1
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Chen Y, Tang F, Cao Z, Zeng J, Qiu Z, Zhang C, Long H, Cheng P, Sun Q, Han W, Tang K, Tang J, Zhao Y, Tian D, Du X. Global pattern and determinant for interaction of seasonal influenza viruses. J Infect Public Health 2024; 17:1086-1094. [PMID: 38705061 DOI: 10.1016/j.jiph.2024.04.024] [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: 01/09/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND The prevalence of different types/subtypes varies across seasons and countries for seasonal influenza viruses, indicating underlying interactions between types/subtypes. The global interaction patterns and determinants for seasonal influenza types/subtypes need to be explored. METHODS Influenza epidemiological surveillance data, as well as multidimensional data that include population-related, environment-related, and virus-related factors from 55 countries worldwide were used to explore type/subtype interactions based on Spearman correlation coefficient. The machine learning method Extreme Gradient Boosting (XGBoost) and interpretable framework SHapley Additive exPlanation (SHAP) were utilized to quantify contributing factors and their effects on interactions among influenza types/subtypes. Additionally, causal relationships between types/subtypes were also explored based on Convergent Cross-mapping (CCM). RESULTS A consistent globally negative correlation exists between influenza A/H3N2 and A/H1N1. Meanwhile, interactions between influenza A (A/H3N2, A/H1N1) and B show significant differences across countries, primarily influenced by population-related factors. Influenza A has a stronger driving force than influenza B, and A/H3N2 has a stronger driving force than A/H1N1. CONCLUSION The research elucidated the globally complex and heterogeneous interaction patterns among influenza type/subtypes, identifying key factors shaping their interactions. This sheds light on better seasonal influenza prediction and model construction, informing targeted prevention strategies and ultimately reducing the global burden of seasonal influenza.
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Affiliation(s)
- Yilin Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Feng Tang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; Foshan Center for Disease Control and Prevention, Foshan 528000, PR China
| | - Zicheng Cao
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health, Shantou University, Shantou 515000, PR China
| | - Jinfeng Zeng
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Zekai Qiu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Chi Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Haoyu Long
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Peiwen Cheng
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Qianru Sun
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Wenjie Han
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Kang Tang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Jing Tang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Yang Zhao
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; Shenzhen Key Laboratory of Pathogenic Microbes & Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Dechao Tian
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; Shenzhen Key Laboratory of Pathogenic Microbes & Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; Shenzhen Key Laboratory of Pathogenic Microbes & Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510030, PR China.
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2
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Sobel Leonard A, Mendoza L, McFarland AG, Marques AD, Everett JK, Moncla L, Bushman FD, Odom John AR, Hensley SE. Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status. Virus Evol 2024; 10:veae034. [PMID: 38859985 PMCID: PMC11163376 DOI: 10.1093/ve/veae034] [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: 11/14/2023] [Revised: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 06/12/2024] Open
Abstract
Seasonal influenza virus predominantly evolves through antigenic drift, marked by the accumulation of mutations at antigenic sites. Because of antigenic drift, influenza vaccines are frequently updated, though their efficacy may still be limited due to strain mismatches. Despite the high levels of viral diversity observed across populations, most human studies reveal limited intrahost diversity, leaving the origin of population-level viral diversity unclear. Previous studies show host characteristics, such as immunity, might affect within-host viral evolution. Here we investigate influenza A viral diversity in children aged between 6 months and 18 years. Influenza virus evolution in children is less well characterized than in adults, yet may be associated with higher levels of viral diversity given the lower level of pre-existing immunity and longer durations of infection in children. We obtained influenza isolates from banked influenza A-positive nasopharyngeal swabs collected at the Children's Hospital of Philadelphia during the 2017-18 influenza season. Using next-generation sequencing, we evaluated the population of influenza viruses present in each sample. We characterized within-host viral diversity using the number and frequency of intrahost single-nucleotide variants (iSNVs) detected in each sample. We related viral diversity to clinical metadata, including subjects' age, vaccination status, and comorbid conditions, as well as sample metadata such as virus strain and cycle threshold. Consistent with previous studies, most samples contained low levels of diversity with no clear association between the subjects' age, vaccine status, or health status. Further, there was no enrichment of iSNVs near known antigenic sites. Taken together, these findings are consistent with previous observations that the majority of intrahost influenza virus infection is characterized by low viral diversity without evidence of diversifying selection.
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Affiliation(s)
- Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Lydia Mendoza
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Alexander G McFarland
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Andrew D Marques
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - John K Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Louise Moncla
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Audrey R Odom John
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
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3
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VanInsberghe D, McBride DS, DaSilva J, Stark TJ, Lau MSY, Shepard SS, Barnes JR, Bowman AS, Lowen AC, Koelle K. Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections. PLoS Pathog 2024; 20:e1012131. [PMID: 38626244 PMCID: PMC11051653 DOI: 10.1371/journal.ppat.1012131] [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: 10/26/2023] [Revised: 04/26/2024] [Accepted: 03/16/2024] [Indexed: 04/18/2024] Open
Abstract
Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized in non-human hosts. Elucidating these dynamics is important to better understand IAV biology and the evolutionary processes that govern spillover into humans. Here, we sampled an IAV outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype swine IAVs. PCR-positive samples with robust Ct values were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Based on higher-depth re-sequenced data from a subset of these initially sequenced samples (260 samples from 168 pigs), we characterized patterns of within-host IAV genetic diversity and evolution. We find that IAV genetic diversity in single-subtype infected pigs is low, with the majority of intrahost Single Nucleotide Variants (iSNVs) present at frequencies of <10%. The ratio of the number of nonsynonymous to the number of synonymous iSNVs is significantly lower than under the neutral expectation, indicating that purifying selection shapes patterns of within-host viral diversity in swine. The dynamic turnover of iSNVs and their pronounced frequency changes further indicate that genetic drift also plays an important role in shaping IAV populations within pigs. Taken together, our results highlight similarities in patterns of IAV genetic diversity and evolution between humans and swine, including the role of stochastic processes in shaping within-host IAV dynamics.
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Affiliation(s)
- David VanInsberghe
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Dillon S. McBride
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Juliana DaSilva
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Thomas J. Stark
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Max S. Y. Lau
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Samuel S. Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Andrew S. Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
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4
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Shi YT, Harris JD, Martin MA, Koelle K. Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation. Mol Biol Evol 2024; 41:msad286. [PMID: 38158742 PMCID: PMC10798134 DOI: 10.1093/molbev/msad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
Sequencing of viral infections has become increasingly common over the last decade. Deep sequencing data in particular have proven useful in characterizing the roles that genetic drift and natural selection play in shaping within-host viral populations. They have also been used to estimate transmission bottleneck sizes from identified donor-recipient pairs. These bottleneck sizes quantify the number of viral particles that establish genetic lineages in the recipient host and are important to estimate due to their impact on viral evolution. Current approaches for estimating bottleneck sizes exclusively consider the subset of viral sites that are observed as polymorphic in the donor individual. However, these approaches have the potential to substantially underestimate true transmission bottleneck sizes. Here, we present a new statistical approach for instead estimating bottleneck sizes using patterns of viral genetic variation that arise de novo within a recipient individual. Specifically, our approach makes use of the number of clonal viral variants observed in a transmission pair, defined as the number of viral sites that are monomorphic in both the donor and the recipient but carry different alleles. We first test our approach on a simulated dataset and then apply it to both influenza A virus sequence data and SARS-CoV-2 sequence data from identified transmission pairs. Our results confirm the existence of extremely tight transmission bottlenecks for these 2 respiratory viruses.
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Affiliation(s)
| | | | - Michael A Martin
- Department of Biology, Emory University, Atlanta, GA, USA
- Graduate Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory Center of Excellence for Influenza Research and Response (CEIRR), Atlanta, GA, USA
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5
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Holmes KE, VanInsberghe D, Ferreri LM, Elie B, Ganti K, Lee CY, Lowen AC. Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567585. [PMID: 38014182 PMCID: PMC10680852 DOI: 10.1101/2023.11.19.567585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
For many viruses, narrow bottlenecks acting during transmission sharply reduce genetic diversity in a recipient host relative to the donor. Since genetic diversity represents adaptive potential, such losses of diversity are though to limit the opportunity for viral populations to undergo antigenic change and other adaptive processes. Thus, a detailed picture of evolutionary dynamics during transmission is critical to understanding the forces driving viral evolution at an epidemiologic scale. To advance this understanding, we used a novel barcoded virus library and a guinea pig model of transmission to decipher where in the transmission process diversity is lost for influenza A viruses. In inoculated guinea pigs, we show that a high level of viral genetic diversity is maintained across time. Continuity in the barcodes detected furthermore indicates that stochastic effects are not pronounced within inoculated hosts. Importantly, in both aerosol-exposed and direct contact-exposed animals, we observed many barcodes at the earliest time point(s) positive for infectious virus, indicating robust transfer of diversity through the environment. This high viral diversity is short-lived, however, with a sharp decline seen 1-2 days after initiation of infection. Although major losses of diversity at transmission are well described for influenza A virus, our data indicate that events that occur following viral transfer and during the earliest stages of natural infection have a predominant role in this process. This finding suggests that immune selection may have greater opportunity to operate during influenza A transmission than previously recognized.
