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Mahesh DN, Sreelatha B, Vinoth S, Nancy S. Clinical profile of children with influenza like illness during pre-monsoon at coastal Karaikal, Puducherry, India. Bioinformation 2024; 20:252-257. [PMID: 38712005 PMCID: PMC11069598 DOI: 10.6026/973206300200252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/31/2024] [Accepted: 03/31/2024] [Indexed: 05/08/2024] Open
Abstract
Influenza infections in developing countries are under reported and WHO estimates that nearly 99% of influenza deaths worldwide occur in children under-five years of age in Asian and African countries. Consequently, this study aims to analyze the use of clinical profile and easily available laboratory parameters to aid identification of the possible viral etiology in the setting of pre-monsoon ILI. A cross-sectional study was carried out for three months among children with ILI attending fever clinic of a tertiary care hospital in Karaikal, South India. In the study population the prevalence of ILI was highest in the age group four to five years followed by school aged children. Adolescents were affected the least. Influenza B was most common virus causing ILI in this region, followed by covid-19 infection. Laboratory parameters depicted a significantly high ESR in COVID-19 infected ILI children. They also exhibited leucopenia and normal platelet counts. Clinical symptoms and laboratory parameters which are easily available and cheaper can be used in resource poor settings of healthcare to identify possible influenza and COVID-19 infected children amongst cases presenting with ILI.
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Affiliation(s)
- Dande Naga Mahesh
- Department of Paediatrics, Vinayaka Mission's Medical College and Hospital, Vinayaka Mission's Research Foundation - Deemed to be University (VMRF-DU), Karaikal, Puducherry, India
| | - B Sreelatha
- Department of Paediatrics, Vinayaka Mission's Medical College and Hospital, Vinayaka Mission's Research Foundation - Deemed to be University (VMRF-DU), Karaikal, Puducherry, India
| | - S Vinoth
- Department of Paediatrics, Vinayaka Mission's Medical College and Hospital, Vinayaka Mission's Research Foundation - Deemed to be University (VMRF-DU), Karaikal, Puducherry, India
| | - S Nancy
- Department of Community Medicine, Vinayaka Mission's Medical College and Hospital, Vinayaka Mission's Research Foundation - Deemed to be University (VMRF-DU), Karaikal, Puducherry, India
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2
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Dey S, Mondal A. Unveiling the role of host kinases at different steps of influenza A virus life cycle. J Virol 2024; 98:e0119223. [PMID: 38174932 PMCID: PMC10805039 DOI: 10.1128/jvi.01192-23] [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] [Indexed: 01/05/2024] Open
Abstract
Influenza viruses remain a major public health concern causing contagious respiratory illnesses that result in around 290,000-650,000 global deaths every year. Their ability to constantly evolve through antigenic shifts and drifts leads to the emergence of newer strains and resistance to existing drugs and vaccines. To combat this, there is a critical need for novel antiviral drugs through the introduction of host-targeted therapeutics. Influenza viruses encode only 14 gene products that get extensively modified through phosphorylation by a diverse array of host kinases. Reversible phosphorylation at serine, threonine, or tyrosine residues dynamically regulates the structure, function, and subcellular localization of viral proteins at different stages of their life cycle. In addition, kinases influence a plethora of signaling pathways that also regulate virus propagation by modulating the host cell environment thus establishing a critical virus-host relationship that is indispensable for executing successful infection. This dependence on host kinases opens up exciting possibilities for developing kinase inhibitors as next-generation anti-influenza therapy. To fully capitalize on this potential, extensive mapping of the influenza virus-host kinase interaction network is essential. The key focus of this review is to outline the molecular mechanisms by which host kinases regulate different steps of the influenza A virus life cycle, starting from attachment-entry to assembly-budding. By assessing the contributions of different host kinases and their specific phosphorylation events during the virus life cycle, we aim to develop a holistic overview of the virus-host kinase interaction network that may shed light on potential targets for novel antiviral interventions.
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Affiliation(s)
- Soumik Dey
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Arindam Mondal
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
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3
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Forghani M, Firstkov AL, Alyannezhadi MM, Danilenko DM, Komissarov AB. Reduced amino acid alphabet-based encoding and its impact on modeling influenza antigenic evolution. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2022. [DOI: 10.15789/2220-7619-raa-1968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Currently, vaccination is one of the most efficient ways to control and prevent influenza infection. Vaccine production largely relies on the results of laboratory assays, including hemagglutination inhibition and microneutralization assays, which are time-consuming and laborious. Viruses can escape from the immune response that results in the need to revise and update vaccines biannually. The hemagglutination inhibition assay can measure how effectively antibodies against a reference strain bind and block an antigen of the test strain. Various computer-aided models have been developed to optimize candidate vaccine strain selection. A general problem in modeling of antigenic evolution is the representation of genetic sequences for input into the research model. Our motivation stems from the well-known problem of encoding genetic information for modeling antigenic evolution. This paper introduces a two-fold encoding approach based on reduced amino acid alphabet and amino acid index databases called AAindex. We propose to apply a simplified amino acid alphabet in modeling of antigenic evolution. A simplified alphabet, also called a sub-alphabet or reduced amino acid alphabet, implies to use the 20 amino acids being clustered and divided into amino acid groups. The proposed encoding allows to redefine mutations termed for amino acid groups located in reduced alphabets. We investigated 40 reduced amino acid sets and their performance in modeling antigenic evolution. The experimental results indicate that the proposed reduced amino acid alphabets can achieve the performance of the standard alphabet in its accuracy. Moreover, these alphabets provide deeper insight into various aspects of the relationship between mutation and antigenic variation. By checking identified high-impact sites in the Influenza Research Database, we found that not only antigenic sites have a significant influence on antigenicity, but also other amino acids located in close proximity. The results indicate that all selected non-antigenic sites are related to immune responses. According to the Influenza Research Database, these have been experimentally determined to be T-cell epitopes, B-cell epitopes, and MHC-binding epitopes of different classes. This highlighted a caveat: while simulating antigenic evolution, the model should consider not only the genetic information on antigenic sites, but also that of neighboring positions, as they may indirectly impact antigenicity. Additionally, our findings indicate that structural and charge characteristics are the most beneficial in modeling antigenic evolution, which is in agreement with previous studies.
