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1.
Future Microbiol ; 16: 1105-1133, 2021 09.
Article in English | MEDLINE | ID: covidwho-1381356

ABSTRACT

SARS-CoV-2 is the etiological agent of the current pandemic worldwide and its associated disease COVID-19. In this review, we have analyzed SARS-CoV-2 characteristics and those ones of other well-known RNA viruses viz. HIV, HCV and Influenza viruses, collecting their historical data, clinical manifestations and pathogenetic mechanisms. The aim of the work is obtaining useful insights and lessons for a better understanding of SARS-CoV-2. These pathogens present a distinct mode of transmission, as SARS-CoV-2 and Influenza viruses are airborne, whereas HIV and HCV are bloodborne. However, these viruses exhibit some potential similar clinical manifestations and pathogenetic mechanisms and their understanding may contribute to establishing preventive measures and new therapies against SARS-CoV-2.


Subject(s)
COVID-19/history , Pandemics/history , SARS-CoV-2/physiology , SARS-CoV-2/pathogenicity , Antiviral Agents/therapeutic use , COVID-19/drug therapy , COVID-19/epidemiology , COVID-19/transmission , Climate , Disease Reservoirs/virology , Genome, Viral , History, 19th Century , History, 20th Century , History, 21st Century , Humans , Mutation , RNA Viruses/pathogenicity , RNA Viruses/physiology , Reinfection/epidemiology , Reinfection/history , Reinfection/transmission , Reinfection/virology , Respiratory Tract Infections/drug therapy , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/history , Respiratory Tract Infections/transmission , Virus Replication
2.
J Biol Chem ; 297(1): 100856, 2021 07.
Article in English | MEDLINE | ID: covidwho-1283409

ABSTRACT

The nuclear pore complex is the sole gateway connecting the nucleoplasm and cytoplasm. In humans, the nuclear pore complex is one of the largest multiprotein assemblies in the cell, with a molecular mass of ∼110 MDa and consisting of 8 to 64 copies of about 34 different nuclear pore proteins, termed nucleoporins, for a total of 1000 subunits per pore. Trafficking events across the nuclear pore are mediated by nuclear transport receptors and are highly regulated. The nuclear pore complex is also used by several RNA viruses and almost all DNA viruses to access the host cell nucleoplasm for replication. Viruses hijack the nuclear pore complex, and nuclear transport receptors, to access the nucleoplasm where they replicate. In addition, the nuclear pore complex is used by the cell innate immune system, a network of signal transduction pathways that coordinates the first response to foreign invaders, including viruses and other pathogens. Several branches of this response depend on dynamic signaling events that involve the nuclear translocation of downstream signal transducers. Mounting evidence has shown that these signaling cascades, especially those steps that involve nucleocytoplasmic trafficking events, are targeted by viruses so that they can evade the innate immune system. This review summarizes how nuclear pore proteins and nuclear transport receptors contribute to the innate immune response and highlights how viruses manipulate this cellular machinery to favor infection. A comprehensive understanding of nuclear pore proteins in antiviral innate immunity will likely contribute to the development of new antiviral therapeutic strategies.


Subject(s)
Immunity, Innate/genetics , Nuclear Pore Complex Proteins/genetics , Nuclear Pore/genetics , Virus Diseases/genetics , Active Transport, Cell Nucleus/genetics , Active Transport, Cell Nucleus/immunology , DNA Viruses/genetics , DNA Viruses/pathogenicity , Humans , Immune Evasion/genetics , Immune Evasion/immunology , NF-kappa B/genetics , Nuclear Pore/immunology , Nuclear Pore Complex Proteins/immunology , RNA Viruses/genetics , RNA Viruses/pathogenicity , Viral Nonstructural Proteins/genetics , Virus Diseases/immunology , Virus Diseases/virology , Virus Replication/genetics , Virus Replication/immunology
3.
Front Immunol ; 11: 573583, 2020.
Article in English | MEDLINE | ID: covidwho-1226976

