium in mallards as compared to guinea pigs. No clear longitudinal patterns in richness, diversity or linkage disequilibrium were present in either host. Our results reveal mallards to be a highly permissive host for IAV reassortment and suggest that reduced viral mixing limits avian IAV reassortment in a mammalian host.
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Affiliation(s)
- Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Anish Bagga
- Emory College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA;
| | - Juliana DaSilva
- Center for Disease Control and Prevention, Influenza Division, Atlanta, GA 30322, USA; (J.D.); (S.S.S.); (J.R.B.)
| | - Samuel S. Shepard
- Center for Disease Control and Prevention, Influenza Division, Atlanta, GA 30322, USA; (J.D.); (S.S.S.); (J.R.B.)
| | - John R. Barnes
- Center for Disease Control and Prevention, Influenza Division, Atlanta, GA 30322, USA; (J.D.); (S.S.S.); (J.R.B.)
| | - Susan Shriner
- National Wildlife Research Center, US Department of Agriculture-Animal and Plant Health Inspection Service, Fort Collins, CO 80521, USA;
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Emory-UGA Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA 30322, USA
- Correspondence: (K.K.); , (A.C.L.)
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Emory-UGA Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA 30322, USA
- Correspondence: (K.K.); , (A.C.L.)
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12
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Gregianini TS, Varella IRS, Fisch P, Martins LG, Veiga ABG. Dual and Triple Infections With Influenza A and B Viruses: A Case-Control Study in Southern Brazil. J Infect Dis 2019; 220:961-968. [DOI: 10.1093/infdis/jiz221] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/27/2019] [Indexed: 01/01/2023] Open
Abstract
Abstract
Influenza surveillance is important for disease control and should consider possible coinfection with different viruses, which can be associated with disease severity. This study analyzed 34 459 patients with respiratory infection from 2009 to 2018, of whom 8011 were positive for influenza A virus (IAV) or influenza B virus (IBV). We found 18 cases of dual influenza virus infection, including coinfection with 2009 pandemic influenza A(H1N1) virus (A[H1N1]pdm09) and influenza A(H3N2) virus (1 case), A(H1N1)pdm09 and IBV (6 cases), A(H3N2) and IBV (8 cases), and nonsubtyped IAV and IBV (3 cases); and 1 case of triple infection with A(H3N2), A(H1N1)pdm09, and IBV. Compared with 76 monoinfected patients, coinfection was significantly associated with cardiopathy and death. Besides demographic characteristics and clinical symptoms, we assessed vaccination status, antiviral treatment, timeliness of antiviral use, hospitalization, and intensive care unit admission, but no significant differences were found between coinfected and monoinfected cases. Our findings indicate that influenza virus coinfection occurs more often than previously reported and that it can lead to a worse disease outcome.
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Affiliation(s)
| | | | | | - Letícia Garay Martins
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana B G Veiga
- Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
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13
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H5N8 and H7N9 packaging signals constrain HA reassortment with a seasonal H3N2 influenza A virus. Proc Natl Acad Sci U S A 2019; 116:4611-4618. [PMID: 30760600 PMCID: PMC6410869 DOI: 10.1073/pnas.1818494116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Influenza A virus (IAV) has a segmented genome, which (i) allows for exchange of gene segments in coinfected cells, termed reassortment, and (ii) necessitates a selective packaging mechanism to ensure incorporation of a complete set of segments into virus particles. Packaging signals serve as segment identifiers and enable segment-specific packaging. We have previously shown that packaging signals limit reassortment between heterologous IAV strains in a segment-dependent manner. Here, we evaluated the extent to which packaging signals prevent reassortment events that would raise concern for pandemic emergence. Specifically, we tested the compatibility of hemagglutinin (HA) packaging signals from H5N8 and H7N9 avian IAVs with a human seasonal H3N2 IAV. By evaluating reassortment outcomes, we demonstrate that HA segments carrying H5 or H7 packaging signals are significantly disfavored for incorporation into a human H3N2 virus in both cell culture and a guinea pig model. However, incorporation of the heterologous HAs was not excluded fully, and variants with heterologous HA packaging signals were detected at low levels in vivo, including in naïve contact animals. This work indicates that the likelihood of reassortment between human seasonal IAV and avian IAV is reduced by divergence in the RNA packaging signals of the HA segment. These findings offer important insight into the molecular mechanisms governing IAV emergence and inform efforts to estimate the risks posed by H7N9 and H5N8 subtype avian IAVs.