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4
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Makau DN, Lycett S, Michalska-Smith M, Paploski IAD, Cheeran MCJ, Craft ME, Kao RR, Schroeder DC, Doeschl-Wilson A, VanderWaal K. Ecological and evolutionary dynamics of multi-strain RNA viruses. Nat Ecol Evol 2022; 6:1414-1422. [PMID: 36138206 DOI: 10.1038/s41559-022-01860-6] [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: 12/21/2021] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
Potential interactions among co-circulating viral strains in host populations are often overlooked in the study of virus transmission. However, these interactions probably shape transmission dynamics by influencing host immune responses or altering the relative fitness among co-circulating strains. In this Review, we describe multi-strain dynamics from ecological and evolutionary perspectives, outline scales in which multi-strain dynamics occur and summarize important immunological, phylogenetic and mathematical modelling approaches used to quantify interactions among strains. We also discuss how host-pathogen interactions influence the co-circulation of pathogens. Finally, we highlight outstanding questions and knowledge gaps in the current theory and study of ecological and evolutionary dynamics of multi-strain viruses.
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Affiliation(s)
- Dennis N Makau
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | | | | | - Igor A D Paploski
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Maxim C-J Cheeran
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Meggan E Craft
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
| | - Rowland R Kao
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
- School of Biological Sciences, University of Reading, Reading, UK
| | | | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA.
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5
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Chauhan NK, Shadrach BJ, Dutt N, Jalandra RN, Deokar K, Garg MK, Nag VL, Bhardwaj P, Jain V, Misra S. Safe Practice of Flexible Bronchoscopy for Non-COVID-19 Indications during the SARS-CoV-2 Pandemic. TANAFFOS 2022; 21:207-213. [PMID: 36879727 PMCID: PMC9985126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/17/2021] [Indexed: 06/18/2023]
Abstract
BACKGROUND Flexible bronchoscopy is an aerosol-generating procedure (AGP), which increases the risk of transmission of SARS-CoV-2 infection. We aimed to find COVID-19 symptoms among healthcare workers (HCWs) involved in flexible bronchoscopies for non-COVID-19 indications during the SARS-CoV-2 pandemic. MATERIALS AND METHODS The participants of this hospital-based single-center descriptive study were HCWs of our hospital involved in flexible bronchoscopies of patients with non-COVID-19 indications. These patients had no clinical features of COVID-19 and were tested negative for SARS-CoV-2 by the real-time polymerase chain reaction of nasopharyngeal and throat swabs before the procedure. The study outcome was the occurrence of COVID-19 in study participants after exposure to bronchoscopies. RESULTS Thirteen HCWs performed 81 bronchoscopies on 62 patients. Indications for bronchoscopies included malignancy (61.30%), suspected infections (19.35%), non-resolving pneumonia (6.45%), mucus plug removal (6.45%), central airway obstruction (4.84%), and hemoptysis (1.61%). The mean age of patients was 50.44 ± 15.00 years, and the majority was males (72.58%). Bronchoscopic procedures included 51 bronchoalveolar lavages, 32 endobronchial ultrasound- transbronchial needle aspiration (EBUS-TBNA), 26 endobronchial biopsies, 10 transbronchial lung biopsy (TBLB), 3 mucus plug removals, 2 conventional TBNA, and 2 radial EBUS-TBLB. Except for two HCWs who complained of transient throat irritation of non-infectious cause, none of the cases developed any clinical features suggestive of COVID-19. CONCLUSION A dedicated bronchoscopy protocol helps in minimizing the risk of transmission of SARS-CoV-2 infection among HCWs involved in flexible bronchoscopies for non-COVID-19 indications during the SARS-CoV-2 pandemic.
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Affiliation(s)
- Nishant Kumar Chauhan
- Department of Pulmonary Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
| | - Benhur Joel Shadrach
- Department of Pulmonary Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
| | - Naveen Dutt
- Department of Pulmonary Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
| | - Ram Niwas Jalandra
- Department of Pulmonary Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
| | - Kunal Deokar
- Department of Pulmonary Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
| | - Mahendra Kumar Garg
- Department of General Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
| | - Vijaya Lakshmi Nag
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
| | - Pankaj Bhardwaj
- Department of Community Medicine and Family Medicine, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
| | - Vidhi Jain
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
| | - Sanjeev Misra
- Department of Surgical Oncology, All India Institute of Medical Sciences (AIIMS), Jodhpur, India
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6
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Oidtman RJ, Arevalo P, Bi Q, McGough L, Russo CJ, Vera Cruz D, Costa Vieira M, Gostic KM. Influenza immune escape under heterogeneous host immune histories. Trends Microbiol 2021; 29:1072-1082. [PMID: 34218981 PMCID: PMC8578193 DOI: 10.1016/j.tim.2021.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 11/30/2022]
Abstract
In a pattern called immune imprinting, individuals gain the strongest immune protection against the influenza strains encountered earliest in life. In many recent examples, differences in early infection history can explain birth year-associated differences in susceptibility (cohort effects). Susceptibility shapes strain fitness, but without a clear conceptual model linking host susceptibility to the identity and order of past infections general conclusions on the evolutionary and epidemic implications of cohort effects are not possible. Failure to differentiate between cohort effects caused by differences in the set, rather than the order (path), of past infections is a current source of confusion. We review and refine hypotheses for path-dependent cohort effects, which include imprinting. We highlight strategies to measure their underlying causes and emergent consequences.