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Affiliation(s)
- Katie E. Holmes
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - David VanInsberghe
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lucas M. Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Baptiste Elie
- MIVEGEC, CNRS, IRD, Université de Montpellier, Montpellier, France
| | - Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Jung-gu, Daegu, Republic of Korea
| | - 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 (CEIRR), Atlanta, GA, USA
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6
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Han AX, de Jong SPJ, Russell CA. Co-evolution of immunity and seasonal influenza viruses. Nat Rev Microbiol 2023; 21:805-817. [PMID: 37532870 DOI: 10.1038/s41579-023-00945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
Seasonal influenza viruses cause recurring global epidemics by continually evolving to escape host immunity. The viral constraints and host immune responses that limit and drive the evolution of these viruses are increasingly well understood. However, it remains unclear how most of these advances improve the capacity to reduce the impact of seasonal influenza viruses on human health. In this Review, we synthesize recent progress made in understanding the interplay between the evolution of immunity induced by previous infections or vaccination and the evolution of seasonal influenza viruses driven by the heterogeneous accumulation of antibody-mediated immunity in humans. We discuss the functional constraints that limit the evolution of the viruses, the within-host evolutionary processes that drive the emergence of new virus variants, as well as current and prospective options for influenza virus control, including the viral and immunological barriers that must be overcome to improve the effectiveness of vaccines and antiviral drugs.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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7
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Terbot JW, Cooper BS, Good JM, Jensen JD. A Simulation Framework for Modeling the Within-Patient Evolutionary Dynamics of SARS-CoV-2. Genome Biol Evol 2023; 15:evad204. [PMID: 37950882 PMCID: PMC10664409 DOI: 10.1093/gbe/evad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/13/2023] Open
Abstract
The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to considerable interest in detecting novel beneficial mutations and other genomic changes that may signal the development of variants of concern (VOCs). The ability to accurately detect these changes within individual patient samples is important in enabling early detection of VOCs. Such genomic scans for rarely acting positive selection are best performed via comparison of empirical data with simulated data wherein commonly acting evolutionary factors, including mutation and recombination, reproductive and infection dynamics, and purifying and background selection, can be carefully accounted for and parameterized. Although there has been work to quantify these factors in SARS-CoV-2, they have yet to be integrated into a baseline model describing intrahost evolutionary dynamics. To construct such a baseline model, we develop a simulation framework that enables one to establish expectations for underlying levels and patterns of patient-level variation. By varying eight key parameters, we evaluated 12,096 different model-parameter combinations and compared them with existing empirical data. Of these, 592 models (∼5%) were plausible based on the resulting mean expected number of segregating variants. These plausible models shared several commonalities shedding light on intrahost SARS-CoV-2 evolutionary dynamics: severe infection bottlenecks, low levels of reproductive skew, and a distribution of fitness effects skewed toward strongly deleterious mutations. We also describe important areas of model uncertainty and highlight additional sequence data that may help to further refine a baseline model. This study lays the groundwork for the improved analysis of existing and future SARS-CoV-2 within-patient data.
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Affiliation(s)
- John W Terbot
- School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, Arizona, USA
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, Arizona, USA
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8
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VanInsberghe D, McBride DS, DaSilva J, Stark TJ, Lau MS, Shepard SS, Barnes JR, Bowman AS, Lowen AC, Koelle K. Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563581. [PMID: 37961583 PMCID: PMC10634741 DOI: 10.1101/2023.10.23.563581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized in non-human hosts. Elucidating these dynamics is important to better understand IAV biology and the evolutionary processes that govern spillover into humans. Here, we sampled an IAV outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype IAVs. PCR-positive samples with robust Ct values were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Based on higher-depth re-sequenced data from a subset of these initially sequenced samples (260 samples from 168 pigs), we characterized patterns of within-host IAV genetic diversity and evolution. We find that IAV genetic diversity in single-subtype infected pigs is low, with the majority of intra-host single nucleotide variants (iSNVs) present at frequencies of <10%. The ratio of the number of nonsynonymous to the number of synonymous iSNVs is significantly lower than under the neutral expectation, indicating that purifying selection shapes patterns of within-host viral diversity in swine. The dynamic turnover of iSNVs and their pronounced frequency changes further indicate that genetic drift also plays an important role in shaping IAV populations within pigs. Taken together, our results highlight similarities in patterns of IAV genetic diversity and evolution between humans and swine, including the role of stochastic processes in shaping within-host IAV dynamics.
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Affiliation(s)
- David VanInsberghe
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, 30322
- Department of Biology, Emory University, Atlanta, GA, 30322
| | - Dillon S. McBride
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Juliana DaSilva
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - Thomas J. Stark
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - Max S.Y. Lau
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322
| | - Samuel S. Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - Andrew S. Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, 30322
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR)
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, 30322
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR)
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9
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Kieran TJ, DaSilva J, Stark TJ, York IA, Pappas C, Barnes JR, Maines TR, Belser JA. Influenza A Virus Multicycle Replication Yields Comparable Viral Population Emergence in Human Respiratory and Ocular Cell Types. Microbiol Spectr 2023; 11:e0116623. [PMID: 37404140 PMCID: PMC10433845 DOI: 10.1128/spectrum.01166-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023] Open
Abstract
While primarily considered a respiratory pathogen, influenza A virus (IAV) is nonetheless capable of spreading to, and replicating in, numerous extrapulmonary tissues in humans. However, within-host assessments of genetic diversity during multicycle replication have been largely limited to respiratory tract tissues and specimens. As selective pressures can vary greatly between anatomical sites, there is a need to examine how measures of viral diversity may vary between influenza viruses exhibiting different tropisms in humans, as well as following influenza virus infection of cells derived from different organ systems. Here, we employed human primary tissue constructs emulative of the human airway or corneal surface, and we infected both with a panel of human- and avian-origin IAV, inclusive of H1 and H3 subtype human viruses and highly pathogenic H5 and H7 subtype viruses, which are associated with both respiratory disease and conjunctivitis following human infection. While both cell types supported productive replication of all viruses, airway-derived tissue constructs elicited greater induction of genes associated with antiviral responses than did corneal-derived constructs. We used next-generation sequencing to examine viral mutations and population diversity, utilizing several metrics. With few exceptions, generally comparable measures of viral diversity and mutational frequency were detected following homologous virus infection of both respiratory-origin and ocular-origin tissue constructs. Expansion of within-host assessments of genetic diversity to include IAV with atypical clinical presentations in humans or in extrapulmonary cell types can provide greater insight into understanding those features most prone to modulation in the context of viral tropism. IMPORTANCE Influenza A virus (IAV) can infect tissues both within and beyond the respiratory tract, leading to extrapulmonary complications, such as conjunctivitis or gastrointestinal disease. Selective pressures governing virus replication and induction of host responses can vary based on the anatomical site of infection, yet studies examining within-host assessments of genetic diversity are typically only conducted in cells derived from the respiratory tract. We examined the contribution of influenza virus tropism on these properties two different ways: by using IAV associated with different tropisms in humans, and by infecting human cell types from two different organ systems susceptible to IAV infection. Despite the diversity of cell types and viruses employed, we observed generally similar measures of viral diversity postinfection across all conditions tested; these findings nonetheless contribute to a greater understanding of the role tissue type contributes to the dynamics of virus evolution within a human host.
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Affiliation(s)
- Troy J. Kieran
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Juliana DaSilva
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thomas J. Stark
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ian A. York
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claudia Pappas
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Taronna R. Maines
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica A. Belser
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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10
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Terbot JW, Cooper BS, Good JM, Jensen JD. A simulation framework for modeling the within-patient evolutionary dynamics of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548462. [PMID: 37503016 PMCID: PMC10370031 DOI: 10.1101/2023.07.13.548462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The global impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to considerable interest in detecting novel beneficial mutations and other genomic changes that may signal the development of variants of concern (VOCs). The ability to accurately detect these changes within individual patient samples is important in enabling early detection of VOCs. Such genomic scans for positive selection are best performed via comparison of empirical data to simulated data wherein evolutionary factors, including mutation and recombination rates, reproductive and infection dynamics, and purifying and background selection, can be carefully accounted for and parameterized. While there has been work to quantify these factors in SARS-CoV-2, they have yet to be integrated into a baseline model describing intra-host evolutionary dynamics. To construct such a baseline model, we develop a simulation framework that enables one to establish expectations for underlying levels and patterns of patient-level variation. By varying eight key parameters, we evaluated 12,096 different model-parameter combinations and compared them to existing empirical data. Of these, 592 models (~5%) were plausible based on the resulting mean expected number of segregating variants. These plausible models shared several commonalities shedding light on intra-host SARS-CoV-2 evolutionary dynamics: severe infection bottlenecks, low levels of reproductive skew, and a distribution of fitness effects skewed towards strongly deleterious mutations. We also describe important areas of model uncertainty and highlight additional sequence data that may help to further refine a baseline model. This study lays the groundwork for the improved analysis of existing and future SARS-CoV-2 within-patient data.