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14
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Vahey MD, Fletcher DA. Low-Fidelity Assembly of Influenza A Virus Promotes Escape from Host Cells. Cell 2018; 176:281-294.e19. [PMID: 30503209 DOI: 10.1016/j.cell.2018.10.056] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 09/05/2018] [Accepted: 10/26/2018] [Indexed: 12/11/2022]
Abstract
Influenza viruses inhabit a wide range of host environments using a limited repertoire of protein components. Unlike viruses with stereotyped shapes, influenza produces virions with significant morphological variability even within clonal populations. Whether this tendency to form pleiomorphic virions is coupled to compositional heterogeneity and whether it affects replicative fitness remains unclear. Here, we address these questions by developing a strain of influenza A virus amenable to rapid compositional characterization through quantitative, site-specific labeling of viral proteins. Using this strain, we find that influenza A produces virions with broad variations in size and composition from even single infected cells. This phenotypic variability contributes to virus survival during environmental challenges, including exposure to antivirals. Complementing genetic adaptations that act over larger populations and longer times, this "low-fidelity" assembly of influenza A virus allows small populations to survive environments that fluctuate over individual replication cycles.
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Affiliation(s)
- Michael D Vahey
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; University of California, Berkeley/University of California, San Francisco Graduate Group in Bioengineering, Berkeley, CA 94720, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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15
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16
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Bourret V. Avian influenza viruses in pigs: An overview. Vet J 2018; 239:7-14. [PMID: 30197112 DOI: 10.1016/j.tvjl.2018.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 05/22/2018] [Accepted: 07/15/2018] [Indexed: 12/11/2022]
Abstract
This paper reviews important aspects of infection of pigs with avian influenza viruses. Wild waterfowl are the main reservoir for influenza A viruses; other species, such as pigs, can be infected, but most avian strains are imperfectly adapted to replication and transmission in such new hosts. However, some avian-to-porcine host jumps have resulted in the emergence of stable swine influenza virus lineages, with major consequences for both animal and human health. Different categories of factors are involved in these cross-species adaptations, both epidemiological (relating to host-host interactions) and virological (relating to host-virus interactions). An understanding of the adaptation of avian influenza viruses to pigs has benefited from a number of recent studies, but more research is warranted to fully appreciate the key molecular and epidemiological factors involved in this intriguing viral host jump.
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Affiliation(s)
- V Bourret
- Université de Montpellier, CEFE, Campus CNRS, 1919 route de Mende, 34293 Montpellier, France.
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17
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Abstract
Influenza A virus (IAV) is an RNA virus with a segmented genome. These viral properties allow for the rapid evolution of IAV under selective pressure, due to mutation occurring from error-prone replication and the exchange of gene segments within a co-infected cell, termed reassortment. Both mutation and reassortment give rise to genetic diversity, but constraints shape their impact on viral evolution: just as most mutations are deleterious, most reassortment events result in genetic incompatibilities. The phenomenon of segment mismatch encompasses both RNA- and protein-based incompatibilities between co-infecting viruses and results in the production of progeny viruses with fitness defects. Segment mismatch is an important determining factor of the outcomes of mixed IAV infections and has been addressed in multiple risk assessment studies undertaken to date. However, due to the complexity of genetic interactions among the eight viral gene segments, our understanding of segment mismatch and its underlying mechanisms remain incomplete. Here, we summarize current knowledge regarding segment mismatch and discuss the implications of this phenomenon for IAV reassortment and diversity.