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Affiliation(s)
- Rachel J Oidtman
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Philip Arevalo
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Qifang Bi
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Diana Vera Cruz
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Marcos Costa Vieira
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Katelyn M Gostic
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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7
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An Antigenic Thrift-Based Approach to Influenza Vaccine Design. Vaccines (Basel) 2021; 9:vaccines9060657. [PMID: 34208489 PMCID: PMC8235769 DOI: 10.3390/vaccines9060657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 11/19/2022] Open
Abstract
The antigenic drift theory states that influenza evolves via the gradual accumulation of mutations, decreasing a host’s immune protection against previous strains. Influenza vaccines are designed accordingly, under the premise of antigenic drift. However, a paradox exists at the centre of influenza research. If influenza evolved primarily through mutation in multiple epitopes, multiple influenza strains should co-circulate. Such a multitude of strains would render influenza vaccines quickly inefficacious. Instead, a single or limited number of strains dominate circulation each influenza season. Unless additional constraints are placed on the evolution of influenza, antigenic drift does not adequately explain these observations. Here, we explore the constraints placed on antigenic drift and a competing theory of influenza evolution – antigenic thrift. In contrast to antigenic drift, antigenic thrift states that immune selection targets epitopes of limited variability, which constrain the variability of the virus. We explain the implications of antigenic drift and antigenic thrift and explore their current and potential uses in the context of influenza vaccine design.
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8
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Khorramdelazad H, Kazemi MH, Najafi A, Keykhaee M, Zolfaghari Emameh R, Falak R. Immunopathological similarities between COVID-19 and influenza: Investigating the consequences of Co-infection. Microb Pathog 2021; 152:104554. [PMID: 33157216 PMCID: PMC7607235 DOI: 10.1016/j.micpath.2020.104554] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a global public health emergency since December 2019, and so far, more than 980,000 people (until September 24, 2020) around the world have died. SARS-CoV-2 mimics the influenza virus regarding methods and modes of transmission, clinical features, related immune responses, and seasonal coincidence. Accordingly, co-infection by these viruses is imaginable because some studies have reported several cases with SARS-CoV-2 and influenza virus co-infection. Given the importance of the mentioned co-infection and the coming influenza season, it is essential to recognize the similarities and differences between the symptoms, immunopathogenesis and treatment of SARS-CoV-2 and influenza virus. Therefore, we reviewed the virology, clinical features, and immunopathogenesis of both influenza virus and SARS-CoV-2 and evaluated outcomes in cases with SARS-CoV-2 and influenza virus co-infection.
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Affiliation(s)
- Hossein Khorramdelazad
- Department of Immunology, School of Medicine, Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Kazemi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Najafi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Keykhaee
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran
| | - Reza Falak
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
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9
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Mtambo SE, Amoako DG, Somboro AM, Agoni C, Lawal MM, Gumede NS, Khan RB, Kumalo HM. Influenza Viruses: Harnessing the Crucial Role of the M2 Ion-Channel and Neuraminidase toward Inhibitor Design. Molecules 2021; 26:880. [PMID: 33562349 PMCID: PMC7916051 DOI: 10.3390/molecules26040880] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/01/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022] Open
Abstract
As a member of the Orthomyxoviridae family of viruses, influenza viruses (IVs) are known causative agents of respiratory infection in vertebrates. They remain a major global threat responsible for the most virulent diseases and global pandemics in humans. The virulence of IVs and the consequential high morbidity and mortality of IV infections are primarily attributed to the high mutation rates in the IVs' genome coupled with the numerous genomic segments, which give rise to antiviral resistant and vaccine evading strains. Current therapeutic options include vaccines and small molecule inhibitors, which therapeutically target various catalytic processes in IVs. However, the periodic emergence of new IV strains necessitates the continuous development of novel anti-influenza therapeutic options. The crux of this review highlights the recent studies on the biology of influenza viruses, focusing on the structure, function, and mechanism of action of the M2 channel and neuraminidase as therapeutic targets. We further provide an update on the development of new M2 channel and neuraminidase inhibitors as an alternative to existing anti-influenza therapy. We conclude by highlighting therapeutic strategies that could be explored further towards the design of novel anti-influenza inhibitors with the ability to inhibit resistant strains.
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Affiliation(s)
- Sphamadla E. Mtambo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (S.E.M.); (A.M.S.); (C.A.); (M.M.L.); (N.S.G.); (R.B.K.)
| | - Daniel G. Amoako
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (S.E.M.); (A.M.S.); (C.A.); (M.M.L.); (N.S.G.); (R.B.K.)
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Anou M. Somboro
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (S.E.M.); (A.M.S.); (C.A.); (M.M.L.); (N.S.G.); (R.B.K.)
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Clement Agoni
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (S.E.M.); (A.M.S.); (C.A.); (M.M.L.); (N.S.G.); (R.B.K.)
| | - Monsurat M. Lawal
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (S.E.M.); (A.M.S.); (C.A.); (M.M.L.); (N.S.G.); (R.B.K.)
| | - Nelisiwe S. Gumede
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (S.E.M.); (A.M.S.); (C.A.); (M.M.L.); (N.S.G.); (R.B.K.)
| | - Rene B. Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (S.E.M.); (A.M.S.); (C.A.); (M.M.L.); (N.S.G.); (R.B.K.)
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (S.E.M.); (A.M.S.); (C.A.); (M.M.L.); (N.S.G.); (R.B.K.)
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10
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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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11
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Abstract
Influenza continues to baffle humans by its constantly changing nature. The twenty-first century has witnessed considerable advances in the understanding of the influenza viral pathogenesis, its synergy with bacterial infections and diagnostic methods. However, challenges continue: to find a less expensive and more reliable point-of-care test for use in developing countries, to produce more efficacious antiviral drugs, to explore ways to combat emerging antiviral resistance and to develop vaccines that can either be produced in a shorter production time or can overcome the need for annual matching with the circulating influenza strains. Most importantly for India, as a nation that suffered the highest mortality in the influenza pandemic 1918, there is an urgent need to gear up our existing preparedness for the next pandemic which is capable to hit at any moment in time.
