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Martin MA, Berg N, Koelle K. Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks. Virus Evol 2024; 10:veae042. [PMID: 38883977 PMCID: PMC11179161 DOI: 10.1093/ve/veae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 05/06/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Influenza infections result in considerable public health and economic impacts each year. One of the contributing factors to the high annual incidence of human influenza is the virus's ability to evade acquired immunity through continual antigenic evolution. Understanding the evolutionary forces that act within and between hosts is therefore critical to interpreting past trends in influenza virus evolution and in predicting future ones. Several studies have analyzed longitudinal patterns of influenza A virus genetic diversity in natural human infections to assess the relative contributions of selection and genetic drift on within-host evolution. However, in these natural infections, within-host viral populations harbor very few single-nucleotide variants, limiting our resolution in understanding the forces acting on these populations in vivo. Furthermore, low levels of within-host viral genetic diversity limit the ability to infer the extent of drift across transmission events. Here, we propose to use influenza virus genomic diversity as an alternative signal to better understand within- and between-host patterns of viral evolution. Specifically, we focus on the dynamics of defective viral genomes (DVGs), which harbor large internal deletions in one or more of influenza virus's eight gene segments. Our longitudinal analyses of DVGs show that influenza A virus populations are highly dynamic within hosts, corroborating previous findings based on viral genetic diversity that point toward the importance of genetic drift in driving within-host viral evolution. Furthermore, our analysis of DVG populations across transmission pairs indicates that DVGs rarely appeared to be shared, indicating the presence of tight transmission bottlenecks. Our analyses demonstrate that viral genomic diversity can be used to complement analyses based on viral genetic diversity to reveal processes that drive viral evolution within and between hosts.
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Affiliation(s)
- Michael A Martin
- Department of Pathology, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, USA
- Graduate Program in Population Biology, Ecology, and Evolution, Emory University, 1462 Clifton Road NE, Atlanta, GA 30322, USA
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Nick Berg
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
- National Institute of Allergy and Infectious Diseases Laboratory of Viral Disease, National Institutes of Health, 33 North Drive, Bethesda, MD 20814, USA
| | - Katia Koelle
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), 1510 Clifton Road NE, Atlanta, GA 30322, USA
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2
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Staheli JP, Neal ML, Navare A, Mast FD, Aitchison JD. Predicting host-based, synthetic lethal antiviral targets from omics data. NAR MOLECULAR MEDICINE 2024; 1:ugad001. [PMID: 38994440 PMCID: PMC11233254 DOI: 10.1093/narmme/ugad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/08/2023] [Accepted: 01/03/2024] [Indexed: 07/13/2024]
Abstract
Traditional antiviral therapies often have limited effectiveness due to toxicity and the emergence of drug resistance. Host-based antivirals are an alternative, but can cause nonspecific effects. Recent evidence shows that virus-infected cells can be selectively eliminated by targeting synthetic lethal (SL) partners of proteins disrupted by viral infection. Thus, we hypothesized that genes depleted in CRISPR knockout (KO) screens of virus-infected cells may be enriched in SL partners of proteins altered by infection. To investigate this, we established a computational pipeline predicting antiviral SL drug targets. First, we identified SARS-CoV-2-induced changes in gene products via a large compendium of omics data. Second, we identified SL partners for each altered gene product. Last, we screened CRISPR KO data for SL partners required for cell viability in infected cells. Despite differences in virus-induced alterations detected by various omics data, they share many predicted SL targets, with significant enrichment in CRISPR KO-depleted datasets. Our comparison of SARS-CoV-2 and influenza infection data revealed potential broad-spectrum, host-based antiviral SL targets. This suggests that CRISPR KO data are replete with common antiviral targets due to their SL relationship with virus-altered states and that such targets can be revealed from analysis of omics datasets and SL predictions.
