A60 Revealing the evolution of virulence in RNA viruses

Abstract A combination of high rates of mutation and replication, coupled with strong natural selection, ensures that RNA viruses experience rapid genotypic and phenotypic evolution. Such a ‘fast-forward’ evolution enables viruses to rapidly adapt to new host species, evade host immune responses, and to develop resistance to anti-viral drugs. Similarly, rapid evolution allows viruses to attain new levels of virulence, defined as the ability to cause severe disease in hosts. We hypothesize that distinct viral groups share genetic determinants that modulate virulence that have been acquired through convergent evolution. Thus, common patterns reflecting changing virulence-related specific viral groups could be detected. The main goals for this project are (1) to understand how genetic and phenotypic diversity can be generated among different viral groups by analyzing the variation patterns and determining the selective forces behind them (impact in viral fitness) and (2) to understand how fixed mutations can modulate virulence within different viral groups by performing comparison of strains with differing virulence within a longitudinal timescale. The subject of the study is key emerging and re-emerging virus families of medical importance. Such groups include: Coronaviridae (severe acute respiratory syndrome and Middle East respiratory syndrome-associated coronaviruses), Picornaviridae (Hepatitis A virus), Flaviviridae (Yellow fever, West Nile, Hepatitis C, Dengue, and Zika viruses), Togaviridae (Rubella and Chikungunya virus), Bornaviridae (Borna-disease virus), Filoviridae (Ebola and Marburg viruses), Paramyxoviridae (Measles, Nipah, and Hendra viruses), Rhabdoviridae (Lyssaviruses), Arenaviridae (Lassa virus), Bunyaviridae (Hanta- and Crimean-Congo hemorrhagic fever viruses), and Orthomyxoviridae (Influenza A viruses). Viral genomes collected at different time points, different hosts (human and their most closely related animal reservoirs) and different locations will be compiled. Extensive molecular evolutionary analyses will be carried out to infer gene expansion/contraction within groups, rates of evolution, and changes in selection pressure, including the detection of positive selected genes and sites (adaptive evolution). Positively selected sites will be mapped onto the viral protein structures to reveal their impact on function, and hence the location of potential virulence determinants. Virulence changes among particular viral strains and types will be defined and measured according to definitions based on an increase in: (1) transmissibility, (2) host tropism, (3) immune evasion, (4) morbidity and mortality, (5) drug resistance, and by the incorporation of epidemiological data to determine whether high or low virulence strains within different hosts and localities are spreading most efficiently in nature.

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Targeting Innate Immunity for Antiviral Therapy through Small Molecule Agonists of the RLR Pathway

Journal of Virology ◽

10.1128/jvi.02202-15 ◽

2015 ◽

Vol 90 (5) ◽

pp. 2372-2387 ◽

Cited By ~ 29

Author(s):

Sowmya Pattabhi ◽

Courtney R. Wilkins ◽

Ran Dong ◽

Megan L. Knoll ◽

Jeffrey Posakony ◽

...

Keyword(s):

Small Molecule ◽

Influenza A ◽

Ebola Virus ◽

Rna Viruses ◽

Nipah Virus ◽

Innate Immune ◽

Lassa Virus ◽

Content Type ◽

Antiviral Responses ◽

Syncytial Virus

ABSTRACTThe cellular response to virus infection is initiated when pathogen recognition receptors (PRR) engage viral pathogen-associated molecular patterns (PAMPs). This process results in induction of downstream signaling pathways that activate the transcription factor interferon regulatory factor 3 (IRF3). IRF3 plays a critical role in antiviral immunity to drive the expression of innate immune response genes, including those encoding antiviral factors, type 1 interferon, and immune modulatory cytokines, that act in concert to restrict virus replication. Thus, small molecule agonists that can promote IRF3 activation and induce innate immune gene expression could serve as antivirals to induce tissue-wide innate immunity for effective control of virus infection. We identified small molecule compounds that activate IRF3 to differentially induce discrete subsets of antiviral genes. We tested a lead compound and derivatives for the ability to suppress infections caused by a broad range of RNA viruses. Compound administration significantly decreased the viral RNA load in cultured cells that were infected with viruses of the familyFlaviviridae, including West Nile virus, dengue virus, and hepatitis C virus, as well as viruses of the familiesFiloviridae(Ebola virus),Orthomyxoviridae(influenza A virus),Arenaviridae(Lassa virus), andParamyxoviridae(respiratory syncytial virus, Nipah virus) to suppress infectious virus production. Knockdown studies mapped this response to the RIG-I-like receptor pathway. This work identifies a novel class of host-directed immune modulatory molecules that activate IRF3 to promote host antiviral responses to broadly suppress infections caused by RNA viruses of distinct genera.IMPORTANCEIncidences of emerging and reemerging RNA viruses highlight a desperate need for broad-spectrum antiviral agents that can effectively control infections caused by viruses of distinct genera. We identified small molecule compounds that can selectively activate IRF3 for the purpose of identifying drug-like molecules that can be developed for the treatment of viral infections. Here, we report the discovery of a hydroxyquinoline family of small molecules that can activate IRF3 to promote cellular antiviral responses. These molecules can prophylactically or therapeutically control infection in cell culture by pathogenic RNA viruses, including West Nile virus, dengue virus, hepatitis C virus, influenza A virus, respiratory syncytial virus, Nipah virus, Lassa virus, and Ebola virus. Our study thus identifies a class of small molecules with a novel mechanism to enhance host immune responses for antiviral activity against a variety of RNA viruses that pose a significant health care burden and/or that are known to cause infections with high case fatality rates.