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12
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Panahi MH, Parsaeian M, Mansournia MA, Khoshabi M, Gouya MM, Hemati P, Fotouhi A. A spatio-temporal analysis of influenza-like illness in Iran from 2011 to 2016. Med J Islam Repub Iran 2020; 34:65. [PMID: 32974231 PMCID: PMC7500421 DOI: 10.34171/mjiri.34.65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Indexed: 11/05/2022] Open
Abstract
Background: Investigating the spatial aspects of the disease can help decision-makers and researchers better understand the pattern of the disease, and is also very important in the implementation of the disease control programs. Given the vast area of Iran, as well as the diverse geographical and climate conditions of the country, using the geographical information system (GIS) is a suitable method for the study of influenza. In this study, we provide a clear picture of the distribution of the influenza-like illness (ILI) in Iranian provinces through the years from 2011 to 2016 by applying a spatio-temporal analysis, using geographic information system (GIS). Disease rates by location and year are estimated, and then hot spots and cold spots are distinguished. Methods: This study was conducted using the ILI incidence rate data recorded in the Iranian Influenza Surveillance System from August 2011 to August 2016. The Choropleth map method and the various equal interval and natural break classifications were used. The local Getis-Ord Gi* method was then used to identify the hot spots and regions where, for some reason, the distribution of the disease had significantly clustered spatially. Statistical analyses were done using the ArcGIS 10.2 software. Results: This study indicates that the highest ILI rate belongs to the period from August 2014 to August 2015 with a rate of 180.26 (95%CI: 177.65 to 182.9) per 100,000 people. The results show that the highest 5-year mean of ILI rate belongs to Zanjan, Markazi, Lorestan, Ilam, North Khorasan, and South Khorasan provinces. Also, results from the local Getis-Ord Gi* method show that ILI has formed a hot spot between the years 2011 and 2013 on the eastern borders of Iran and afterward during the years 2014 to 2016 in the western regions of the country. Conclusion: Given the importance of influenza and its huge economic burden on the society, identifying the hot spot regions can help better manage the disease. This study indicates the distribution of the disease has formed a hot spot in the western regions of the country.
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Affiliation(s)
- Mohammad Hossein Panahi
- 1Epidemiology and Biostatistics Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahboubeh Parsaeian
- 1Epidemiology and Biostatistics Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Mansournia
- 1Epidemiology and Biostatistics Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Khoshabi
- 2Department of Geo-Spatial Information System (GIS), Center of Excellence in GIS, K.N. Toosi University of Technology, Tehran, Iran
| | - Mohammad Mehdi Gouya
- 3Center for Communicable Disease Control, Ministry of Health & Medical Education, Tehran, Iran,4Iran University of Medical Sciences, Tehran, Iran
| | - Payman Hemati
- 3Center for Communicable Disease Control, Ministry of Health & Medical Education, Tehran, Iran
| | - Akbar Fotouhi
- 1Epidemiology and Biostatistics Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran,Corresponding author: Dr Akbar Fotouhi,
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13
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Pease (1987): The evolutionary epidemiology of influenza A. Theor Popul Biol 2020; 133:29-32. [DOI: 10.1016/j.tpb.2019.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/26/2022]
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14
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Kissler SM, Tedijanto C, Goldstein E, Grad YH, Lipsitch M. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science 2020; 368:860-868. [PMID: 32291278 PMCID: PMC7164482 DOI: 10.1126/science.abb5793] [Citation(s) in RCA: 1517] [Impact Index Per Article: 379.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022]
Abstract
It is urgent to understand the future of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) transmission. We used estimates of seasonality, immunity, and cross-immunity for human coronavirus OC43 (HCoV-OC43) and HCoV-HKU1 using time-series data from the United States to inform a model of SARS-CoV-2 transmission. We projected that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after the initial, most severe pandemic wave. Absent other interventions, a key metric for the success of social distancing is whether critical care capacities are exceeded. To avoid this, prolonged or intermittent social distancing may be necessary into 2022. Additional interventions, including expanded critical care capacity and an effective therapeutic, would improve the success of intermittent distancing and hasten the acquisition of herd immunity. Longitudinal serological studies are urgently needed to determine the extent and duration of immunity to SARS-CoV-2. Even in the event of apparent elimination, SARS-CoV-2 surveillance should be maintained because a resurgence in contagion could be possible as late as 2024.
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Affiliation(s)
- Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christine Tedijanto
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward Goldstein
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Marc Lipsitch
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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15
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Kissler SM, Tedijanto C, Goldstein E, Grad YH, Lipsitch M. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science 2020; 368:860-868. [PMID: 32291278 DOI: 10.1101/2020.03.04.20031112] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/09/2020] [Indexed: 05/20/2023]
Abstract
It is urgent to understand the future of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) transmission. We used estimates of seasonality, immunity, and cross-immunity for human coronavirus OC43 (HCoV-OC43) and HCoV-HKU1 using time-series data from the United States to inform a model of SARS-CoV-2 transmission. We projected that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after the initial, most severe pandemic wave. Absent other interventions, a key metric for the success of social distancing is whether critical care capacities are exceeded. To avoid this, prolonged or intermittent social distancing may be necessary into 2022. Additional interventions, including expanded critical care capacity and an effective therapeutic, would improve the success of intermittent distancing and hasten the acquisition of herd immunity. Longitudinal serological studies are urgently needed to determine the extent and duration of immunity to SARS-CoV-2. Even in the event of apparent elimination, SARS-CoV-2 surveillance should be maintained because a resurgence in contagion could be possible as late as 2024.
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Affiliation(s)
- Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christine Tedijanto
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward Goldstein
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Marc Lipsitch
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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16
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Kissler SM, Tedijanto C, Goldstein E, Grad YH, Lipsitch M. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science 2020. [PMID: 32291278 DOI: 10.1126/science.abb5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
It is urgent to understand the future of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) transmission. We used estimates of seasonality, immunity, and cross-immunity for human coronavirus OC43 (HCoV-OC43) and HCoV-HKU1 using time-series data from the United States to inform a model of SARS-CoV-2 transmission. We projected that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after the initial, most severe pandemic wave. Absent other interventions, a key metric for the success of social distancing is whether critical care capacities are exceeded. To avoid this, prolonged or intermittent social distancing may be necessary into 2022. Additional interventions, including expanded critical care capacity and an effective therapeutic, would improve the success of intermittent distancing and hasten the acquisition of herd immunity. Longitudinal serological studies are urgently needed to determine the extent and duration of immunity to SARS-CoV-2. Even in the event of apparent elimination, SARS-CoV-2 surveillance should be maintained because a resurgence in contagion could be possible as late as 2024.