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Affiliation(s)
- John W Terbot
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Brandon S. Cooper
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey D. Jensen
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
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11
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Alotaibi BS, Tantry BA, Bandy A, Ahmad R, Khursheed SQ, Ahmad A, Hakami MA, Shah NN. Simultaneous Detection of Influenza A/B, Respiratory Syncytial Virus, and SARS-CoV-2 in Nasopharyngeal Swabs by One-Tube Multiplex Reverse Transcription Polymerase Chain Reaction. Trop Med Infect Dis 2023; 8:326. [PMID: 37368744 DOI: 10.3390/tropicalmed8060326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
The treatment and outcome of respiratory virus infections differ. SARS-CoV-2, as well as other respiratory viruses such as influenza virus (A and B) and respiratory syncytial virus (RSV), require simultaneous, cost-effective, and rapid differential detection. We used a gold standard five-target single-step RT-PCR to detect influenza viruses, RSV, and SARS-CoV-2, and this method can be extended to detect influenza virus subtypes. As a result, this five-target single-step RT-PCR method is ideal for differentiating respiratory viruses. The 5' nuclease activity of Taq DNA polymerase is used in the real-time reverse transcription PCR assay. The Taq man fast viral 1-step enzyme is a 4× Master mix and five-target primer probe mix that detects influenza A, influenza B, SARS-CoV-2 ORF1ab, respiratory syncytial viruses A/B and actin. When compared with TaqMan TM and Invitrogen superscript TM III Platinum and the Meril Kit for SARS-CoV-2, the assay demonstrated 100% sensitivity, specificity, and amplification efficiency of 90.1% for target genes. In conclusion, our one-tube multiplex RT-PCR assay offers a rapid and reliable method for the simultaneous detection of influenza A/B, RSV, and SARS-CoV-2 from nasopharyngeal swabs. This assay has the potential to enhance diagnostic capabilities and improve public health responses during respiratory outbreaks, enabling timely interventions and informed decision making.
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Affiliation(s)
- Bader S Alotaibi
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 19257, Saudi Arabia
| | - Bilal Ahmad Tantry
- Department of Microbiology, Government Medical College, Srinagar 190010, India
| | - Altaf Bandy
- Department of Community Medicine, College of Medicine, Shaqra University, Shaqra 15273, Saudi Arabia
| | - Reyaz Ahmad
- Department of Microbiology, Government Medical College, Srinagar 190010, India
| | | | - Arshid Ahmad
- Department of Pulmonary Medicine, Government Medical College, Srinagar 190001, India
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 19257, Saudi Arabia
| | - Naveed Nazir Shah
- Department of Pulmonary Medicine, Government Medical College, Srinagar 190001, India
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12
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Xiong D, Zhang X, Yu J, Wei H. Distribution of intra‐host variations and mutations in the genomes of SARS‐CoV‐2 and their implications on detection and therapeutics. MedComm (Beijing) 2022; 3:e186. [DOI: 10.1002/mco2.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety Center for Biosafety Mega‐Science Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China
- CAS Key Laboratory of Special Pathogens and Biosafety University of Chinese Academy of Sciences Beijing China
| | - Xiaoxu Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety Center for Biosafety Mega‐Science Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety Center for Biosafety Mega‐Science Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China
- CAS Key Laboratory of Special Pathogens and Biosafety University of Chinese Academy of Sciences Beijing China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety Center for Biosafety Mega‐Science Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China
- CAS Key Laboratory of Special Pathogens and Biosafety University of Chinese Academy of Sciences Beijing China
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13
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Malosh RE, McGovern I, Monto AS. Influenza During the 2010-2020 Decade in the United States: Seasonal Outbreaks and Vaccine Interventions. Clin Infect Dis 2022; 76:540-549. [PMID: 36219562 PMCID: PMC9619714 DOI: 10.1093/cid/ciac653] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Indexed: 11/14/2022] Open
Abstract
The 10 years between the last influenza pandemic and start of the severe acute respiratory syndrome coronavirus 2 pandemic have been marked by great advances in our ability to follow influenza occurrence and determine vaccine effectiveness (VE), largely based on widespread use of the polymerase chain reaction assay. We examine the results, focusing mainly on data from the United States and inactivated vaccines. Surveillance has expanded, resulting in increased ability to characterize circulating viruses and their impact. The surveillance has often confirmed previous observations on timing of outbreaks and age groups affected, which can now be examined in greater detail. Selection of strains for vaccines is now based on enhanced viral characterization using immunologic, virologic, and computational techniques not previously available. Vaccine coverage has been largely stable, but VE has remained modest and, in some years, very low. We discuss ways to improve VE based on existing technology while we work toward supraseasonal vaccines.
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Affiliation(s)
| | | | - Arnold S Monto
- Correspondence: A. S. Monto, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029 ()
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14
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Hannon WW, Roychoudhury P, Xie H, Shrestha L, Addetia A, Jerome KR, Greninger AL, Bloom JD. Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat. Virus Evol 2022; 8:veac052. [PMID: 35799885 PMCID: PMC9257191 DOI: 10.1093/ve/veac052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/12/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. Here, we use deep sequencing to investigate the transmission of viral genetic variation among individuals during a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak that infected the vast majority of crew members on a fishing boat. We deep-sequenced nasal swabs to characterize the within-host viral population of infected crew members, using experimental duplicates and strict computational filters to ensure accurate variant calling. We find that within-host viral diversity is low in infected crew members. The mutations that did fix in some crew members during the outbreak are not observed at detectable frequencies in any of the sampled crew members in which they are not fixed, suggesting that viral evolution involves occasional fixation of low-frequency mutations during transmission rather than persistent maintenance of within-host viral diversity. Overall, our results show that strong transmission bottlenecks dominate viral evolution even during a superspreading event with a very high attack rate.
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Affiliation(s)
- William W Hannon
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA,Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA
| | | | - Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA
| | | | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195, USA
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15
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Amato KA, Haddock LA, Braun KM, Meliopoulos V, Livingston B, Honce R, Schaack GA, Boehm E, Higgins CA, Barry GL, Koelle K, Schultz-Cherry S, Friedrich TC, Mehle A. Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks. Nat Commun 2022; 13:3416. [PMID: 35701424 PMCID: PMC9197827 DOI: 10.1038/s41467-022-31147-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/03/2022] [Indexed: 11/09/2022] Open
Abstract
Transmission of influenza A viruses (IAV) between hosts is subject to numerous physical and biological barriers that impose genetic bottlenecks, constraining viral diversity and adaptation. The bottlenecks within hosts and their potential impacts on evolutionary pathways taken during infection are poorly understood. To address this, we created highly diverse IAV libraries bearing molecular barcodes on two gene segments, enabling high-resolution tracking and quantification of unique virus lineages within hosts. Here we show that IAV infection in lungs is characterized by multiple within-host bottlenecks that result in “islands” of infection in lung lobes, each with genetically distinct populations. We perform site-specific inoculation of barcoded IAV in the upper respiratory tract of ferrets and track viral diversity as infection spreads to the trachea and lungs. We detect extensive compartmentalization of discrete populations within lung lobes. Bottleneck events and localized replication stochastically sample individual viruses from the upper respiratory tract or the trachea that become the dominant genotype in a particular lobe. These populations are shaped strongly by founder effects, with limited evidence for positive selection. The segregated sites of replication highlight the jackpot-style events that contribute to within-host influenza virus evolution and may account for low rates of intrahost adaptation. Transmission of influenza A viruses (IAV) between hosts and replication within host impose genetic bottlenecks, constraining viral diversity and adaptation. Here, Amato et al. perform site-specific inoculation of barcoded IAV of ferrets and track viral diversity as infection spreads to the lower respiratory tract and conclude that narrow population bottlenecks are an important feature of the within-host infection dynamics.