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Affiliation(s)
- Jeannette P Staheli
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Maxwell L Neal
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Arti Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
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3
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Staheli JP, Neal ML, Navare A, Mast FD, Aitchison JD. Predicting host-based, synthetic lethal antiviral targets from omics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553430. [PMID: 37645861 PMCID: PMC10462099 DOI: 10.1101/2023.08.15.553430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Traditional antiviral therapies often have limited effectiveness due to toxicity and development of drug resistance. Host-based antivirals, while an alternative, may lead to non-specific effects. Recent evidence shows that virus-infected cells can be selectively eliminated by targeting synthetic lethal (SL) partners of proteins disrupted by viral infection. Thus, we hypothesized that genes depleted in CRISPR KO screens of virus-infected cells may be enriched in SL partners of proteins altered by infection. To investigate this, we established a computational pipeline predicting SL drug targets of viral infections. First, we identified SARS-CoV-2-induced changes in gene products via a large compendium of omics data. Second, we identified SL partners for each altered gene product. Last, we screened CRISPR KO data for SL partners required for cell viability in infected cells. Despite differences in virus-induced alterations detected by various omics data, they share many predicted SL targets, with significant enrichment in CRISPR KO-depleted datasets. Comparing data from SARS-CoV-2 and influenza infections, we found possible broad-spectrum, host-based antiviral SL targets. This suggests that CRISPR KO data are replete with common antiviral targets due to their SL relationship with virus-altered states and that such targets can be revealed from analysis of omics datasets and SL predictions.
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Affiliation(s)
- Jeannette P. Staheli
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - Maxwell L. Neal
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - Arti Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
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4
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Beesley LJ, Moran KR, Wagh K, Castro LA, Theiler J, Yoon H, Fischer W, Hengartner NW, Korber B, Del Valle SY. SARS-CoV-2 variant transition dynamics are associated with vaccination rates, number of co-circulating variants, and convalescent immunity. EBioMedicine 2023; 91:104534. [PMID: 37004335 PMCID: PMC10065418 DOI: 10.1016/j.ebiom.2023.104534] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Throughout the COVID-19 pandemic, the SARS-CoV-2 virus has continued to evolve, with new variants outcompeting existing variants and often leading to different dynamics of disease spread. METHODS In this paper, we performed a retrospective analysis using longitudinal sequencing data to characterize differences in the speed, calendar timing, and magnitude of 16 SARS-CoV-2 variant waves/transitions for 230 countries and sub-country regions, between October 2020 and January 2023. We then clustered geographic locations in terms of their variant behavior across several Omicron variants, allowing us to identify groups of locations exhibiting similar variant transitions. Finally, we explored relationships between heterogeneity in these variant waves and time-varying factors, including vaccination status of the population, governmental policy, and the number of variants in simultaneous competition. FINDINGS This work demonstrates associations between the behavior of an emerging variant and the number of co-circulating variants as well as the demographic context of the population. We also observed an association between high vaccination rates and variant transition dynamics prior to the Mu and Delta variant transitions. INTERPRETATION These results suggest the behavior of an emergent variant may be sensitive to the immunologic and demographic context of its location. Additionally, this work represents the most comprehensive characterization of variant transitions globally to date. FUNDING Laboratory Directed Research and Development (LDRD), Los Alamos National Laboratory.
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Affiliation(s)
- Lauren J Beesley
- Statistical Sciences, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Kelly R Moran
- Statistical Sciences, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Lauren A Castro
- Information Systems and Modeling, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - James Theiler
- Space Data Science and Systems, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Will Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Nick W Hengartner
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA; The New Mexico Consortium, Los Alamos, NM, USA
| | - Sara Y Del Valle
- Information Systems and Modeling, Los Alamos National Laboratory, Los Alamos, NM, USA
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5
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Wang Y, Tang CY, Wan XF. Antigenic characterization of influenza and SARS-CoV-2 viruses. Anal Bioanal Chem 2022; 414:2841-2881. [PMID: 34905077 PMCID: PMC8669429 DOI: 10.1007/s00216-021-03806-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.
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Affiliation(s)
- Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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6
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Miller JK, Elenberg K, Dubrawski A. Forecasting emergence of COVID-19 variants of concern. PLoS One 2022; 17:e0264198. [PMID: 35202422 PMCID: PMC8870573 DOI: 10.1371/journal.pone.0264198] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 02/04/2022] [Indexed: 12/02/2022] Open
Abstract
We consider whether one can forecast the emergence of variants of concern in the SARS-CoV-2 outbreak and similar pandemics. We explore methods of population genetics and identify key relevant principles in both deterministic and stochastic models of spread of infectious disease. Finally, we demonstrate that fitness variation, defined as a trait for which an increase in its value is associated with an increase in net Darwinian fitness if the value of other traits are held constant, is a strong indicator of imminent transition in the viral population.
