scholarly journals On the origin and evolution of SARS-CoV-2

2021 ◽  
Author(s):  
Devika Singh ◽  
Soojin V. Yi
Keyword(s):  
Mammalian Cells ◽  
Genetic Recombination ◽  
Disease Outbreaks ◽  
Purifying Selection ◽  
Host Cells ◽  
Human Populations ◽  
S Protein ◽  
Origin And Evolution ◽  
Multiple Species ◽  
The Impact

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global outbreak of a coronavirus disease (herein referred to as COVID-19). Other viruses in the same phylogenetic group have been responsible for previous regional outbreaks, including SARS and MERS. SARS-CoV-2 has a zoonotic origin, similar to the causative viruses of these previous outbreaks. The repetitive introduction of animal viruses into human populations resulting in disease outbreaks suggests that similar future epidemics are inevitable. Therefore, understanding the molecular origin and ongoing evolution of SARS-CoV-2 will provide critical insights for preparing for and preventing future outbreaks. A key feature of SARS-CoV-2 is its propensity for genetic recombination across host species boundaries. Consequently, the genome of SARS-CoV-2 harbors signatures of multiple recombination events, likely encompassing multiple species and broad geographic regions. Other regions of the SARS-CoV-2 genome show the impact of purifying selection. The spike (S) protein of SARS-CoV-2, which enables the virus to enter host cells, exhibits signatures of both purifying selection and ancestral recombination events, leading to an effective S protein capable of infecting human and many other mammalian cells. The global spread and explosive growth of the SARS-CoV-2 population (within human hosts) has contributed additional mutational variability into this genome, increasing opportunities for future recombination.

scholarly journals Bacteria facilitate viral co-infection of mammalian cells and promote genetic recombination

2017 ◽  
Author(s):  
A.K. Erickson ◽  
P.R. Jesudhasan ◽  
M.J. Mayer ◽  
A. Narbad ◽  
S.E. Winter ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Genetic Recombination ◽  
Enteric Viruses ◽  
Intestinal Bacteria ◽  
Enteric Virus ◽  
Viral Fitness ◽  
Host Cells ◽  
Bacterial Strains ◽  
Viral Recombination ◽  
Viral Genomes

SUMMARYIntestinal bacteria promote infection of several mammalian enteric viruses, but the mechanisms and consequences are unclear. We screened a panel of 41 bacterial strains as a platform to determine how different bacteria impact enteric viruses. We found that most bacterial strains bound poliovirus, a model enteric virus. Given that each bacterium bound multiple virions, we hypothesized that bacteria may deliver multiple viral genomes to a mammalian cell even when very few virions are present, such as during the first replication cycle after inter-host transmission. We found that exposure to certain bacterial strains increased viral co-infection even when the ratio of virus to host cells was low. Bacteria-mediated viral co-infection correlated with bacterial adherence to cells. Importantly, bacterial strains that induced viral co-infection facilitated viral fitness restoration through genetic recombination. Thus, bacteria-virus interactions may increase viral fitness through viral recombination at initial sites of infection, potentially limiting abortive infections.

scholarly journals Evolutionary Origin of SARS-CoV-2 (COVID-19 Virus) and SARS Viruses through the Identification of Novel Protein/DNA Sequence Features Specific for Different Clades of Sarbecoviruses

2020 ◽  
Author(s):  
Radhey S. Gupta ◽  
Bijendra Khadka
Keyword(s):  
Host Cells ◽  
Spike Protein ◽  
The Novel ◽  
Terminal Sequence ◽  
S Protein ◽  
Origin And Evolution ◽  
Novel Interactions ◽  
Surface Loops ◽  
Relationship Of ◽  
Novel Protein