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Affiliation(s)
- Katherine A Amato
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Luis A Haddock
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA
| | - Victoria Meliopoulos
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brandi Livingston
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Rebekah Honce
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Grace A Schaack
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emma Boehm
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA
| | - Christina A Higgins
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gabrielle L Barry
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706, USA.,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Andrew Mehle
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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16
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Soldevila N, Basile L, Martínez A, Torner N, Marcos MÁ, Mosquera MM, Antón A, Andrés C, Rius C, Pumarola T, Domínguez Á. Surveillance of influenza B severe hospitalized cases during ten seasons in Catalonia. Does the lineage make a difference? J Med Virol 2022; 94:4417-4424. [PMID: 35593301 DOI: 10.1002/jmv.27876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/07/2022] [Accepted: 05/17/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Influenza B viruses circulates in two lineages (B/Victoria and B/Yamagata). Although classically affecting children, recently it has shown high rate of infection and increased hospitalization in the elderly. OBJECTIVE To describe and analyze the clinical and epidemiological characteristics of severe hospitalized laboratory confirmed influenza B virus (SHLCI-B) cases in Catalonia associated to mismatch from Influenza B virus strain included in the trivalent influenza vaccine (TIV). METHODS SHLCI-B registered by the influenza sentinel surveillance system of Catalonia (PIDIRAC) during ten surveillance seasons from 2010 to 2020. Variables age, comorbidities, vaccination status were recorded. Vaccine effectiveness was estimated as (1-OR) for intensive care unit (ICU) admission. Statistical significance was established at p <0.05. RESULTS A total of 1159 SHLCI-B were registered, of these 68.2% (791) corresponded to the 2017-18 season; 21.8% (253) were admitted to ICU and 13.8% (160) were exitus; 62.5% (725) cases occurred in those aged > 64 years; most frequent risk factor was cardiovascular disease (35.1%, 407) followed by chronic pulmonary obstructive disease-COPD (24.6%, 285) and diabetes (24.1%, 279). In 4 seasons, the predominant circulating lineage was B/Victoria, in 2 seasons the B/Yamagata lineage and 4 seasons had no IBV activity. Four seasons presented discordance with the strain included within the TIV. Vaccine effectiveness (VE) to prevent ICU admission was 31% (95% CI: 4-51%; p=0.03); being 29% (95%CI: -3%, 51%) in discordant and 43% (95% CI:-43%, 77%) in concordant seasons. Significant differences were observed in the number of affected aged > 64 years (OR=2.5; 95% CI: 1.9-3.4; p <0.001) and in patients with heart disease (OR = 2.40 95% CI: 1.7-3.4; p <0.001), COPD (OR = 1.6 95% CI: 1.1-2.3; p = 0.01) and diabetes (OR = 1.5 95% CI: 1.1-2.1; p = 0.04) between discordant and concordant seasons. CONCLUSIONS The increase in hospitalization rate in people> 64 years of age and those presenting comorbidities in seasons with circulating influenza B virus belonging to a lineage discordant with the strain included in the TIV and the decrease of VE to prevent ICU admissions evidences the vital need to administer the quadrivalent influenza vaccine regardless of the findings of predominant circulation in the previous season. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Núria Soldevila
- Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Luca Basile
- Public Health Agency of Catalonia, Barcelona, Spain
| | - Ana Martínez
- Public Health Agency of Catalonia, Barcelona, Spain.,Ciber Epidemiology and Public Health CIBERESP, Instituto de Salud Carlos III, Madrid
| | - Núria Torner
- Department of Medicine, University of Barcelona, Barcelona, Spain.,Ciber Epidemiology and Public Health CIBERESP, Instituto de Salud Carlos III, Madrid
| | | | - MMar Mosquera
- Department of Microbiology, Hospital Clínic of Barcelona
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
| | - Cristina Rius
- Ciber Epidemiology and Public Health CIBERESP, Instituto de Salud Carlos III, Madrid.,Public Health Agency of Barcelona, Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid
| | - Ángela Domínguez
- Department of Medicine, University of Barcelona, Barcelona, Spain.,Ciber Epidemiology and Public Health CIBERESP, Instituto de Salud Carlos III, Madrid
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17
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Low Pathogenicity H7N3 Avian Influenza Viruses Have Higher Within-Host Genetic Diversity Than a Closely Related High Pathogenicity H7N3 Virus in Infected Turkeys and Chickens. Viruses 2022; 14:v14030554. [PMID: 35336961 PMCID: PMC8951284 DOI: 10.3390/v14030554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/11/2022] Open
Abstract
Within-host viral diversity offers a view into the early stages of viral evolution occurring after a virus infects a host. In recent years, advances in deep sequencing have allowed for routine identification of low-frequency variants, which are important sources of viral genetic diversity and can potentially emerge as a major virus population under certain conditions. We examined within-host viral diversity in turkeys and chickens experimentally infected with closely related H7N3 avian influenza viruses (AIVs), specifically one high pathogenicity AIV (HPAIV) and two low pathogenicity AIV (LPAIVs) with different neuraminidase protein stalk lengths. Consistent with the high mutation rates of AIVs, an abundance of intra-host single nucleotide variants (iSNVs) at low frequencies of 2–10% was observed in all samples collected. Furthermore, a small number of common iSNVs were observed between turkeys and chickens, and between directly inoculated and contact-exposed birds. Notably, the LPAIVs have significantly higher iSNV diversities and frequencies of nonsynonymous changes than the HPAIV in both turkeys and chickens. These findings highlight the dynamics of AIV populations within hosts and the potential impact of genetic changes, including mutations in the hemagglutinin gene that confers the high pathogenicity pathotype, on AIV virus populations and evolution.
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18
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Hannon WW, Roychoudhury P, Xie H, Shrestha L, Addetia A, Jerome KR, Greninger AL, Bloom JD. Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat.. [PMID: 35169803 PMCID: PMC8845427 DOI: 10.1101/2022.02.09.479546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. Here we use deep sequencing to investigate the transmission of viral genetic variation among individuals during a SARS-CoV-2 outbreak that infected the vast majority of crew members on a fishing boat. We deep-sequenced nasal swabs to characterize the within-host viral population of infected crew members, using experimental duplicates and strict computational filters to ensure accurate variant calling. We find that within-host viral diversity is low in infected crew members. The mutations that did fix in some crew members during the outbreak are not observed at detectable frequencies in any of the sampled crew members in which they are not fixed, suggesting viral evolution involves occasional fixation of low-frequency mutations during transmission rather than persistent maintenance of within-host viral diversity. Overall, our results show that strong transmission bottlenecks dominate viral evolution even during a superspreading event with a very high attack rate.
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19
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Ferreri LM, Geiger G, Seibert B, Obadan A, Rajao D, Lowen AC, Perez DR. Intra- and inter-host evolution of H9N2 influenza A virus in Japanese quail. Virus Evol 2022; 8:veac001. [PMID: 35223084 PMCID: PMC8865083 DOI: 10.1093/ve/veac001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Influenza A viruses (IAVs) are constantly evolving. Crucial steps in the infection cycle, such as sialic acid (SA) receptor binding on the host cell surface, can either promote or hamper the emergence of new variants. We previously assessed the relative fitness in Japanese quail of H9N2 variant viruses differing at a single amino acid position, residue 216 in the hemagglutinin (HA) viral surface protein. This site is known to modulate SA recognition. Our prior study generated a valuable set of longitudinal samples from quail transmission groups where the inoculum comprised different mixed populations of HA 216 variant viruses. Here, we leveraged these samples to examine the evolutionary dynamics of viral populations within and between inoculated and naïve contact quails. We found that positive selection dominated HA gene evolution, but fixation of the fittest variant depended on the competition mixture. Analysis of the whole genome revealed further evidence of positive selection acting both within and between hosts. Positive selection drove fixation of variants in non-HA segments within inoculated and contact quails. Importantly, transmission bottlenecks were modulated by the molecular signature at HA 216, revealing viral receptor usage as a determinant of transmitted diversity. Overall, we show that selection strongly shaped the evolutionary dynamics within and between quails. These findings support the notion that selective processes act effectively on IAV populations in poultry hosts, facilitating rapid viral evolution in this ecological niche.
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Affiliation(s)
| | - Ginger Geiger
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA 30602, USA
| | - Brittany Seibert
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA 30602, USA
| | | | - Daniela Rajao
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA 30602, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
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20
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Efficacy of the commercial plant products acting against influenza-a review. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021; 7:238. [PMID: 34926706 PMCID: PMC8669228 DOI: 10.1186/s43094-021-00385-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Influenza infection always poses a threat to human and animal health. Vaccines and antiviral drugs are recommended to deal with the situation. The drawback of these remedial agents made the scientist change their focus on an alternative therapy. The anti-influenza effects of plants have been extensively studied, and many pharmaceutical companies have prepared their products on this basis.
Main body The present review documents the successfully launched anti-influenza commercial products. In specific, it exposes the scientifically validated and evidence-based supporting inhibitory action of influenza and its strains. Conclusion This review highlighted the efficacy of the commercial products which effectively combat influenza. It provides a complementary strategy to deal with the worst-case scenario of flu. Meanwhile, to face the emerging strains, brand new products are in great necessity besides prevailing and available drugs.