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Affiliation(s)
- James Kyle Miller
- Auton Systems LLC, Pittsburgh, PA, United States of America
- * E-mail:
| | - Kimberly Elenberg
- United States Department of Defense Covid Task Force, Washington, DC, United States of America
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7
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Allen JD, Ross TM. Evaluation of Next-Generation H3 Influenza Vaccines in Ferrets Pre-Immune to Historical H3N2 Viruses. Front Immunol 2021; 12:707339. [PMID: 34475872 PMCID: PMC8406686 DOI: 10.3389/fimmu.2021.707339] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Each person has a unique immune history to past influenza virus infections. Exposure to influenza viruses early in life establishes memory B cell populations that influence future immune responses to influenza vaccination. Current influenza vaccines elicit antibodies that are typically strain specific and do not offer broad protection against antigenically drifted influenza strains in all age groups of people. This is particularly true for vaccine antigens of the A(H3N2) influenza virus subtype, where continual antigenic drift necessitates frequent vaccine reformulation. Broadly-reactive influenza virus vaccine antigens offer a solution to combat antigenic drift, but they also need to be equally effective in all populations, regardless of prior influenza virus exposure history. This study examined the role that pre-existing immunity plays on influenza virus vaccination. Ferrets were infected with historical A(H3N2) influenza viruses isolated from either the 1970’s, 1980’s, or 1990’s and then vaccinated with computationally optimized broadly reactive antigens (COBRA) or wild-type (WT) influenza virus like particles (VLPs) expressing hemagglutinin (HA) vaccine antigens to examine the expansion of immune breadth. Vaccines with the H3 COBRA HA antigens had more cross-reactive antibodies following a single vaccination in all three pre-immune regimens than vaccines with WT H3 HA antigens against historical, contemporary, and future drifted A(H3N2) influenza viruses. The H3 COBRA HA vaccines also induced antibodies capable of neutralizing live virus infections against modern drifted A(H3N2) strains at higher titers than the WT H3 HA vaccine comparators.
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Affiliation(s)
- James D Allen
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States.,Department of Infectious Diseases, University of Georgia, Athens, GA, United States
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8
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Piantham C, Ito K. Modeling the selective advantage of new amino acids on the hemagglutinin of H1N1 influenza viruses using their patient age distributions. Virus Evol 2021; 7:veab049. [PMID: 34285812 PMCID: PMC8286795 DOI: 10.1093/ve/veab049] [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] [Indexed: 12/21/2022] Open
Abstract
In 2009, a new strain of H1N1 influenza A virus caused a pandemic, and its descendant strains are causing seasonal epidemics worldwide. Given the high mutation rate of influenza viruses, variant strains having different amino acids on hemagglutinin (HA) continuously emerge. To prepare vaccine strains for the next influenza seasons, it is an urgent task to predict which variants will be selected in the viral population. An analysis of 24,681 pairs of an amino acid sequence of HA of H1N1pdm2009 viruses and its patient age showed that the empirical fixation probability of new amino acids on HA significantly differed depending on their frequencies in the population, patient age distributions, and epitope flags. The selective advantage of a variant strain having a new amino acid was modeled by linear combinations of patients age distributions and epitope flags, and then the fixation probability of the new amino acid was modeled using Kimura’s formula for advantageous selection. The parameters of models were estimated from the sequence data and models were tested with four-fold cross validations. The frequency of new amino acids alone can achieve high sensitivity, specificity, and precision in predicting the fixation of a new amino acid of which frequency is more than 0.11. The estimated parameter suggested that viruses with a new amino acid having a frequency in the population higher than 0.11 have a significantly higher selective advantage compared to viruses with the old amino acid at the same position. The model considering the Z-value of patient age rank-sums of new amino acids predicted amino acid substitutions on HA with a sensitivity of 0.78, specificity of 0.86, and precision of 0.83, showing significant improvement compared to the constant selective advantage model, which used only the frequency of the amino acid. These results suggested that H1N1 viruses tend to be selected in the adult population, and frequency of viruses having new amino acids and their patient ages are useful to predict amino acid substitutions on HA.