ABSTRACT

Complement, a part of the innate arm of the immune system, is integral to the frontline defense of the host against innumerable pathogens, which includes RNA viruses. Among the major groups of viruses, RNA viruses contribute significantly to the global mortality and morbidity index associated with viral infection. Despite multiple routes of entry adopted by these viruses, facing complement is inevitable. The initial interaction with complement and the nature of this interaction play an important role in determining host resistance versus susceptibility to the viral infection. Many RNA viruses are potent activators of complement, often resulting in virus neutralization. Yet, another facet of virus-induced activation is the exacerbation in pathogenesis contributing to the overall morbidity. The severity in disease and death associated with RNA virus infections shows a tip in the scale favoring viruses. Growing evidence suggest that like their DNA counterparts, RNA viruses have co-evolved to master ingenious strategies to remarkably restrict complement. Modulation of host genes involved in antiviral responses contributed prominently to the adoption of unique strategies to keep complement at bay, which included either down regulation of activation components (C3, C4) or up regulation of complement regulatory proteins. All this hints at a possible "hijacking" of the cross-talk mechanism of the host immune system. Enveloped RNA viruses have a selective advantage of not only modulating the host responses but also recruiting membrane-associated regulators of complement activation (RCAs). This review aims to highlight the significant progress in the understanding of RNA virus-complement interactions.


Subject(s)
Adaptive Immunity , Complement Activation , Complement System Proteins/immunology , Immunity, Innate , RNA Virus Infections/virology , RNA Viruses/pathogenicity , Animals , Complement System Proteins/genetics , Complement System Proteins/metabolism , Evolution, Molecular , Gene Expression Regulation, Viral , Host-Pathogen Interactions , Humans , RNA Virus Infections/genetics , RNA Virus Infections/immunology , RNA Virus Infections/mortality , RNA Viruses/genetics , RNA Viruses/immunology , Severity of Illness Index
4.
Int J Mol Sci ; 22(1)2020 Dec 30.
Article in English | MEDLINE | ID: covidwho-1006614

ABSTRACT

Being opportunistic intracellular pathogens, viruses are dependent on the host for their replication. They hijack host cellular machinery for their replication and survival by targeting crucial cellular physiological pathways, including transcription, translation, immune pathways, and apoptosis. Immediately after translation, the host and viral proteins undergo a process called post-translational modification (PTM). PTMs of proteins involves the attachment of small proteins, carbohydrates/lipids, or chemical groups to the proteins and are crucial for the proteins' functioning. During viral infection, host proteins utilize PTMs to control the virus replication, using strategies like activating immune response pathways, inhibiting viral protein synthesis, and ultimately eliminating the virus from the host. PTM of viral proteins increases solubility, enhances antigenicity and virulence properties. However, RNA viruses are devoid of enzymes capable of introducing PTMs to their proteins. Hence, they utilize the host PTM machinery to promote their survival. Proteins from viruses belonging to the family: Togaviridae, Flaviviridae, Retroviridae, and Coronaviridae such as chikungunya, dengue, zika, HIV, and coronavirus are a few that are well-known to be modified. This review discusses various host and virus-mediated PTMs that play a role in the outcome during the infection.


Subject(s)
Protein Processing, Post-Translational , RNA Virus Infections/enzymology , RNA Virus Infections/virology , RNA Viruses/metabolism , RNA Viruses/pathogenicity , Viral Proteins/metabolism , Acetylation , Chikungunya virus/metabolism , Coronavirus/metabolism , Coronavirus/pathogenicity , Cytopathogenic Effect, Viral , Glycosylation , HIV/metabolism , HIV/pathogenicity , Host Microbial Interactions , Humans , Phosphorylation , RNA Virus Infections/immunology , RNA Virus Infections/metabolism , RNA Viruses/immunology , Ubiquitination , Virus Replication/physiology , Zika Virus/metabolism , Zika Virus/pathogenicity
5.
Viruses ; 13(4)2021 03 24.
Article in English | MEDLINE | ID: covidwho-1151757

ABSTRACT

Viruses play a primary role as etiological agents of pandemics worldwide. Although there has been progress in identifying the molecular features of both viruses and hosts, the extent of the impact these and other factors have that contribute to interspecies transmission and their relationship with the emergence of diseases are poorly understood. The objective of this review was to analyze the factors related to the characteristics inherent to RNA viruses accountable for pandemics in the last 20 years which facilitate infection, promote interspecies jump, and assist in the generation of zoonotic infections with pandemic potential. The search resulted in 48 research articles that met the inclusion criteria. Changes adopted by RNA viruses are influenced by environmental and host-related factors, which define their ability to adapt. Population density, host distribution, migration patterns, and the loss of natural habitats, among others, have been associated as factors in the virus-host interaction. This review also included a critical analysis of the Latin American context, considering its diverse and unique social, cultural, and biodiversity characteristics. The scarcity of scientific information is striking, thus, a call to local institutions and governments to invest more resources and efforts to the study of these factors in the region is key.