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Molecular Evolution of the Influenza A Virus Non-structural Protein 1 in Interspecies Transmission and Adaptation

Frontiers in Microbiology ◽

10.3389/fmicb.2021.693204 ◽

2021 ◽

Vol 12 ◽

Author(s):

Danyel Evseev ◽

Katharine E. Magor

Keyword(s):

Viral Replication ◽

Influenza A Virus ◽

Host Species ◽

Influenza A ◽

Viral Fitness ◽

Interferon Signaling ◽

Structural Protein ◽

New Host ◽

Viral Adaptation ◽

New Host Species

The non-structural protein 1 (NS1) of influenza A viruses plays important roles in viral fitness and in the process of interspecies adaptation. It is one of the most polymorphic and mutation-tolerant proteins of the influenza A genome, but its evolutionary patterns in different host species and the selective pressures that underlie them are hard to define. In this review, we highlight some of the species-specific molecular signatures apparent in different NS1 proteins and discuss two functions of NS1 in the process of viral adaptation to new host species. First, we consider the ability of NS1 proteins to broadly suppress host protein expression through interaction with CPSF4. This NS1 function can be spontaneously lost and regained through mutation and must be balanced against the need for host co-factors to aid efficient viral replication. Evidence suggests that this function of NS1 may be selectively lost in the initial stages of viral adaptation to some new host species. Second, we explore the ability of NS1 proteins to inhibit antiviral interferon signaling, an essential function for viral replication without which the virus is severely attenuated in any host. Innate immune suppression by NS1 not only enables viral replication in tissues, but also dampens the adaptive immune response and immunological memory. NS1 proteins suppress interferon signaling and effector functions through a variety of protein-protein interactions that may differ from host to host but must achieve similar goals. The multifunctional influenza A virus NS1 protein is highly plastic, highly versatile, and demonstrates a diversity of context-dependent solutions to the problem of interspecies adaptation.

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Intra- and Cross-Species Transmission of Astroviruses

Viruses ◽

10.3390/v13061127 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1127

Author(s):

Shanley N. Roach ◽

Ryan A. Langlois

Keyword(s):

Rna Viruses ◽

Neurological Complications ◽

Avian Species ◽

Future Research ◽

Zoonotic Potential ◽

Extensive Disease ◽

New Host ◽

Viral Spread ◽

Common Causes ◽

New Host Species

Astroviruses are non-enveloped, single-stranded RNA viruses that infect mammalian and avian species. In humans, astrovirus infections are one of the most common causes of gastroenteritis in children. Infection has also been linked to serious neurological complications, especially in immunocompromised individuals. More extensive disease has also been characterized in non-human mammalian and avian species. To date, astroviruses have been detected in over 80 different avian and mammalian hosts. As the number of hosts continues to rise, the need to understand how astroviruses transmit within a given species as well as to new host species becomes increasingly important. Here, we review the current understanding of astrovirus transmission, the factors that influence viral spread, and the potential for cross-species transmission. Additionally, we highlight the current gaps in knowledge and areas of future research that will be key to understanding astrovirus transmission and zoonotic potential.

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Structure Unveils Relationships between RNA Virus Polymerases

Viruses ◽

10.3390/v13020313 ◽

2021 ◽

Vol 13 (2) ◽

pp. 313

Author(s):

Heli A. M. Mönttinen ◽

Janne J. Ravantti ◽

Minna M. Poranen

Keyword(s):

Phylogenetic Tree ◽

Rna Viruses ◽

Rna Virus ◽

Sequence Similarity ◽

Protein Structures ◽

Structural Similarity ◽

Functional Differentiation ◽

Comparison Method ◽

Homologous Structure ◽

Biological Entities

RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.

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Characteristics of Critically Ill Patients with COVID-19 Compared to Patients with Influenza—A Single Center Experience

Journal of Clinical Medicine ◽

10.3390/jcm10102056 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2056

Author(s):

Frank Herbstreit ◽

Marvin Overbeck ◽

Marc Moritz Berger ◽

Annabell Skarabis ◽

Thorsten Brenner ◽

...