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Affiliation(s)
- Chayada Piantham
- Division of Bioinformatics, Graduate School of Infectious Diseases, Hokkaido University, Sapporo 0600818, Japan
| | - Kimihito Ito
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo 0010020, Japan
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9
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Next generation methodology for updating HA vaccines against emerging human seasonal influenza A(H3N2) viruses. Sci Rep 2021; 11:4554. [PMID: 33654128 PMCID: PMC7925519 DOI: 10.1038/s41598-020-79590-7] [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: 09/27/2020] [Accepted: 12/10/2020] [Indexed: 01/31/2023] Open
Abstract
While vaccines remain the best tool for preventing influenza virus infections, they have demonstrated low to moderate effectiveness in recent years. Seasonal influenza vaccines typically consist of wild-type influenza A and B viruses that are limited in their ability to elicit protective immune responses against co-circulating influenza virus variant strains. Improved influenza virus vaccines need to elicit protective immune responses against multiple influenza virus drift variants within each season. Broadly reactive vaccine candidates potentially provide a solution to this problem, but their efficacy may begin to wane as influenza viruses naturally mutate through processes that mediates drift. Thus, it is necessary to develop a method that commercial vaccine manufacturers can use to update broadly reactive vaccine antigens to better protect against future and currently circulating viral variants. Building upon the COBRA technology, nine next-generation H3N2 influenza hemagglutinin (HA) vaccines were designed using a next generation algorithm and design methodology. These next-generation broadly reactive COBRA H3 HA vaccines were superior to wild-type HA vaccines at eliciting antibodies with high HAI activity against a panel of historical and co-circulating H3N2 influenza viruses isolated over the last 15 years, as well as the ability to neutralize future emerging H3N2 isolates.
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10
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Ravina, Manjeet, Mohan H, Narang J, Pundir S, Pundir CS. A changing trend in diagnostic methods of Influenza A (H3N2) virus in human: a review. 3 Biotech 2021; 11:87. [PMID: 33495723 PMCID: PMC7816835 DOI: 10.1007/s13205-021-02642-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/03/2021] [Indexed: 12/11/2022] Open
Abstract
The influenza virus is classified into four types A, B, C, and D, but type A and B are responsible for major illnesses in people with influenza A being the only virus responsible for flu pandemics due to the presence of two surface proteins called hemagglutinin (H) and neuraminidase (N) on the virus. The two subtypes of influenza A virus, H1N1 and H3N2, have been known to cause many flu pandemics. Both subtypes change genetically and antigenically to produce variants (clades and subclades, also know as groups and subgroups). H3N2 tends to change rapidly, both genetically and antigenically whereas that of H1N1 generally tends to have smaller changes. Influenza A (H3N2) viruses have evolved to form many separate, genetically different clades that continue to co-circulate. Influenza A(H3N2) viruses have caused significant deaths as per WHO report. The review describes methods for detection of influenza A(H3N2) viruses by conventional serological methods as well as the advanced methods of molecular biology and biosensors. All these methods are based on different parameters and have different targets but the goal is to improve specificity and increase sensitivity. Amongst the molecular methods, real-time polymerase chain reaction (RT-PCR) is considered a gold standard test due to its many advantages whereas a number of other molecular methods are time-consuming, complex to perform or lack specificity. The review also considers bio-sensing methods for simple, rapid, highly sensitive, and specific detection of H3N2. The classification and principle of various H3N2 biosensors are also discussed.