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21
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Tohma K, Saito M, Pajuelo MJ, Mayta H, Zimic M, Lepore CJ, Ford-Siltz LA, Gilman RH, Parra GI. Viral intra-host evolution in immunocompetent children contributes to human norovirus diversification at the global scale. Emerg Microbes Infect 2021; 10:1717-1730. [PMID: 34376124 PMCID: PMC8425682 DOI: 10.1080/22221751.2021.1967706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/30/2021] [Accepted: 08/08/2021] [Indexed: 11/03/2022]
Abstract
Norovirus is a major cause of acute gastroenteritis. Human noroviruses present >30 different genotypes, with a single genotype (GII.4) predominating worldwide. Concurrent outbreaks of norovirus are often associated with the emergence of new viruses. While different hypotheses have been presented, the source of new mutations in noroviruses is still unknown. In this study, we applied high-resolution sequencing to determine the intra-host viral diversity presented by noroviruses during the acute and shedding phase of infection in children. Profiling viral intra-host diversification at nearly full genome level indicated that GII.4 viruses presented dynamic intra-host variation, while non-GII.4 viruses presented minimal variation throughout the infection. Notably, the intra-host genetic variation during the shedding phase recapitulates the genetic diversity observed at the global level, particularly those mapping at the VP1 antigenic sites. Thus the intra-host evolution in healthy children explains the source of norovirus mutations that results in diversification at the global scale.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Monica J. Pajuelo
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Holger Mayta
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cara J Lepore
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | | | - Robert H. Gilman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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22
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Lin GL, Drysdale SB, Snape MD, O’Connor D, Brown A, MacIntyre-Cockett G, Mellado-Gomez E, de Cesare M, Bonsall D, Ansari MA, Öner D, Aerssens J, Butler C, Bont L, Openshaw P, Martinón-Torres F, Nair H, Bowden R, Golubchik T, Pollard AJ. Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus. Nat Commun 2021; 12:5125. [PMID: 34446722 PMCID: PMC8390747 DOI: 10.1038/s41467-021-25265-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection in young children globally, but little is known about within-host RSV diversity. Here, we characterised within-host RSV populations using deep-sequencing data from 319 nasopharyngeal swabs collected during 2017-2020. RSV-B had lower consensus diversity than RSV-A at the population level, while exhibiting greater within-host diversity. Two RSV-B consensus sequences had an amino acid alteration (K68N) in the fusion (F) protein, which has been associated with reduced susceptibility to nirsevimab (MEDI8897), a novel RSV monoclonal antibody under development. In addition, several minor variants were identified in the antigenic sites of the F protein, one of which may confer resistance to palivizumab, the only licensed RSV monoclonal antibody. The differences in within-host virus populations emphasise the importance of monitoring for vaccine efficacy and may help to explain the different prevalences of monoclonal antibody-escape mutants between the two subgroups.
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Affiliation(s)
- Gu-Lung Lin
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Simon B. Drysdale
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK ,grid.4464.20000 0001 2161 2573Present Address: Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George’s, University of London, London, UK
| | - Matthew D. Snape
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O’Connor
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anthony Brown
- grid.4991.50000 0004 1936 8948Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Esther Mellado-Gomez
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Mariateresa de Cesare
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Bonsall
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M. Azim Ansari
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Deniz Öner
- grid.419619.20000 0004 0623 0341Translational Biomarkers, Infectious Diseases Therapeutic Area, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Jeroen Aerssens
- grid.419619.20000 0004 0623 0341Translational Biomarkers, Infectious Diseases Therapeutic Area, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Christopher Butler
- grid.4991.50000 0004 1936 8948Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Louis Bont
- grid.7692.a0000000090126352Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands ,ReSViNET Foundation, Zeist, Netherlands
| | - Peter Openshaw
- grid.7445.20000 0001 2113 8111National Heart and Lung Institute, Imperial College London, London, UK
| | - Federico Martinón-Torres
- grid.411048.80000 0000 8816 6945Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain ,grid.488911.d0000 0004 0408 4897Genetics, Vaccines, Infectious Diseases, and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Harish Nair
- grid.4305.20000 0004 1936 7988Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Rory Bowden
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK ,grid.1042.7Present Address: Division of Advanced Technology and Biology, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC Australia
| | | | - Tanya Golubchik
- grid.4991.50000 0004 1936 8948Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J. Pollard
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.cNIHR Oxford Biomedical Research Centre, Oxford, UK
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23
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Faleye TOC, Adams D, Adhikari S, Sandrolini H, Halden RU, Varsani A, Scotch M. Use of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university setting. BMC Infect Dis 2021; 21:810. [PMID: 34388979 PMCID: PMC8360813 DOI: 10.1186/s12879-021-06526-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/04/2021] [Indexed: 11/25/2022] Open
Abstract
Background Local transmission of seasonal influenza viruses (IVs) can be difficult to resolve. Here, we study if coupling high-throughput sequencing (HTS) of hemagglutinin (HA) and neuraminidase (NA) genes with variant analysis can resolve strains from local transmission that have identical consensus genome. We analyzed 24 samples collected over four days in January 2020 at a large university in the US. We amplified complete hemagglutinin (HA) and neuraminidase (NA) genomic segments followed by Illumina sequencing. We identified consensus complete HA and NA segments using BLASTn and performed variant analysis on strains whose HA and NA segments were 100% similar. Results Twelve of the 24 samples were PCR positive, and we detected complete HA and/or NA segments by de novo assembly in 83.33% (10/12) of them. Similarity and phylogenetic analysis showed that 70% (7/10) of the strains were distinct while the remaining 30% had identical consensus sequences. These three samples also had IAV and IBV co-infection. However, subsequent variant analysis showed that they had distinct variant profiles. While the IAV HA of one sample had no variant, another had a T663C mutation and another had both C1379T and C1589A. Conclusion In this study, we showed that HTS coupled with variant analysis of only HA and NA genes can help resolve variants that are closely related. We also provide evidence that during a short time period in the 2019–2020 season, co-infection of IAV and IBV occurred on the university campus and both 2020/2021 and 2021/2022 WHO recommended H1N1 vaccine strains were co-circulating. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06526-5.
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Affiliation(s)
- Temitope O C Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Deborah Adams
- Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, 85287, USA
| | - Helen Sandrolini
- Arizona State University Health Services, Arizona State University, Tempe, AZ, 85287, USA
| | - Rolf U Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,College of Health Solutions, Arizona State University, Phoenix, AZ, 85004, USA.
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24
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Han AX, Felix Garza ZC, Welkers MRA, Vigeveno RM, Tran ND, Le TQM, Pham Quang T, Dang DT, Tran TNA, Ha MT, Nguyen TH, Le QT, Le TH, Hoang TBN, Chokephaibulkit K, Puthavathana P, Nguyen VVC, Nghiem MN, Nguyen VK, Dao TT, Tran TH, Wertheim HFL, Horby PW, Fox A, van Doorn HR, Eggink D, de Jong MD, Russell CA. Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children. eLife 2021; 10:e68917. [PMID: 34342576 PMCID: PMC8382297 DOI: 10.7554/elife.68917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/02/2021] [Indexed: 01/14/2023] Open
Abstract
The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on infections in healthy adults based on single timepoint data. Here, we analyzed the within-host evolution of 82 longitudinally sampled individuals, mostly young children, infected with A/H1N1pdm09 or A/H3N2 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous minority variants were more prevalent than synonymous ones. For A/H3N2 viruses in young children, early infection was dominated by purifying selection. As these infections progressed, nonsynonymous variants typically increased in frequency even when within-host virus titers decreased. Unlike the short-lived infections of adults where de novo within-host variants are rare, longer infections in young children allow for the maintenance of virus diversity via mutation-selection balance creating potentially important opportunities for within-host virus evolution.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Zandra C Felix Garza
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Matthijs RA Welkers
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - René M Vigeveno
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Nhu Duong Tran
- National Institute of Hygiene and EpidemiologyHanoiViet Nam
| | | | | | | | | | | | | | | | - Thanh Hai Le
- Vietnam National Children's HospitalHanoiViet Nam
| | | | | | | | | | | | | | | | - Tinh Hien Tran
- Siriraj Hospital, Mahidol UniversityBangkokThailand
- Oxford University Clinical Research UnitHo Chi Minh cityViet Nam
| | - Heiman FL Wertheim
- Oxford University Clinical Research UnitHo Chi Minh cityViet Nam
- Radboud Medical Centre, Radboud UniversityNijmegenNetherlands
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Peter W Horby
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Oxford University Clinical Research UnitHanoiViet Nam
| | - Annette Fox
- Oxford University Clinical Research UnitHanoiViet Nam
- Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
- WHO Collaborating Centre for Reference and Research on InfluenzaMelbourneAustralia
| | - H Rogier van Doorn
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Oxford University Clinical Research UnitHanoiViet Nam
| | - Dirk Eggink
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the EnvironmentBilthovenNetherlands
| | - Menno D de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
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25
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Braun KM, Moreno GK, Wagner C, Accola MA, Rehrauer WM, Baker DA, Koelle K, O’Connor DH, Bedford T, Friedrich TC, Moncla LH. Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks. PLoS Pathog 2021; 17:e1009849. [PMID: 34424945 PMCID: PMC8412271 DOI: 10.1371/journal.ppat.1009849] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/02/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023] Open
Abstract
The emergence of divergent SARS-CoV-2 lineages has raised concern that novel variants eliciting immune escape or the ability to displace circulating lineages could emerge within individual hosts. Though growing evidence suggests that novel variants arise during prolonged infections, most infections are acute. Understanding how efficiently variants emerge and transmit among acutely-infected hosts is therefore critical for predicting the pace of long-term SARS-CoV-2 evolution. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely-infected individuals. We find that within-host diversity is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household, and are rarely detected along phylogenetically linked infections in the broader community. These findings suggest that most variation generated within-host is lost during transmission.