Keyword(s):

Influenza A ◽

Health Care Systems ◽

Severe Disease ◽

Tertiary Care ◽

Care Facility ◽

High Volume ◽

Single Center Experience ◽

Severe Influenza ◽

Tertiary Care Facility ◽

Care Systems

Infections with SARS-CoV-2 spread worldwide early in 2020. In previous winters, we had been treating patients with seasonal influenza. While creating a larger impact on the health care systems, comparisons regarding the intensive care unit (ICU) courses of both diseases are lacking. We compared patients with influenza and SARS-CoV-2 infections treated at a tertiary care facility offering treatment for acute respiratory distress syndrome (ARDS) and being a high-volume facility for extracorporeal membrane oxygenation (ECMO). Patients with COVID-19 during the first wave of the pandemic (n = 64) were compared to 64 patients with severe influenza from 2016 to 2020 at our ICU. All patients were treated using a standardized protocol. ECMO was used in cases of severe ARDS. Both groups had similar comorbidities. Time in ICU and mortality were not significantly different, yet mortality with ECMO was high amongst COVID-19 patients with approximately two-thirds not surviving. This is in contrast to a mortality of less than 40% in influenza patients with ECMO. Mortality was higher than estimated by SAPSII score on admission in both groups. Patients with COVID-19 were more likely to be male and non-smokers than those with influenza. The outcomes for patients with severe disease were similar. The study helps to understand similarities and differences between patients treated for severe influenza infections and COVID-19.

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De-Coding the Contributions of the Viral RNAs to Alphaviral Pathogenesis

Pathogens ◽

10.3390/pathogens10060771 ◽

2021 ◽

Vol 10 (6) ◽

pp. 771

Author(s):

Autumn T. LaPointe ◽

Kevin J. Sokoloski

Keyword(s):

Host Response ◽

Severe Disease ◽

Review Article ◽

Structural Proteins ◽

Virulence Determinants ◽

Healthy Individuals ◽

Viral Rnas ◽

Positive Sense ◽

Identification And Characterization

Alphaviruses are positive-sense RNA arboviruses that are capable of causing severe disease in otherwise healthy individuals. There are many aspects of viral infection that determine pathogenesis and major efforts regarding the identification and characterization of virulence determinants have largely focused on the roles of the nonstructural and structural proteins. Nonetheless, the viral RNAs of the alphaviruses themselves play important roles in regard to virulence and pathogenesis. In particular, many sequences and secondary structures within the viral RNAs play an important part in the development of disease and may be considered important determinants of virulence. In this review article, we summarize the known RNA-based virulence traits and host:RNA interactions that influence alphaviral pathogenesis for each of the viral RNA species produced during infection. Overall, the viral RNAs produced during infection are important contributors to alphaviral pathogenesis and more research is needed to fully understand how each RNA species impacts the host response to infection as well as the development of disease.

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S-Acylation of Proteins of Coronavirus and Influenza Virus: Conservation of Acylation Sites in Animal Viruses and DHHC Acyltransferases in Their Animal Reservoirs

Pathogens ◽

10.3390/pathogens10060669 ◽

2021 ◽

Vol 10 (6) ◽

pp. 669

Author(s):

Dina A. Abdulrahman ◽

Xiaorong Meng ◽

Michael Veit

Keyword(s):

Influenza Virus ◽

Amino Acid ◽

Ion Channels ◽

Substrate Specificity ◽

Influenza A ◽

3D Structure ◽

Viral Fitness ◽

Amino Acid Substitutions ◽

Essential Function ◽

Animal Reservoirs

Recent pandemics of zoonotic origin were caused by members of coronavirus (CoV) and influenza A (Flu A) viruses. Their glycoproteins (S in CoV, HA in Flu A) and ion channels (E in CoV, M2 in Flu A) are S-acylated. We show that viruses of all genera and from all hosts contain clusters of acylated cysteines in HA, S and E, consistent with the essential function of the modification. In contrast, some Flu viruses lost the acylated cysteine in M2 during evolution, suggesting that it does not affect viral fitness. Members of the DHHC family catalyze palmitoylation. Twenty-three DHHCs exist in humans, but the number varies between vertebrates. SARS-CoV-2 and Flu A proteins are acylated by an overlapping set of DHHCs in human cells. We show that these DHHC genes also exist in other virus hosts. Localization of amino acid substitutions in the 3D structure of DHHCs provided no evidence that their activity or substrate specificity is disturbed. We speculate that newly emerged CoVs or Flu viruses also depend on S-acylation for replication and will use the human DHHCs for that purpose. This feature makes these DHHCs attractive targets for pan-antiviral drugs.