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Affiliation(s)
- Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christine Tedijanto
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward Goldstein
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Marc Lipsitch
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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17
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Kissler SM, Tedijanto C, Goldstein E, Grad YH, Lipsitch M. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science 2020. [PMID: 32291278 DOI: 10.1126/science:abb5793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
It is urgent to understand the future of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) transmission. We used estimates of seasonality, immunity, and cross-immunity for human coronavirus OC43 (HCoV-OC43) and HCoV-HKU1 using time-series data from the United States to inform a model of SARS-CoV-2 transmission. We projected that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after the initial, most severe pandemic wave. Absent other interventions, a key metric for the success of social distancing is whether critical care capacities are exceeded. To avoid this, prolonged or intermittent social distancing may be necessary into 2022. Additional interventions, including expanded critical care capacity and an effective therapeutic, would improve the success of intermittent distancing and hasten the acquisition of herd immunity. Longitudinal serological studies are urgently needed to determine the extent and duration of immunity to SARS-CoV-2. Even in the event of apparent elimination, SARS-CoV-2 surveillance should be maintained because a resurgence in contagion could be possible as late as 2024.
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Affiliation(s)
- Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christine Tedijanto
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward Goldstein
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Marc Lipsitch
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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18
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Xia Y, Mi F, Du G, Qin S. Analysis of protective immune responses to seasonal influenza vaccination in HIV-infected individuals. Hum Vaccin Immunother 2020; 17:124-132. [PMID: 32412824 DOI: 10.1080/21645515.2020.1754701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Owing to their increased susceptibility to influenza infection, HIV+ individuals are recommended to receive annual influenza vaccination. However, influenza vaccination induced production of anti-influenza neutralization antibodies (Nab) is successful only in some viral-suppressed antiretroviral therapy (ART) treated HIV+ subjects. Additionally, the mechanism of antibody response induced by influenza vaccine in antiretroviral-treated HIV+ subjects is unclear. In this study, we conducted a cohort study which contains 40 HIV+ ART-treated individuals to whom one dose of seasonal influenza vaccine was administered. Blood samples were collected on day 0, 7, 14, and 28 post-vaccination, and serologic responses were characterized by ELISA and micro-neutralization to measure the total antibodies and Nab against influenza vaccines. Transcriptional profiling of peripheral blood mononuclear cells (PBMCs) and immunological assays was measured. Increased levels of proliferation of CD4+T cells and B cells with their corresponding subtypes were observed in HIV-infected subjects at day 7 (D7) following vaccination compared to pre-vaccination. Moreover, proliferation of CD4+T cells and B cells (D7) was correlated with influenza-specific H1N1 Nab at day 28 (D28). Our study could also demonstrate that apoptosis of CD4+T cells and B cells (D7) were inversely correlated with influenza-specific H1N1 Nab. Based on the Nab response after vaccination to each influenza subtypes (D28), HIV+ subjects were stratified as influenza vaccine responders and influenza vaccine non-responders ("responders" ≥ 4-fold increase from day 0; "non-responders" < 4-fold increase from day 0). A selected list of biological pathways (H1N1and H3N2: olfactory transduction, B: phagosome) enriched with transcripts were significantly altered in (ART) treated HIV+ subjects among Nab production responders. This study demonstrated a more detailed mechanism of immune regulation on influenza induced antibody response and revealed some knowledge regarding bioinformatics of vaccine responders and non-responder in influenza induced antibody production in ART-treated HIV patients.
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Affiliation(s)
- Ying Xia
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
| | - Fuli Mi
- Shandong Provincial Qianfoshan Hospital, The First Hospital Affiliated with Shandong First Medical University , Shandong, China
| | - Guoqiang Du
- Pediatric Surgery, Shandong Provincial Hospital, Shandong, China
| | - Shenghui Qin
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, China
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19
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Daoud M. Detecting outliers in segmented genomes of flu virus using an alignment-free approach. Genomics Inform 2020; 18:e2. [PMID: 32224835 PMCID: PMC7120353 DOI: 10.5808/gi.2020.18.1.e2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/21/2019] [Indexed: 11/29/2022] Open
Abstract
In this paper, we propose a new approach to detecting outliers in a set of segmented genomes of the flu virus, a data set with a heterogeneous set of sequences. The approach has the following computational phases: feature extraction, which is a mapping into feature space, alignment-free distance measure to measure the distance between any two segmented genomes, and a mapping into distance space to analyze a quantum of distance values. The approach is implemented using supervised and unsupervised learning modes. The experiments show robustness in detecting outliers of the segmented genome of the flu virus.
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Affiliation(s)
- Mosaab Daoud
- Independent Research Scientist, Toronto, ON M1S1G2, Canada
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20
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Recombinant GII.P16/GII.4 Sydney 2012 Was the Dominant Norovirus Identified in Australia and New Zealand in 2017. Viruses 2018; 10:v10100548. [PMID: 30304780 PMCID: PMC6213408 DOI: 10.3390/v10100548] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/05/2018] [Accepted: 10/06/2018] [Indexed: 01/16/2023] Open
Abstract
For the past two decades, norovirus pandemic variants have emerged every 3–5 years, and dominate until they are replaced by alternate strains. However, this scenario changed in 2016 with the co-circulation of six prevalent viruses, three of which possessed the pandemic GII.4 Sydney 2012 capsid. An increased number of institutional gastroenteritis outbreaks were reported within the Oceania region in mid-2017. This study identified emerging noroviruses circulating in Australia and New Zealand in 2017 to assess the changing dynamics of the virus infection. RT-PCR-based methods, next generation sequencing, and phylogenetic analyses were used to genotype noroviruses from both clinical and wastewater samples. Antigenic changes were observed between the capsid of pandemic Sydney 2012 variant and the two new Sydney recombinant viruses. The combination of these antigenic changes and the acquisition of a new ORF1 through recombination could both facilitate their ongoing persistence in the population. Overall, an increased prevalence of GII.P16/GII.4 Sydney 2012 viruses was observed in 2017, replacing the GII.P16/GII.2 recombinant that dominated in the region at the end of 2016. This shift in strain dominance was also observed in wastewater samples, demonstrating the reliability of wastewater as a molecular surveillance tool.