Both SARS-CoV-2 (COVID-19) and SARS coronaviruses (CoVs) are members of the subgenus Sarbecovirus. To understand the origin of SARS-CoV-2 and its relation to other viruses, protein sequences from sarbecoviruses were analyzed to identify conserved inserts or deletions (termed CSIs) demarcating either particular clusters/lineages of sarbecoviruses or those shared by specific lineages shedding light on their interrelationships. We report several clade-specific CSIs in the spike (S) and nucleocapsid (N) proteins that reliably demarcate distinct sarbecoviruses clades providing important insights into the origin and evolution of SARS-CoV-2. Two CSIs in the N-terminal domain (NTD) of S-protein are uniquely shared by SARS-CoV-2, BatCoV-RaTG13 and most pangolin CoVs (SARS-CoV-2r cluster); another CSI supports a closer relationship of SARS-CoV-2 to BatCov-RaTG13. Three additional CSIs in the NTD are specific for two Bat-SARS-like CoVs (viz. CoVZXC21 and CoVZC45; CoVZC cluster) which form an outgroup of the SARS-CoV-2r cluster. Interestingly, one of the pangolin-CoV-MP789 also shares these CSIs but lack the CSIs specific for the SARS-CoV-2r cluster. The N-terminal sequence (aa 1-320) of the S-protein for pangolin-CoV-MP789 shows highest similarity (85.94%) to the CoVZC cluster, while its C-terminal region including the receptor binding domain (RBD) is most similar (97-98% identity) to the SARS-CoV-2 virus. These observations indicate that the spike protein sequence for the strain MP789 is of chimeric origin. Multiple CSIs described here also distinguish two bat SARS-CoVs strains (BM48-31/BGR/2008 and SARS_BtKY72) from all others. Our work also clarifies that two large CSIs (5 aa and 13 aa) found in the RBD of S-protein are mainly specific for the SARS and SARS-CoV-2r clusters of CoVs. The surface loops formed by these CSIs are predicted to be important in the binding of S-protein with the human ACE-2 receptor. Lastly, we have mapped the locations of different CSIs in the structure of the S-protein. These studies reveal that the three CSIs specific for the SARS-CoV-2r cluster form distinct surface-exposed loops/patches on the S-protein. As the surface-exposed loops play important roles in mediating novel interactions, the novel lobes/patches formed by the SARS-CoV-2-specific CSIs in the spike protein are predicted to play important roles in the interaction of this protein with other surface-exposed components in the host cells thereby enhancing the binding/infectivity of this virus to humans.

scholarly journals Purinergic Antagonist Suramin Aggravates Myocarditis and Increases Mortality by Enhancing Parasitism, Inflammation, and Reactive Tissue Damage in Trypanosoma cruzi-Infected Mice

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Rômulo D. Novaes ◽  
Eliziária C. Santos ◽  
Marli C. Cupertino ◽  
Daniel S. S. Bastos ◽  
Andréa A. S. Mendonça ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Tissue Damage ◽  
Mammalian Cells ◽  
Negative Impact ◽  
Purinergic Signaling ◽  
Host Cells ◽  
Antioxidant Defenses ◽  
The Impact

Suramin (Sur) acts as an ecto-NTPDase inhibitor in Trypanosoma cruzi and a P2-purinoceptor antagonist in mammalian cells. Although the potent antitrypanosomal effect of Sur has been shown in vitro, limited evidence in vivo suggests that this drug can be dangerous to T. cruzi-infected hosts. Therefore, we investigated the dose-dependent effect of Sur-based chemotherapy in a murine model of Chagas disease. Seventy uninfected and T. cruzi-infected male C57BL/6 mice were randomized into five groups: SAL = uninfected; INF = infected; SR5, SR10, and SR20 = infected treated with 5, 10, or 20 mg/kg Sur. In addition to its effect on blood and heart parasitism, the impact of Sur-based chemotherapy on leucocytes myocardial infiltration, cytokine levels, antioxidant defenses, reactive tissue damage, and mortality was analyzed. Our results indicated that animals treated with 10 and 20 mg/kg Sur were disproportionally susceptible to T. cruzi, exhibiting increased parasitemia and cardiac parasitism (amastigote nests and parasite load (T. cruzi DNA)), intense protein, lipid and DNA oxidation, marked myocarditis, and mortality. Animals treated with Sur also exhibited reduced levels of nonprotein antioxidants. However, the upregulation of catalase, superoxide dismutase, and glutathione-S-transferase was insufficient to counteract reactive tissue damage and pathological myocardial remodeling. It is still poorly understood whether Sur exerts a negative impact on the purinergic signaling of T. cruzi-infected host cells. However, our findings clearly demonstrated that through enhanced parasitism, inflammation, and reactive tissue damage, Sur-based chemotherapy contributes to aggravating myocarditis and increasing mortality rates in T. cruzi-infected mice, contradicting the supposed relevance attributed to this drug for the treatment of Chagas disease.

scholarly journals Molecular properties and evolutionary origins of a parvovirus-derived myosin fusion gene in guinea pigs

2019 ◽  
Author(s):  
Ignacio Valencia-Herrera ◽  
Eduardo Cena-Ahumada ◽  
Fernando Faunes ◽  
Rodrigo Ibarra-Karmy ◽  
Robert J. Gifford ◽  
...  
Keyword(s):  
Guinea Pig ◽  
Guinea Pigs ◽  
Fusion Gene ◽  
Purifying Selection ◽  
Evolutionary Origins ◽  
Evolutionarily Conserved ◽  
Mammalian Genomes ◽  
Multiple Species ◽  
The Impact