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Affiliation(s)
- Ravina
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Manjeet
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Hari Mohan
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Jagriti Narang
- Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Shikha Pundir
- Liggins Institute, The University of Auckland, Auckland, New Zealand
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11
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Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J Cell Biol 2020; 219:e202006159. [PMID: 32785687 PMCID: PMC7659715 DOI: 10.1083/jcb.202006159] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
With the rapid global spread of SARS-CoV-2, we have become acutely aware of the inadequacies of our ability to respond to viral epidemics. Although disrupting the viral life cycle is critical for limiting viral spread and disease, it has proven challenging to develop targeted and selective therapeutics. Synthetic lethality offers a promising but largely unexploited strategy against infectious viral disease; as viruses infect cells, they abnormally alter the cell state, unwittingly exposing new vulnerabilities in the infected cell. Therefore, we propose that effective therapies can be developed to selectively target the virally reconfigured host cell networks that accompany altered cellular states to cripple the host cell that has been converted into a virus factory, thus disrupting the viral life cycle.
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Affiliation(s)
- Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
| | - Arti T. Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
| | - Almer M. van der Sloot
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | | | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY
| | | | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Alan Aderem
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
- Department of Biochemistry, University of Washington, Seattle, WA
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12
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Forghani M, Khachay M. Convolutional Neural Network Based Approach to in Silico Non-Anticipating Prediction of Antigenic Distance for Influenza Virus. Viruses 2020; 12:E1019. [PMID: 32932748 PMCID: PMC7551508 DOI: 10.3390/v12091019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
Evaluation of the antigenic similarity degree between the strains of the influenza virus is highly important for vaccine production. The conventional method used to measure such a degree is related to performing the immunological assays of hemagglutinin inhibition. Namely, the antigenic distance between two strains is calculated on the basis of HI assays. Usually, such distances are visualized by using some kind of antigenic cartography method. The known drawback of the HI assay is that it is rather time-consuming and expensive. In this paper, we propose a novel approach for antigenic distance approximation based on deep learning in the feature spaces induced by hemagglutinin protein sequences and Convolutional Neural Networks (CNNs). To apply a CNN to compare the protein sequences, we utilize the encoding based on the physical and chemical characteristics of amino acids. By varying (hyper)parameters of the CNN architecture design, we find the most robust network. Further, we provide insight into the relationship between approximated antigenic distance and antigenicity by evaluating the network on the HI assay database for the H1N1 subtype. The results indicate that the best-trained network gives a high-precision approximation for the ground-truth antigenic distances, and can be used as a good exploratory tool in practical tasks.
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13
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Rowaiye AB, Onuh OA, Oli AN, Okpalefe OA, Oni S, Nwankwo EJ. The pandemic COVID-19: a tale of viremia, cellular oxidation and immune dysfunction. Pan Afr Med J 2020; 36:188. [PMID: 32952832 PMCID: PMC7467617 DOI: 10.11604/pamj.2020.36.188.23476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2 is a tester of the immune system. While it spares the healthy, it brings severe morbidity and in a few cases, mortality to its victims. This article aims at critically reviewing the key virulence factors of COVID-19 which are the viremia, cellular oxidation and immune dysfunction. The averse economic effect of certain disease control measures such as national lock-downs and social distancing, though beneficial, makes them unsustainable. Worse still is the fact that wild animals and domestic pets are carriers of SARS-CoV-2 suggesting that the disease would take longer than expected to be eradicated globally. A better understanding of the pathological dynamics of COVID-19 would help the general populace to prepare for possible infection by the invisible enemy. While the world prospects for vaccines and therapeutic agents against the SARS-CoV-2, clinicians should also seek to modulate the immune system for optimum performance. Immunoprophylactic and immunomodulatory strategies are recommended for the different strata of stakeholders combating the pandemic with the hope that morbidities and mortalities associated with COVID-19 would be drastically reduced.
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Affiliation(s)
- Adekunle Babajide Rowaiye
- Department of Medical Biotechnology, National Biotechnology Development Agency, Abuja, Nigeria.,Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharm Scs, Nnamdi Azikiwe University, Awka, Nigeria
| | - Olukemi Adejoke Onuh
- Department of Medical Biotechnology, National Biotechnology Development Agency, Abuja, Nigeria
| | - Angus Nnamdi Oli
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharm Scs, Nnamdi Azikiwe University, Awka, Nigeria
| | | | - Solomon Oni
- Bioresources Development Centre, Isanlu, National Biotechnology Development Agency, Abuja, Nigeria
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