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21
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Moore J, Ahmed H, Antia R. High dimensional random walks can appear low dimensional: Application to influenza H3N2 evolution. J Theor Biol 2018; 447:56-64. [PMID: 29571708 DOI: 10.1016/j.jtbi.2018.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 02/26/2018] [Accepted: 03/15/2018] [Indexed: 11/19/2022]
Abstract
One important feature of the mammalian immune system is the highly specific binding of antigens to antibodies. Antibodies generated in response to one infection may also provide some level of cross immunity to other infections. One model to describe this cross immunity is the notion of antigenic space, which assigns each antibody and each virus a point in Rn. Past studies using hemagglutination data have suggested the dimensionality of antigenic space, n, is low. We propose that influenza evolution may be modeled as a Gaussian random walk. We then show that hemagluttination data would be consistent with a walk in very high dimensions. The discrepancy between our result and prior studies is due to the fact that random walks can appear low dimensional according to a variety of analyses including principal component analysis (PCA) and multidimensional scaling (MDS). A high dimensionality of antigenic space is of importance to modelers, as it suggests a smaller role for pre-existing immunity within the host population.
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Affiliation(s)
- James Moore
- Department of Biology, Emory University, Atlanta, GA, USA.
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
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22
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Morris DH, Gostic KM, Pompei S, Bedford T, Łuksza M, Neher RA, Grenfell BT, Lässig M, McCauley JW. Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology. Trends Microbiol 2018; 26:102-118. [PMID: 29097090 PMCID: PMC5830126 DOI: 10.1016/j.tim.2017.09.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/06/2017] [Accepted: 09/19/2017] [Indexed: 01/16/2023]
Abstract
Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza virus antigens means that vaccines must be updated to match novel strains, and vaccine effectiveness depends on the ability of scientists to predict nearly a year in advance which influenza variants will dominate in upcoming seasons. In this review, we highlight a promising new surveillance tool: predictive models. Based on data-sharing and close collaboration between the World Health Organization and academic scientists, these models use surveillance data to make quantitative predictions regarding influenza evolution. Predictive models demonstrate the potential of applied evolutionary biology to improve public health and disease control. We review the state of influenza predictive modeling and discuss next steps and recommendations to ensure that these models deliver upon their considerable biomedical promise.
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Affiliation(s)
- Dylan H Morris
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Katelyn M Gostic
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Simone Pompei
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marta Łuksza
- Institute for Advanced Study, Princeton, NJ, USA
| | - Richard A Neher
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael Lässig
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
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23
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Shin WJ, Seong BL. Type II transmembrane serine proteases as potential target for anti-influenza drug discovery. Expert Opin Drug Discov 2017; 12:1139-1152. [DOI: 10.1080/17460441.2017.1372417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Woo-Jin Shin
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
- Vaccine Translational Research Center, Yonsei University, Seoul, South Korea
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24
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Abstract
The distinctive features of human influenza A phylogeny have inspired many mathematical and computational studies of viral infections spreading in a host population, but our understanding of the mechanisms that shape the coupled evolution of host immunity, disease incidence and viral antigenic properties is far from complete. In this paper we explore the epidemiology and the phylogeny of a rapidly mutating pathogen in a host population with a weak immune response, that allows re-infection by the same strain and provides little cross-immunity. We find that mutation generates explosive diversity and that, as diversity grows, the system is driven to a very high prevalence level. This is in stark contrast with the behavior of similar models where mutation gives rise to a large epidemic followed by disease extinction, under the assumption that infection with a strain provides lifelong immunity. For low mutation rates, the behavior of the system shows the main qualitative features of influenza evolution. Our results highlight the importance of heterogeneity in the human immune response for understanding influenza A phenomenology. They are meant as a first step toward computationally affordable, individual based models including more complex host-pathogen interactions.
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Affiliation(s)
- Tomás Aquino
- a Department of Civil & Environmental Engineering and Earth Sciences ; University of Notre Dame ; Notre Dame , IN USA
| | - Ana Nunes
- b BioISI Biosystems & Integrative Sciences Institute and Departamento de Física; Faculdade de Ciências da Universidade de Lisboa ; Lisboa , Portugal
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25
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Chan CHS, Sanders LP, Tanaka MM. Modelling the role of immunity in reversion of viral antigenic sites. J Theor Biol 2015; 392:23-34. [PMID: 26723535 DOI: 10.1016/j.jtbi.2015.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/14/2015] [Accepted: 12/16/2015] [Indexed: 12/22/2022]
Abstract
Antigenic sites in viral pathogens exhibit distinctive evolutionary dynamics due to their role in evading recognition by host immunity. Antigenic selection is known to drive higher rates of non-synonymous substitution; less well understood is why differences are observed between viruses in their propensity to mutate to a novel or previously encountered amino acid. Here, we present a model to explain patterns of antigenic reversion and forward substitution in terms of the epidemiological and molecular processes of the viral population. We develop an analytical three-strain model and extend the analysis to a multi-site model to predict characteristics of observed sequence samples. Our model provides insight into how the balance between selection to escape immunity and to maintain viability is affected by the rate of mutational input. We also show that while low probabilities of reversion may be due to either a low cost of immune escape or slowly decaying host immunity, these two scenarios can be differentiated by the frequency patterns at antigenic sites. Comparison between frequency patterns of human influenza A (H3N2) and human RSV-A suggests that the increased rates of antigenic reversion in RSV-A is due to faster decaying immunity and not higher costs of escape.