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Affiliation(s)
- Maria C White
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
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18
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Affiliation(s)
- Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322
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19
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Seasonal H3N2 and 2009 Pandemic H1N1 Influenza A Viruses Reassort Efficiently but Produce Attenuated Progeny. J Virol 2017. [PMID: 28637755 DOI: 10.1128/jvi.00830-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Reassortment of gene segments between coinfecting influenza A viruses (IAVs) facilitates viral diversification and has a significant epidemiological impact on seasonal and pandemic influenza. Since 1977, human IAVs of H1N1 and H3N2 subtypes have cocirculated with relatively few documented cases of reassortment. We evaluated the potential for viruses of the 2009 pandemic H1N1 (pH1N1) and seasonal H3N2 lineages to reassort under experimental conditions. Results of heterologous coinfections with pH1N1 and H3N2 viruses were compared to those obtained following coinfection with homologous, genetically tagged, pH1N1 viruses as a control. High genotype diversity was observed among progeny of both coinfections; however, diversity was more limited following heterologous coinfection. Pairwise analysis of genotype patterns revealed that homologous reassortment was random while heterologous reassortment was characterized by specific biases. pH1N1/H3N2 reassortant genotypes produced under single-cycle coinfection conditions showed a strong preference for homologous PB2-PA combinations and general preferences for the H3N2 NA, pH1N1 M, and H3N2 PB2 except when paired with the pH1N1 PA or NP. Multicycle coinfection results corroborated these findings and revealed an additional preference for the H3N2 HA. Segment compatibility was further investigated by measuring chimeric polymerase activity and growth of selected reassortants in human tracheobronchial epithelial cells. In guinea pigs inoculated with a mixture of viruses, parental H3N2 viruses dominated but reassortants also infected and transmitted to cage mates. Taken together, our results indicate that strong intrinsic barriers to reassortment between seasonal H3N2 and pH1N1 viruses are few but that the reassortants formed are attenuated relative to parental strains.IMPORTANCE The genome of IAV is relatively simple, comprising eight RNA segments, each of which typically encodes one or two proteins. Each viral protein carries out multiple functions in coordination with other viral components and the machinery of the cell. When two IAVs coinfect a cell, they can exchange genes through reassortment. The resultant progeny viruses often suffer fitness defects due to suboptimal interactions among divergent viral components. The genetic diversity generated through reassortment can facilitate the emergence of novel outbreak strains. Thus, it is important to understand the efficiency of reassortment and the factors that limit its potential. The research described here offers new tools for studying reassortment between two strains of interest and applies those tools to viruses of the 2009 pandemic H1N1 and seasonal H3N2 lineages, which currently cocirculate in humans and therefore have the potential to give rise to novel epidemic strains.
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20
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Hurst CJ. Of Ducks and Men: Ecology and Evolution of a Zoonotic Pathogen in a Wild Reservoir Host. MODELING THE TRANSMISSION AND PREVENTION OF INFECTIOUS DISEASE 2017. [PMCID: PMC7123570 DOI: 10.1007/978-3-319-60616-3_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A hallmark of disease is that most pathogens are able to infect more than one host species. However, for most pathogens, we still have a limited understanding of how this affects epidemiology, persistence and virulence of infections—including several zoonotic pathogens that reside in wild animal reservoirs and spillover into humans. In this chapter, we review the current knowledge of mallard (Anas platyrhynchos) as host for pathogens. This species is widely distributed, often occupying habitats close to humans and livestock, and is an important game bird species and the ancestor to domestic ducks—thereby being an excellent model species to highlight aspects of the wildlife, domestic animal interface and the relevance for human health. We discuss mallard as host for a range of pathogens but focus more in depth of it as a reservoir host for influenza A virus (IAV). Over the last decades, IAV research has surged, prompted in part to the genesis and spread of highly pathogenic virus variants that have been devastating to domestic poultry and caused a number of human spillover infections. The aim of this chapter is to synthesise and review the intricate interactions of virus, host and environmental factors governing IAV epidemiology and evolution.
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