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Intercellular Transmission of Naked Viruses through Extracellular Vesicles: Focus on Polyomaviruses

Viruses ◽

10.3390/v12101086 ◽

2020 ◽

Vol 12 (10) ◽

pp. 1086

Author(s):

Francois Helle ◽

Lynda Handala ◽

Marine Bentz ◽

Gilles Duverlie ◽

Etienne Brochot

Keyword(s):

Immune System ◽

Extracellular Vesicles ◽

Rna Viruses ◽

Viral Transmission ◽

Viral Fitness ◽

Host Cells ◽

Dna Viruses ◽

Recent Advances ◽

Viral Particles ◽

Similar Strategy

Extracellular vesicles have recently emerged as a novel mode of viral transmission exploited by naked viruses to exit host cells through a nonlytic pathway. Extracellular vesicles can allow multiple viral particles to collectively traffic in and out of cells, thus enhancing the viral fitness and diversifying the transmission routes while evading the immune system. This has been shown for several RNA viruses that belong to the Picornaviridae, Hepeviridae, Reoviridae, and Caliciviridae families; however, recent studies also demonstrated that the BK and JC viruses, two DNA viruses that belong to the Polyomaviridae family, use a similar strategy. In this review, we provide an update on recent advances in understanding the mechanisms used by naked viruses to hijack extracellular vesicles, and we discuss the implications for the biology of polyomaviruses.

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Multiple Influenza A (H3N2) Mutations Conferring Resistance to Neuraminidase Inhibitors in a Bone Marrow Transplant Recipient

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.03667-14 ◽

2014 ◽

Vol 58 (12) ◽

pp. 7188-7197 ◽

Cited By ~ 37

Author(s):

Alireza Eshaghi ◽

Sarah Shalhoub ◽

Paul Rosenfeld ◽

Aimin Li ◽

Rachel R. Higgins ◽

...

Keyword(s):

Influenza Virus ◽

Antiviral Therapy ◽

Influenza A ◽

Antiviral Treatment ◽

Marrow Transplant ◽

Viral Fitness ◽

H3n2 Virus ◽

Resistance Mutations ◽

Depth Analysis ◽

Resistant Strains

ABSTRACTImmunocompromised patients are predisposed to infections caused by influenza virus. Influenza virus may produce considerable morbidity, including protracted illness and prolonged viral shedding in these patients, thus prompting higher doses and prolonged courses of antiviral therapy. This approach may promote the emergence of resistant strains. Characterization of neuraminidase (NA) inhibitor (NAI)-resistant strains of influenza A virus is essential for documenting causes of resistance. In this study, using quantitative real-time PCR along with conventional Sanger sequencing, we identified an NAI-resistant strain of influenza A (H3N2) virus in an immunocompromised patient. In-depth analysis by deep gene sequencing revealed that various known markers of antiviral resistance, including transient R292K and Q136K substitutions and a sustained E119K (N2 numbering) substitution in the NA protein emerged during prolonged antiviral therapy. In addition, a combination of a 4-amino-acid deletion at residues 245 to 248 (Δ245-248) accompanied by the E119V substitution occurred, causing resistance to or reduced inhibition by NAIs (oseltamivir, zanamivir, and peramivir). Resistant variants within a pool of viral quasispecies arose during combined antiviral treatment. More research is needed to understand the interplay of drug resistance mutations, viral fitness, and transmission.

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Computed tomography findings in patients with H1N1 influenza A infection

Radiologia Brasileira ◽

10.1590/s0100-39842013000500006 ◽

2013 ◽

Vol 46 (5) ◽

pp. 299-306 ◽

Cited By ~ 6

Author(s):

Viviane Brandão Amorim ◽

Rosana Souza Rodrigues ◽

Miriam Menna Barreto ◽

Gláucia Zanetti ◽

Edson Marchiori

Keyword(s):

Computed Tomography ◽

Influenza A ◽

H1n1 Virus ◽

Severe Disease ◽

H1n1 Influenza ◽

Wall Thickening ◽

High Resolution Computed Tomography ◽

Air Trapping ◽

Bronchial Wall

The present study aimed to review high resolution computed tomography findings in patients with H1N1 influenza A infection. The most common tomographic findings include ground-glass opacities, areas of consolidation or a combination of both patterns. Some patients may also present bronchial wall thickening, airspace nodules, crazy-paving pattern, perilobular opacity, air trapping and findings related to organizing pneumonia. These abnormalities are frequently bilateral, with subpleural distribution. Despite their nonspecificity, it is important to recognize the main tomographic findings in patients affected by H1N1 virus in order to include this possibility in the differential diagnosis, characterize complications and contribute in the follow-up, particularly in cases of severe disease.

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