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Affiliation(s)
- Carmen H S Chan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; Evolution & Ecology Research Centre, University of New South Wales, Sydney, NSW, Australia.
| | - Lloyd P Sanders
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; Evolution & Ecology Research Centre, University of New South Wales, Sydney, NSW, Australia; Computational Social Science, ETH, Zürich, Switzerland
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; Evolution & Ecology Research Centre, University of New South Wales, Sydney, NSW, Australia
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26
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Wikramaratna PS, Rambaut A. Relationship between haemagglutination inhibition titre and immunity to influenza in ferrets. Vaccine 2015; 33:5380-5385. [PMID: 26342848 PMCID: PMC4582772 DOI: 10.1016/j.vaccine.2015.08.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/21/2015] [Accepted: 08/18/2015] [Indexed: 11/22/2022]
Abstract
Our understanding of the antigenic evolution of the human influenza virus is chiefly derived from experiments in which serum from influenza infected ferrets is tested against panels of virus isolates in the haemagglutination inhibition (HI) assay. The interpretation of these results has been much aided by the development of antigenic mapping techniques, which suppose that the antigenic distance between two different influenza viruses is directly proportional to their fold-difference in titre in this assay. Yet, antigenic distance is not necessarily the same as cross-protection, and high levels of protection have been observed in humans against strains to which they have low HI titres. However, no study has previously addressed the relationship between HI titre and cross-protection in ferrets: the standard animal model. This study fills this gap by analysing published data where pre-challenge HI titres are available for individual ferrets, and post-challenge outcomes have been recorded. Ultimately, this work confirms that it is the absolute, rather than relative, HI titre that determines the extent of immunity and that there is a threshold HI titre beyond which ferrets are completely protected from infection. Nevertheless, this titre is much higher in ferrets than has been suggested for humans. Further, we are consequently able to show that using distance between strains within an antigenic map to predict cross-protection between influenza viruses can be misleading.
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Affiliation(s)
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, UK; Fogarty International Center, National Institute of Health, Bethesda, MD, USA; Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
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27
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Lourenço J, Wikramaratna PS, Gupta S. MANTIS: an R package that simulates multilocus models of pathogen evolution. BMC Bioinformatics 2015; 16:176. [PMID: 26017358 PMCID: PMC4445977 DOI: 10.1186/s12859-015-0598-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/27/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In host-pathogen systems the development of immunity by the host places pressure on pathogens, by setting up competition between genetic variants due to the establishment of cross-protective responses. These pressures can lead to pathogen-specific, ubiquitous dynamic behaviours. Understanding the evolutionary forces that shape these patterns is one of the key goals of computationally simulated epidemiological models. Despite the contribution of such research methods in recent years to our current understanding of pathogen evolution, the availability of free software tools for the general public remains scarce. RESULTS We developed the Multilocus ANTIgenic Simulator (MANTIS) software package for the R statistical environment. MANTIS can simulate and analyse epidemiological time-series generated under the biological assumptions of the strain theory of host-pathogen systems by Gupta et al. CONCLUSIONS MANTIS wraps a C/C++ ordinary-differential equations system and Runge-Kutta solver into a set of user-friendly R functions. These include routines to numerically simulate the system and others to analyse, visualize and export results. For this, the package offers its own set of time-series plotting and exportation functions. MANTIS's main goal is to serve as a free, ready-to-use academic software tool. Its open source nature further provides an opportunity for users with advanced programming skills to expand its capabilities. Here, we describe the background theory, implementation, basic functionality and usage of this package. MANTIS is freely available from http://www.eeid.ox.ac.uk/mantis under the GPL license.
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Affiliation(s)
- José Lourenço
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK.
| | | | - Sunetra Gupta
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK.
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28
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Meeyai A, Praditsitthikorn N, Kotirum S, Kulpeng W, Putthasri W, Cooper BS, Teerawattananon Y. Seasonal influenza vaccination for children in Thailand: a cost-effectiveness analysis. PLoS Med 2015; 12:e1001829; discussion e1001829. [PMID: 26011712 PMCID: PMC4444096 DOI: 10.1371/journal.pmed.1001829] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 04/13/2015] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Seasonal influenza is a major cause of mortality worldwide. Routine immunization of children has the potential to reduce this mortality through both direct and indirect protection, but has not been adopted by any low- or middle-income countries. We developed a framework to evaluate the cost-effectiveness of influenza vaccination policies in developing countries and used it to consider annual vaccination of school- and preschool-aged children with either trivalent inactivated influenza vaccine (TIV) or trivalent live-attenuated influenza vaccine (LAIV) in Thailand. We also compared these approaches with a policy of expanding TIV coverage in the elderly. METHODS AND FINDINGS We developed an age-structured model to evaluate the cost-effectiveness of eight vaccination policies parameterized using country-level data from Thailand. For policies using LAIV, we considered five different age groups of children to vaccinate. We adopted a Bayesian evidence-synthesis framework, expressing uncertainty in parameters through probability distributions derived by fitting the model to prospectively collected laboratory-confirmed influenza data from 2005-2009, by meta-analysis of clinical trial data, and by using prior probability distributions derived from literature review and elicitation of expert opinion. We performed sensitivity analyses using alternative assumptions about prior immunity, contact patterns between age groups, the proportion of infections that are symptomatic, cost per unit vaccine, and vaccine effectiveness. Vaccination of children with LAIV was found to be highly cost-effective, with incremental cost-effectiveness ratios between about 2,000 and 5,000 international dollars per disability-adjusted life year averted, and was consistently preferred to TIV-based policies. These findings were robust to extensive sensitivity analyses. The optimal age group to vaccinate with LAIV, however, was sensitive both to the willingness to pay for health benefits and to assumptions about contact patterns between age groups. CONCLUSIONS Vaccinating school-aged children with LAIV is likely to be cost-effective in Thailand in the short term, though the long-term consequences of such a policy cannot be reliably predicted given current knowledge of influenza epidemiology and immunology. Our work provides a coherent framework that can be used for similar analyses in other low- and middle-income countries.