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Affiliation(s)
- Katarina M. Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gage K. Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cassia Wagner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Molly A. Accola
- University of Wisconsin School of Medicine and Public Health and the William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, United States of America
| | - William M. Rehrauer
- University of Wisconsin School of Medicine and Public Health and the William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, United States of America
| | - David A. Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Louise H. Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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26
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Barnard KN, Wasik BR, Alford BK, Hayward JJ, Weichert WS, Voorhees IEH, Holmes EC, Parrish CR. Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors. J Evol Biol 2021; 34:1878-1900. [PMID: 34114711 DOI: 10.1111/jeb.13890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022]
Abstract
Viruses are often cultured in cell lines for research and vaccine development, and those often differ from the natural hosts or tissues. Cell lines can also differ in the presence of virus receptors, such as the sialic acid (Sia) receptors used by influenza A viruses (IAV), which can vary in linkage (α2,3- or α2,6-linkage) and form (N-glycolylneuraminic acid [Neu5Gc] or N-acetylneuraminic acid [Neu5Ac]). The selective pressures resulting from passaging viruses in cell types with host-specific variations in viral receptors are still only partially understood. IAV are commonly cultured in MDCK cells which are both derived from canine kidney tubule epithelium and inherently heterogeneous. MDCK cells naturally present Neu5Ac and α2,3-linked Sia forms. Here, we examine natural MDCK variant lineages, as well as engineered variants that synthesize Neu5Gc and/or α2,6-linkages. We determined how viral genetic variation occurred within human H3N2, H1N1 pandemic and canine H3N2 IAV populations when serially passaged in MDCK cell lines that vary in cell type (MDCK-Type I or MDCK-Type II clones) and in Sia display. Deep sequencing of viral genomes showed small numbers of consensus-level mutations, mostly within the hemagglutinin (HA) gene. Both human IAV showed variants in the HA stem and the HA receptor-binding site of populations passaged in cells displaying Neu5Gc. Canine H3N2 showed variants near the receptor-binding site when passaged in cells displaying Neu5Gc or α2,6-linkages. Viruses replicated to low titres in MDCK-Type II cells, suggesting that not all cell types in heterogeneous MDCK cell populations are equally permissive to infection.
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Affiliation(s)
- Karen N Barnard
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brian R Wasik
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Brynn K Alford
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Jessica J Hayward
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Wendy S Weichert
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Ian E H Voorhees
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Colin R Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
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27
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Wang Y, Wang D, Zhang L, Sun W, Zhang Z, Chen W, Zhu A, Huang Y, Xiao F, Yao J, Gan M, Li F, Luo L, Huang X, Zhang Y, Wong SS, Cheng X, Ji J, Ou Z, Xiao M, Li M, Li J, Ren P, Deng Z, Zhong H, Xu X, Song T, Mok CKP, Peiris M, Zhong N, Zhao J, Li Y, Li J, Zhao J. Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients. Genome Med 2021; 13:30. [PMID: 33618765 PMCID: PMC7898256 DOI: 10.1186/s13073-021-00847-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/05/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Since early February 2021, the causative agent of COVID-19, SARS-CoV-2, has infected over 104 million people with more than 2 million deaths according to official reports. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. METHODS Using high-throughput sequencing of metatranscriptomic and hybrid captured libraries, we characterized consensus genomes and intra-host single nucleotide variations (iSNVs) of serial samples collected from eight patients with COVID-19. The distribution of iSNVs along the SARS-CoV-2 genome was analyzed and co-occurring iSNVs among COVID-19 patients were identified. We also compared the evolutionary dynamics of SARS-CoV-2 population in the respiratory tract (RT) and gastrointestinal tract (GIT). RESULTS The 32 consensus genomes revealed the co-existence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in a single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparing allele frequencies of the iSNVs revealed a clear genetic differentiation between intra-host populations from the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events during intra-host migrations. Compared to RT populations, the GIT populations showed a better maintenance and rapid development of viral genetic diversity following the suspected intra-host bottlenecks. CONCLUSIONS Our findings here illustrate the intra-host bottlenecks and evolutionary dynamics of SARS-CoV-2 in different anatomic sites and may provide new insights to understand the virus-host interactions of coronaviruses and other RNA viruses.
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Affiliation(s)
- Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lu Zhang
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510060, Guangdong, China
| | - Wanying Sun
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Weijun Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen, Shenzhen, 518083, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yongbo Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Fei Xiao
- Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China
| | - Jinxiu Yao
- Yangjiang People's Hospital, Yangjiang, Guangdong, China
| | - Mian Gan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Ling Luo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Xiaofang Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Sook-San Wong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Xinyi Cheng
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jingkai Ji
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Zhihua Ou
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Min Li
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Jiandong Li
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Peidi Ren
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huanzi Zhong
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Tie Song
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, Guangdong, China
| | - Chris Ka Pun Mok
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
- The HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, 19406, China
| | - Malik Peiris
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
- The HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, 19406, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
| | - Yimin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China.
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510060, Guangdong, China.
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Braun KM, Moreno GK, Halfmann PJ, Hodcroft EB, Baker DA, Boehm EC, Weiler AM, Haj AK, Hatta M, Chiba S, Maemura T, Kawaoka Y, Koelle K, O’Connor DH, Friedrich TC. Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. PLoS Pathog 2021; 17:e1009373. [PMID: 33635912 PMCID: PMC7946358 DOI: 10.1371/journal.ppat.1009373] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/10/2021] [Accepted: 02/12/2021] [Indexed: 01/08/2023] Open
Abstract
The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems.
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Affiliation(s)
- Katarina M. Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gage K. Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter J. Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Emma B. Hodcroft
- Institute of Social and Preventative Medicine, University of Bern, Bern, Switzerland
| | - David A. Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Emma C. Boehm
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Amelia K. Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Masato Hatta
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shiho Chiba
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Tadashi Maemura
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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29
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Stepanova E, Krutikova E, Wong PF, Matyushenko V, Bazhenova E, Isakova-Sivak I, Rudenko L. Safety, Immunogenicity, and Protective Efficacy of a Chimeric A/B Live Attenuated Influenza Vaccine in a Mouse Model. Microorganisms 2021; 9:microorganisms9020259. [PMID: 33513862 PMCID: PMC7910998 DOI: 10.3390/microorganisms9020259] [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: 12/07/2020] [Revised: 01/06/2021] [Accepted: 01/25/2021] [Indexed: 01/20/2023] Open
Abstract
Influenza A and B viruses cause significant morbidity and mortality worldwide. Current influenza vaccines are composed of three or four strains: A/H1N1, A/H3N2, and B (Victoria and Yamagata lineages). It is of great interest if immunization against both type A and B influenza viruses can be combined in a single vaccine strain, thus reducing the cost of vaccine production and the possibility of strain interference within the multicomponent vaccine. In the current study, we developed an experimental live cold-adapted influenza intertype reassortant (influenza A and B) vaccine on the live attenuated influenza vaccine (LAIV) A/Leningrad/134/17/57 backbone. Hemagglutinin (HA) and neuraminidase (NA) functional domains were inherited from the influenza B/Brisbane/60/2008 strain, whereas their packaging signals were substituted with appropriate fragments of influenza A virus genes. The recombinant A/B virus efficiently replicated in eggs and Madin–Darby Canine Kidney (MDCK) cells under optimal conditions, temperature-sensitive phenotype was maintained, and its antigenic properties matched the influenza B parental virus. The chimeric vaccine was attenuated in mice: after intranasal immunization, viral replication was seen only in nasal turbinates but not in the lungs. Immunological studies demonstrated the induction of IgG antibody responses against the influenza A and B virus, whereas hemagglutination inhibition (HAI) and neutralizing antibodies were detected only against the influenza B virus, resulting in significant protection of immunized animals against influenza B virus challenge. IFNγ-secreting CD8 effector memory T cells (CD44+CD62L−) were detected in mouse splenocytes after stimulation with the specific influenza A peptide (NP366); however, the T-cell response was not sufficient to protect animals against infection with a high-dose mouse-adapted A/California/07/2009 (H1N1pdm09) virus, most probably due to the mismatch of key T-cell epitopes of the H1N1 virus and the LAIV backbone. Overall, generation of the chimeric A/B LAIV virus on a licensed LAIV backbone demonstrated prospects for the development of safe and efficacious vaccine candidates that afford combined protection against both type A and type B influenza viruses; however, further optimization of the T-cell epitope content within the LAIV backbone may be required.