Subject(s)
Host-Pathogen Interactions , Pandemics/statistics & numerical data , RNA Virus Infections/transmission , RNA Viruses/pathogenicity , Viral Zoonoses/transmission , Animals , Genome, Viral , Humans , Latin America/epidemiology , Pandemics/prevention & control , RNA Virus Infections/epidemiology , RNA Viruses/genetics
6.
Sci Rep ; 10(1): 3963, 2020 03 03.
Article in English | MEDLINE | ID: covidwho-659769

ABSTRACT

The diversity of pathogens associated with acute respiratory infection (ARI) makes diagnosis challenging. Traditional pathogen screening tests have a limited detection range and provide little additional information. We used total RNA sequencing ("meta-transcriptomics") to reveal the full spectrum of microbes associated with paediatric ARI. Throat swabs were collected from 48 paediatric ARI patients and 7 healthy controls. Samples were subjected to meta-transcriptomics to determine the presence and abundance of viral, bacterial, and eukaryotic pathogens, and to reveal mixed infections, pathogen genotypes/subtypes, evolutionary origins, epidemiological history, and antimicrobial resistance. We identified 11 RNA viruses, 4 DNA viruses, 4 species of bacteria, and 1 fungus. While most are known to cause ARIs, others, such as echovirus 6, are rarely associated with respiratory disease. Co-infection of viruses and bacteria and of multiple viruses were commonplace (9/48), with one patient harboring 5 different pathogens, and genome sequence data revealed large intra-species diversity. Expressed resistance against eight classes of antibiotic was detected, with those for MLS, Bla, Tet, Phe at relatively high abundance. In summary, we used a simple total RNA sequencing approach to reveal the complex polymicrobial infectome in ARI. This provided comprehensive and clinically informative information relevant to understanding respiratory disease.


Subject(s)
Metagenome/genetics , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/virology , Bacteria/classification , Bacteria/genetics , Bacteria/pathogenicity , DNA Viruses/classification , DNA Viruses/genetics , DNA Viruses/pathogenicity , Drug Resistance, Microbial/genetics , Female , Fungi/classification , Fungi/genetics , Fungi/pathogenicity , Humans , Male , Phylogeny , RNA Viruses/classification , RNA Viruses/genetics , RNA Viruses/pathogenicity , Viruses/classification , Viruses/genetics , Viruses/pathogenicity
7.
Clin Immunol ; 226: 108699, 2021 05.
Article in English | MEDLINE | ID: covidwho-1101151

ABSTRACT

RNA editing is a fundamental biological process with 2 major forms, namely adenosine-to-inosine (A-to-I, recognized as A-to-G) and cytosine-to-uracil (C-to-U) deamination, mediated by ADAR and APOBEC enzyme families, respectively. A-to-I RNA editing has been shown to directly affect the genome/transcriptome of RNA viruses with significant repercussions for viral protein synthesis, proliferation and infectivity, while it also affects recognition of double-stranded RNAs by cytosolic receptors controlling the host innate immune response. Recent evidence suggests that RNA editing may be present in SARS-CoV-2 genome/transcriptome. The majority of mapped mutations in SARS-CoV-2 genome are A-to-G/U-to-C(opposite strand) and C-to-U/G-to-A(opposite strand) substitutions comprising potential ADAR-/APOBEC-mediated deamination events. A single nucleotide substitution can have dramatic effects on SARS-CoV-2 infectivity as shown by the D614G(A-to-G) substitution in the spike protein. Future studies utilizing serial sampling from patients with COVID-19 are warranted to delineate whether RNA editing affects viral replication and/or the host immune response to SARS-CoV-2.