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Affiliation(s)
- Aronrag Meeyai
- Health Intervention and Technology Assessment Program, Nonthaburi, Thailand
- Department of Epidemiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Naiyana Praditsitthikorn
- Health Intervention and Technology Assessment Program, Nonthaburi, Thailand
- Bureau of AIDS, TB, and STI, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Surachai Kotirum
- Health Intervention and Technology Assessment Program, Nonthaburi, Thailand
| | - Wantanee Kulpeng
- Health Intervention and Technology Assessment Program, Nonthaburi, Thailand
| | - Weerasak Putthasri
- International Health Policy Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Ben S. Cooper
- Mahidol Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Wagner A. A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin. Proc Biol Sci 2015; 281:rspb.2013.2763. [PMID: 24827434 DOI: 10.1098/rspb.2013.2763] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Networks of evolving genotypes can be constructed from the worldwide time-resolved genotyping of pathogens like influenza viruses. Such genotype networks are graphs where neighbouring vertices (viral strains) differ in a single nucleotide or amino acid. A rich trove of network analysis methods can help understand the evolutionary dynamics reflected in the structure of these networks. Here, I analyse a genotype network comprising hundreds of influenza A (H3N2) haemagglutinin genes. The network is rife with cycles that reflect non-random parallel or convergent (homoplastic) evolution. These cycles also show patterns of sequence change characteristic for strong and local evolutionary constraints, positive selection and mutation-limited evolution. Such cycles would not be visible on a phylogenetic tree, illustrating that genotype network analysis can complement phylogenetic analyses. The network also shows a distinct modular or community structure that reflects temporal more than spatial proximity of viral strains, where lowly connected bridge strains connect different modules. These and other organizational patterns illustrate that genotype networks can help us study evolution in action at an unprecedented level of resolution.
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Affiliation(s)
- Andreas Wagner
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Building Y27, Winterthurerstrasse 190, Zurich 8057, Switzerland The Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne 1015, Switzerland The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Wikramaratna PS, Pybus OG, Gupta S. Contact between bird species of different lifespans can promote the emergence of highly pathogenic avian influenza strains. Proc Natl Acad Sci U S A 2014; 111:10767-72. [PMID: 24958867 PMCID: PMC4115569 DOI: 10.1073/pnas.1401849111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Outbreaks of highly pathogenic strains of avian influenza viruses (AIVs) cause considerable economic losses to the poultry industry and also pose a threat to human life. The possibility that one of these strains will evolve to become transmissible between humans, sparking a major influenza pandemic, is a matter of great concern. Most studies so far have focused on assessing these odds from the perspective of the intrinsic mutability of AIV rather than the ecological constraints to invasion faced by the virus population. Here we present an alternative multihost model for the evolution of AIV in which the mode and tempo of mutation play a limited role, with the emergence of strains being determined instead principally by the prevailing profile of population-level immunity. We show that (i) many of the observed differences in influenza virus dynamics among species can be captured by our model by simply varying host lifespan and (ii) increased contact between species of different lifespans can promote the emergence of potentially more virulent strains that were hitherto suppressed in one of the species.
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Affiliation(s)
- Paul S Wikramaratna
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; andInstitute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; and
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; and
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31
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Chhajer R, Ali N. Genetically modified organisms and visceral leishmaniasis. Front Immunol 2014; 5:213. [PMID: 24860575 PMCID: PMC4030198 DOI: 10.3389/fimmu.2014.00213] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/28/2014] [Indexed: 11/18/2022] Open
Abstract
Vaccination is the most effective method of preventing infectious diseases. Since the eradication of small pox in 1976, many other potentially life compromising if not threatening diseases have been dealt with subsequently. This event was a major leap not only in the scientific world already burdened with many diseases but also in the mindset of the common man who became more receptive to novel treatment options. Among the many protozoan diseases, the leishmaniases have emerged as one of the largest parasite killers of the world, second only to malaria. There are three types of leishmaniasis namely cutaneous (CL), mucocutaneous (ML), and visceral (VL), caused by a group of more than 20 species of Leishmania parasites. Visceral leishmaniasis, also known as kala-azar is the most severe form and almost fatal if untreated. Since the first attempts at leishmanization, we have killed parasite vaccines, subunit protein, or DNA vaccines, and now we have live recombinant carrier vaccines and live attenuated parasite vaccines under various stages of development. Although some research has shown promising results, many more potential genes need to be evaluated as live attenuated vaccine candidates. This mini-review attempts to summarize the success and failures of genetically modified organisms used in vaccination against some of major parasitic diseases for their application in leishmaniasis.
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Affiliation(s)
- Rudra Chhajer
- Infectious Diseases and Immunology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology , Kolkata , India
| | - Nahid Ali
- Infectious Diseases and Immunology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology , Kolkata , India
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32
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Pybus OG, Fraser C, Rambaut A. Evolutionary epidemiology: preparing for an age of genomic plenty. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120193. [PMID: 23382418 DOI: 10.1098/rstb.2012.0193] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- O G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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Zinder D, Bedford T, Gupta S, Pascual M. The roles of competition and mutation in shaping antigenic and genetic diversity in influenza. PLoS Pathog 2013; 9:e1003104. [PMID: 23300455 PMCID: PMC3536651 DOI: 10.1371/journal.ppat.1003104] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 11/10/2012] [Indexed: 01/05/2023] Open
Abstract
Influenza A (H3N2) offers a well-studied, yet not fully understood, disease in terms of the interactions between pathogen population dynamics, epidemiology and genetics. A major open question is why the virus population is globally dominated by a single and very recently diverged (2-8 years) lineage. Classically, this has been modeled by limiting the generation of new successful antigenic variants, such that only a small subset of progeny acquire the necessary mutations to evade host immunity. An alternative approach was recently suggested by Recker et al. in which a limited number of antigenic variants are continuously generated, but most of these are suppressed by pre-existing host population immunity. Here we develop a framework spanning the regimes described above to explore the impact of rates of mutation and levels of competition on phylodynamic patterns. We find that the evolutionary dynamics of the subtype H3N2 influenza is most easily generated within this framework when it is mutation limited as well as being under strong immune selection at a number of epitope regions of limited diversity.
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Affiliation(s)
- Daniel Zinder
- University of Michigan, Department of Computational Medicine and Bioinformatics, Department of Ecology and Evolutionary Biology, Ann Arbor, Michigan, United States of America
| | - Trevor Bedford
- University of Edinburgh, Institute of Evolutionary Biology, Edinburgh, United Kingdom
| | - Sunetra Gupta
- University of Oxford, Department of Zoology, Oxford, United Kingdom
| | - Mercedes Pascual
- University of Michigan, Department of Computational Medicine and Bioinformatics, Department of Ecology and Evolutionary Biology, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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