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30
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Braun KM, Moreno GK, Halfmann PJ, Hodcroft EB, Baker DA, Boehm EC, Weiler AM, Haj AK, Hatta M, Chiba S, Maemura T, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.11.16.384917. [PMID: 33236011 PMCID: PMC7685321 DOI: 10.1101/2020.11.16.384917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems.
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Affiliation(s)
- Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Emma B Hodcroft
- Institute of Social and Preventative Medicine, University of Bern, Bern, Switzerland
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Emma C Boehm
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Amelia K Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Masato Hatta
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Shiho Chiba
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Tadashi Maemura
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Katia Koelle
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
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31
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Schreiber SJ, Ke R, Loverdo C, Park M, Ahsan P, Lloyd-Smith JO. Cross-scale dynamics and the evolutionary emergence of infectious diseases. Virus Evol 2021; 7:veaa105. [PMID: 35186322 PMCID: PMC8087961 DOI: 10.1093/ve/veaa105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
When emerging pathogens encounter new host species for which they are poorly adapted, they must evolve to escape extinction. Pathogens experience selection on traits at multiple scales, including replication rates within host individuals and transmissibility between hosts. We analyze a stochastic model linking pathogen growth and competition within individuals to transmission between individuals. Our analysis reveals a new factor, the cross-scale reproductive number of a mutant virion, that quantifies how quickly mutant strains increase in frequency when they initially appear in the infected host population. This cross-scale reproductive number combines with viral mutation rates, single-strain reproductive numbers, and transmission bottleneck width to determine the likelihood of evolutionary emergence, and whether evolution occurs swiftly or gradually within chains of transmission. We find that wider transmission bottlenecks facilitate emergence of pathogens with short-term infections, but hinder emergence of pathogens exhibiting cross-scale selective conflict and long-term infections. Our results provide a framework to advance the integration of laboratory, clinical, and field data in the context of evolutionary theory, laying the foundation for a new generation of evidence-based risk assessment of emergence threats.
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Affiliation(s)
| | - Ruian Ke
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Claude Loverdo
- Laboratoire Jean Perrin, Sorbonne Université, CNRS, Paris 75005, France
| | - Miran Park
- Department of Ecology & Evolution, University of California, Los Angeles, CA 90095, USA
| | - Prianna Ahsan
- Department of Ecology & Evolution, University of California, Los Angeles, CA 90095, USA
| | - James O Lloyd-Smith
- Department of Ecology & Evolution, University of California, Los Angeles, CA 90095, USA
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32
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The Early Evolution of Oral Poliovirus Vaccine Is Shaped by Strong Positive Selection and Tight Transmission Bottlenecks. Cell Host Microbe 2020; 29:32-43.e4. [PMID: 33212020 PMCID: PMC7815045 DOI: 10.1016/j.chom.2020.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/12/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023]
Abstract
The emergence of circulating vaccine-derived polioviruses through evolution of the oral polio vaccine (OPV) poses a significant obstacle to polio eradication. Understanding the early genetic changes that occur as OPV evolves and transmits is important for preventing future outbreaks. Here, we use deep sequencing to define the evolutionary trajectories of type 2 OPV in a vaccine trial. By sequencing 497 longitudinal stool samples from 271 OPV2 recipients and household contacts, we were able to examine the extent of convergent evolution in vaccinated individuals and the amount of viral diversity that is transmitted. In addition to rapid reversion of key attenuating mutations, we identify strong selection at 19 sites across the genome. We find that a tight transmission bottleneck limits the onward transmission of these early adaptive mutations. Our results highlight the distinct evolutionary dynamics of live attenuated virus vaccines and have important implications for the success of next-generation OPV.
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33
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Morris DH, Petrova VN, Rossine FW, Parker E, Grenfell BT, Neher RA, Levin SA, Russell CA. Asynchrony between virus diversity and antibody selection limits influenza virus evolution. eLife 2020; 9:e62105. [PMID: 33174838 PMCID: PMC7748417 DOI: 10.7554/elife.62105] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
Seasonal influenza viruses create a persistent global disease burden by evolving to escape immunity induced by prior infections and vaccinations. New antigenic variants have a substantial selective advantage at the population level, but these variants are rarely selected within-host, even in previously immune individuals. Using a mathematical model, we show that the temporal asynchrony between within-host virus exponential growth and antibody-mediated selection could limit within-host antigenic evolution. If selection for new antigenic variants acts principally at the point of initial virus inoculation, where small virus populations encounter well-matched mucosal antibodies in previously-infected individuals, there can exist protection against reinfection that does not regularly produce observable new antigenic variants within individual infected hosts. Our results provide a theoretical explanation for how virus antigenic evolution can be highly selective at the global level but nearly neutral within-host. They also suggest new avenues for improving influenza control.
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MESH Headings
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Biological Evolution
- Genetic Variation/genetics
- Humans
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza A virus/genetics
- Influenza A virus/immunology
- Influenza, Human/immunology
- Influenza, Human/transmission
- Influenza, Human/virology
- Models, Statistical
- Selection, Genetic/genetics
- Selection, Genetic/immunology
- Virion/genetics
- Virion/immunology
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Affiliation(s)
- Dylan H Morris
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Velislava N Petrova
- Department of Human Genetics, Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Fernando W Rossine
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Edyth Parker
- Department of Veterinary Medicine, University of CambridgeCambridgeUnited Kingdom
- Department of Medical Microbiology, Academic Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Bryan T Grenfell
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
- Fogarty International Center, National Institutes of HealthBethesdaUnited States
| | | | - Simon A Levin
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Colin A Russell
- Department of Medical Microbiology, Academic Medical Center, University of AmsterdamAmsterdamNetherlands
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34
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Abstract
Seasonal influenza vaccines prevent influenza-related illnesses, hospitalizations, and deaths. However, these vaccines are not as effective as other viral vaccines, and there is clearly room for improvement. Here, we review the history of seasonal influenza vaccines, describe challenges associated with producing influenza vaccine antigens, and discuss the inherent difficulties of updating influenza vaccine strains each influenza season. We argue that seasonal influenza vaccines can be dramatically improved by modernizing antigen production processes and developing models that are better at predicting viral evolution. Resources should be specifically dedicated to improving seasonal influenza vaccines while developing entirely new vaccine platforms.
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Affiliation(s)
- Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , ,
| | - Elizabeth M Anderson
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , ,
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , ,
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35
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Plant EP, Manukyan H, Laassri M, Ye Z. Insights from the comparison of genomic variants from two influenza B viruses grown in the presence of human antibodies in cell culture. PLoS One 2020; 15:e0239015. [PMID: 32925936 PMCID: PMC7489522 DOI: 10.1371/journal.pone.0239015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022] Open
Abstract
Understanding the extent and limitation of viral genome evolution can provide insight about potential drug and vaccine targets. Influenza B Viruses (IBVs) infect humans in a seasonal manner and causes significant morbidity and mortality. IBVs are negative-sense single-stranded RNA viruses with a segmented genome and can be divided into two antigenically distinct lineages. The two lineages have been circulating and further evolving for almost four decades. The immune response to IBV infection can lead to antibodies that target the strain causing the infection. Some antibodies are cross-reactive and are able to bind strains from both lineages but, because of antigenic drift and immunodominance, both lineages continue to evolve and challenge human health. Here we investigate changes in the genomes of an IBVs from each lineage after passage in tissue culture in the presence of human sera containing polyclonal antibodies directed toward antigenically and temporally distinct viruses. Our previous analysis of the fourth segment, which encodes the major surface protein HA, revealed a pattern of change in which signature sequences from one lineage mutated to the signature sequences of the other lineage. Here we analyze genes from the other genomic segments and observe that most of the quasispecies’ heterogeneity occurs at the same loci in each lineage. The nature of the variants at these loci are investigated and possible reasons for this pattern are discussed. This work expands our understanding of the extent and limitations of genomic change in IBV.
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Affiliation(s)
- Ewan P. Plant
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Hasmik Manukyan
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Majid Laassri
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Zhiping Ye
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
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36
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Lumby CK, Zhao L, Breuer J, Illingworth CJR. A large effective population size for established within-host influenza virus infection. eLife 2020; 9:e56915. [PMID: 32773034 PMCID: PMC7431133 DOI: 10.7554/elife.56915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection Ne for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an Ne of 2.5 × 107 (95% confidence range 1.0 × 107 to 9.0 × 107) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.