Subject(s)
APOBEC Deaminases/metabolism , Adenosine Deaminase/metabolism , COVID-19/immunology , Immunity, Innate , RNA Editing , RNA Viruses/genetics , RNA-Binding Proteins/metabolism , SARS-CoV-2/genetics , APOBEC Deaminases/genetics , Adenosine Deaminase/genetics , COVID-19/enzymology , COVID-19/virology , Humans , Mutation , RNA Viruses/pathogenicity , RNA, Double-Stranded/metabolism , RNA-Binding Proteins/genetics , SARS-CoV-2/metabolism
8.
Eye (Lond) ; 35(4): 1117-1139, 2021 04.
Article in English | MEDLINE | ID: covidwho-1054017

ABSTRACT

Emerging infectious diseases (EIDs) are an increasing threat to public health on a global scale. In recent times, the most prominent outbreaks have constituted RNA viruses, spreading via droplets (COVID-19 and Influenza A H1N1), directly between humans (Ebola and Marburg), via arthropod vectors (Dengue, Zika, West Nile, Chikungunya, Crimean Congo) and zoonotically (Lassa fever, Nipah, Rift Valley fever, Hantaviruses). However, specific approved antiviral therapies and vaccine availability are scarce, and public health measures remain critical. Patients can present with a spectrum of ocular manifestations. Emerging infectious diseases should therefore be considered in the differential diagnosis of ocular inflammatory conditions in patients inhabiting or returning from endemic territories, and more general vigilance is advisable in the context of a global pandemic. Eye specialists are in a position to facilitate swift diagnosis, improve clinical outcomes, and contribute to wider public health efforts during outbreaks. This article reviews those emerging viral diseases associated with reports of ocular manifestations and summarizes details pertinent to practicing eye specialists.


Subject(s)
Communicable Diseases, Emerging/diagnosis , Eye Infections, Viral/diagnosis , Virus Diseases/diagnosis , Animals , Arthropod Vectors , Communicable Diseases, Emerging/epidemiology , Disease Outbreaks , Eye Infections, Viral/epidemiology , Humans , RNA Viruses/pathogenicity , Viral Zoonoses , Virus Diseases/epidemiology
9.
J Med Virol ; 93(4): 1843-1846, 2021 04.
Article in English | MEDLINE | ID: covidwho-971501

ABSTRACT

In this commentary, we shed light on the role of the mammalian target of rapamycin (mTOR) pathway in viral infections. The mTOR pathway has been demonstrated to be modulated in numerous RNA viruses. Frequently, inhibiting mTOR results in suppression of virus growth and replication. Recent evidence points towards modulation of mTOR in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We discuss the current literature on mTOR in SARS-CoV-2 and highlight evidence in support of a role for mTOR inhibitors in the treatment of coronavirus disease 2019.


Subject(s)
COVID-19/drug therapy , RNA Viruses/physiology , SARS-CoV-2/physiology , TOR Serine-Threonine Kinases/antagonists & inhibitors , Animals , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/virology , Humans , Middle East Respiratory Syndrome Coronavirus/genetics , Middle East Respiratory Syndrome Coronavirus/pathogenicity , Middle East Respiratory Syndrome Coronavirus/physiology , RNA Viruses/genetics , RNA Viruses/pathogenicity , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Signal Transduction/drug effects , TOR Serine-Threonine Kinases/metabolism , Virus Replication
10.
Viruses ; 12(12)2020 12 06.
Article in English | MEDLINE | ID: covidwho-967147

ABSTRACT

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.


Subject(s)
Computational Biology , RNA Viruses/genetics , Virology , COVID-19 , Congresses as Topic , Evolution, Molecular , Genome, Viral , Humans , Metagenomics , RNA Viruses/pathogenicity
11.
J Neurovirol ; 26(6): 929-940, 2020 12.
Article in English | MEDLINE | ID: covidwho-871580

ABSTRACT

The emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing global health crises. Children can be infected, but are less likely to develop severe neurological abnormalities compared with adults. However, whether SARS-CoV-2 can directly cause neurological impairments in pediatric patients is not known. The possible evolutionary and molecular relationship between SARS-CoV-2 and non-segmented RNA viruses were examined with reference to neurological disorders in pediatric patients. SARS-CoV-2 shares similar functional domains with neuroinvasive and neurotropic RNA viruses. The Spike 1 (S1) receptor binding domain and the cleavage sites at S1/S2 boundary are less conserved compared with the S2 among coronaviruses.


Subject(s)
COVID-19 , Nervous System Diseases/virology , RNA Viruses/genetics , SARS-CoV-2/genetics , Child , Child, Preschool , Computational Biology , Female , Humans , Infant , Male , Phylogeny , RNA Viruses/pathogenicity , Spike Glycoprotein, Coronavirus , Virulence
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