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Affiliation(s)
- Casper K Lumby
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Lei Zhao
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Judith Breuer
- Great Ormond Street HospitalLondonUnited Kingdom
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Christopher JR Illingworth
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of CambridgeCambridgeUnited Kingdom
- Department of Computer Science, Institute of Biotechnology, University of HelsinkiHelsinkiFinland
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37
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Collective interactions augment influenza A virus replication in a host-dependent manner. Nat Microbiol 2020; 5:1158-1169. [PMID: 32632248 PMCID: PMC7484227 DOI: 10.1038/s41564-020-0749-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/01/2020] [Indexed: 11/08/2022]
Abstract
Infection with a single influenza A virus (IAV) is only rarely sufficient to initiate productive infection. Instead, multiple viral genomes are often required in a given cell. Here, we show that the reliance of IAV on multiple infection can form an important species barrier. Namely, we find that avian H9N2 viruses representative of those circulating widely at the poultry-human interface exhibit acute dependence on collective interactions in mammalian systems. This need for multiple infection is greatly reduced in the natural host. Quantification of incomplete viral genomes showed that their complementation accounts for the moderate reliance on multiple infection seen in avian cells but not the added reliance seen in mammalian cells. An additional form of virus-virus interaction is needed in mammals. We find that the PA gene segment is a major driver of this phenotype and that both viral replication and transcription are affected. These data indicate that multiple distinct mechanisms underlie the reliance of IAV on multiple infection and underscore the importance of virus-virus interactions in IAV infection, evolution and emergence.
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38
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Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method. J Virol 2020; 94:JVI.00014-20. [PMID: 32295920 PMCID: PMC7307158 DOI: 10.1128/jvi.00014-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/08/2020] [Indexed: 12/12/2022] Open
Abstract
Viral populations undergo a repeated cycle of within-host growth followed by transmission. Viral evolution is affected by each stage of this cycle. The number of viral particles transmitted from one host to another, known as the transmission bottleneck, is an important factor in determining how the evolutionary dynamics of the population play out, restricting the extent to which the evolved diversity of the population can be passed from one host to another. Previous study of viral sequence data has suggested that the transmission bottleneck size for influenza A transmission between human hosts is small. Reevaluating these data using a novel and improved method, we largely confirm this result, albeit that we infer a slightly higher bottleneck size in some cases, of between 1 and 13 virions. While a tight bottleneck operates in human influenza transmission, it is not extreme in nature; some diversity can be meaningfully retained between hosts. The transmission bottleneck is defined as the number of viral particles that transmit from one host to establish an infection in another. Genome sequence data have been used to evaluate the size of the transmission bottleneck between humans infected with the influenza virus; however, the methods used to make these estimates have some limitations. Specifically, viral allele frequencies, which form the basis of many calculations, may not fully capture a process which involves the transmission of entire viral genomes. Here, we set out a novel approach for inferring viral transmission bottlenecks; our method combines an algorithm for haplotype reconstruction with maximum likelihood methods for bottleneck inference. This approach allows for rapid calculation and performs well when applied to data from simulated transmission events; errors in the haplotype reconstruction step did not adversely affect inferences of the population bottleneck. Applied to data from a previous household transmission study of influenza A infection, we confirm the result that the majority of transmission events involve a small number of viruses, albeit with slightly looser bottlenecks being inferred, with between 1 and 13 particles transmitted in the majority of cases. While influenza A transmission involves a tight population bottleneck, the bottleneck is not so tight as to universally prevent the transmission of within-host viral diversity. IMPORTANCE Viral populations undergo a repeated cycle of within-host growth followed by transmission. Viral evolution is affected by each stage of this cycle. The number of viral particles transmitted from one host to another, known as the transmission bottleneck, is an important factor in determining how the evolutionary dynamics of the population play out, restricting the extent to which the evolved diversity of the population can be passed from one host to another. Previous study of viral sequence data has suggested that the transmission bottleneck size for influenza A transmission between human hosts is small. Reevaluating these data using a novel and improved method, we largely confirm this result, albeit that we infer a slightly higher bottleneck size in some cases, of between 1 and 13 virions. While a tight bottleneck operates in human influenza transmission, it is not extreme in nature; some diversity can be meaningfully retained between hosts.
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39
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Abstract
The evolutionary dynamics of a virus can differ within hosts and across populations. Studies of within-host evolution provide an important link between experimental studies of virus evolution and large-scale phylodynamic analyses. They can determine the extent to which global processes are recapitulated on local scales and how accurately experimental infections model natural ones. They may also inform epidemiologic models of disease spread and reveal how host-level dynamics contribute to a virus's evolution at a larger scale. Over the last decade, advances in viral sequencing have enabled detailed studies of viral genetic diversity within hosts. I review how within-host diversity is sampled, measured, and expressed, and how comparative studies of viral diversity can be leveraged to elucidate a virus's evolutionary dynamics. These concepts are illustrated with detailed reviews of recent research on the within-host evolution of influenza virus, dengue virus, and cytomegalovirus.
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Affiliation(s)
- Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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Plant EP, Manukyan H, Sanchez JL, Laassri M, Ye Z. Immune Pressure on Polymorphous Influenza B Populations Results in Diverse Hemagglutinin Escape Mutants and Lineage Switching. Vaccines (Basel) 2020; 8:vaccines8010125. [PMID: 32168968 PMCID: PMC7157493 DOI: 10.3390/vaccines8010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/27/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Mutations arise in the genomes of progeny viruses during infection. Mutations that occur in epitopes targeted by host antibodies allow the progeny virus to escape the host adaptive, B-cell mediated antibody immune response. Major epitopes have been identified in influenza B virus (IBV) hemagglutinin (HA) protein. However, IBV strains maintain a seasonal presence in the human population and changes in IBV genomes in response to immune pressure are not well characterized. There are two lineages of IBV that have circulated in the human population since the 1980s, B-Victoria and B-Yamagata. It is hypothesized that early exposure to one influenza subtype leads to immunodominance. Subsequent seasonal vaccination or exposure to new subtypes may modify subsequent immune responses, which, in turn, results in selection of escape mutations in the viral genome. Here we show that while some mutations do occur in known epitopes suggesting antibody escape, many mutations occur in other parts of the HA protein. Analysis of mutations outside of the known epitopes revealed that these mutations occurred at the same amino acid position in viruses from each of the two IBV lineages. Interestingly, where the amino acid sequence differed between viruses from each lineage, reciprocal amino acid changes were observed. That is, the virus from the Yamagata lineage become more like the Victoria lineage virus and vice versa. Our results suggest that some IBV HA sequences are constrained to specific amino acid codons when viruses are cultured in the presence of antibodies. Some changes to the known antigenic regions may also be restricted in a lineage-dependent manner. Questions remain regarding the mechanisms underlying these results. The presence of amino acid residues that are constrained within the HA may provide a new target for universal vaccines for IBV.
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Affiliation(s)
- Ewan P. Plant
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
- Correspondence: ; Tel.: +1-240-402-7319
| | - Hasmik Manukyan
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
| | - Jose L. Sanchez
- Armed Forces Health Surveillance Branch, Public Health Division, Assistant Director for Combat Support (AD-CS), Defense Health Agency, Silver Spring, MD 20904, USA;
| | - Majid Laassri
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
| | - Zhiping Ye
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
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Valesano AL, Fitzsimmons WJ, McCrone JT, Petrie JG, Monto AS, Martin ET, Lauring AS. Influenza B Viruses Exhibit Lower Within-Host Diversity than Influenza A Viruses in Human Hosts. J Virol 2020; 94:e01710-19. [PMID: 31801858 PMCID: PMC7022338 DOI: 10.1128/jvi.01710-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022] Open
Abstract
Influenza B virus (IBV) undergoes seasonal antigenic drift more slowly than influenza A virus, but the reasons for this difference are unclear. While the evolutionary dynamics of influenza viruses play out globally, they are fundamentally driven by mutation, reassortment, drift, and selection at the level of individual hosts. These processes have recently been described for influenza A virus, but little is known about the evolutionary dynamics of IBV during individual infections and transmission events. Here, we define the within-host evolutionary dynamics of IBV by sequencing virus populations from naturally infected individuals enrolled in a prospective, community-based cohort over 8,176 person-seasons of observation. Through analysis of high depth-of-coverage sequencing data from samples from 91 individuals with influenza B, we find that IBV accumulates lower genetic diversity than previously observed for influenza A virus during acute infections. Consistent with studies of influenza A viruses, the within-host evolution of IBVs is characterized by purifying selection and the general absence of widespread positive selection of within-host variants. Analysis of shared genetic diversity across 15 sequence-validated transmission pairs suggests that IBV experiences a tight transmission bottleneck similar to that of influenza A virus. These patterns of local-scale evolution are consistent with the lower global evolutionary rate of IBV.IMPORTANCE The evolution of influenza virus is a significant public health problem and necessitates the annual evaluation of influenza vaccine formulation to keep pace with viral escape from herd immunity. Influenza B virus is a serious health concern for children, in particular, yet remains understudied compared to influenza A virus. Influenza B virus evolves more slowly than influenza A virus, but the factors underlying this are not completely understood. We studied how the within-host diversity of influenza B virus relates to its global evolution by sequencing viruses from a community-based cohort. We found that influenza B virus populations have lower within-host genetic diversity than influenza A virus and experience a tight genetic bottleneck during transmission. Our work provides insights into the varying dynamics of influenza viruses in human infection.
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Affiliation(s)
- Andrew L Valesano
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, USA
| | - William J Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joshua G Petrie
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Arnold S Monto
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily T Martin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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