AbstractSequences derived from parvoviruses (familyParvoviridae) are relatively common in animal genomes, but the functional significance of these endogenous parvoviral element (EPV) sequences remains unclear. In this study we use a combination ofin silicoand molecular biological approaches to investigate a fusion gene encoded by guinea pigs (genusCavia) that is partially derived from an EPV. This gene, namedenRep-Myo9, encodes a predicted polypeptide gene product comprising a partialmyosin9 (Myo9)-like gene fused to a 3’ truncated, EPV- encoded replicase. We first examined the genomic and phylogenetic characteristics of the EPV locus that encodes the viral portions ofenRep-Myo9. We show that this locus, named enRep, is specific to guinea pigs and derives from an ancient representative of the parvoviral genusDependoparvovirusthat integrated into the guinea pig germline 22-35 million years ago. Despite these ancient origins, however, the regions of enRep that are incorporated into the coding sequence of theenRep-Myo9gene are conserved across multiple species in the family Caviidae (guinea pigs and cavies) consistent with purifying selection. Using molecular biological approaches, we further demonstrate that: (i)enRep-Myo9mRNA is broadly transcribed in guinea pig cells; (ii) the clonedenRep-Myo9transcript can express a protein of the expected size in guinea pig cellsin vitro, and; (iii) the expressed protein localizes to the cytosol. Our findings demonstrate that, consistent with a functional role, theenRep-Myo9fusion gene is evolutionarily conserved, broadly transcribed, and capable of expressing protein.ImportanceDNA from viruses has been ‘horizontally transferred’ to mammalian genomes during evolution, but the impact of this process on mammalian biology remains poorly understood. The findings of our study indicate that in guinea pigs a novel gene has evolved through fusion of host and virus genes.

scholarly journals Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 880
Author(s):  
Ismail Celik ◽  
Rohitash Yadav ◽  
Zekeriya Duzgun ◽  
Sarah Albogami ◽  
Ahmed M. El-Shehawi ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Experimental Studies ◽  
Point Mutations ◽  
Protein Docking ◽  
Binding Domain ◽  
Host Cells ◽  
Dynamics Simulation ◽  
Receptor Binding Domain ◽  
S Protein ◽  
The Impact

Since the beginning of the coronavirus 19 (COVID-19) pandemic in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving through the acquisition of genomic mutations, leading to the emergence of multiple variants of concern (VOCs) and variants of interest (VOIs). Currently, four VOCs (Alpha, Beta, Delta, and Gamma) and seven VOIs (Epsilon, Zeta, Eta, Theta, Iota, Kappa, and Lambda) of SARS-CoV-2 have been identified in worldwide circulation. Here, we investigated the interactions of the receptor-binding domain (RBD) of five SARS-CoV-2 variants with the human angiotensin-converting enzyme 2 (hACE2) receptor in host cells, to determine the extent of molecular divergence and the impact of mutation, using protein-protein docking and dynamics simulation approaches. Along with the wild-type (WT) SARS-CoV-2, this study included the Brazilian (BR/lineage P.1/Gamma), Indian (IN/lineage B.1.617/Delta), South African (SA/lineage B.1.351/Beta), United Kingdom (UK/lineage B.1.1.7/Alpha), and United States (US/lineage B.1.429/Epsilon) variants. The protein-protein docking and dynamics simulation studies revealed that these point mutations considerably affected the structural behavior of the spike (S) protein compared to the WT, which also affected the binding of RBD with hACE2 at the respective sites. Additional experimental studies are required to determine whether these effects have an influence on drug–S protein binding and its potential therapeutic effect.

scholarly journals The impact of genetic modifiers on variation in germline mutation rates within and among human populations

2021 ◽  
Author(s):  
William R. Milligan ◽  
Guy Amster ◽  
Guy Sella
Keyword(s):  
Genetic Modifier ◽  
Purifying Selection ◽  
Mutation Rates ◽  
Ancestral Population ◽  
Human Populations ◽  
Demographic Model ◽  
Genetic Modifiers ◽  
Genome Wide ◽  
Demographic Processes ◽  
The Impact

AbstractMutation rates and spectra differ among human populations. Here, we examine whether this variation could be explained by evolution at mutation modifiers. To this end, we consider genetic modifier sites at which mutations, “mutator alleles”, increase genome-wide mutation rates and model their evolution under purifying selection due to the additional deleterious mutations that they cause, genetic drift, and demographic processes. We solve the model analytically for a constant population size and characterize how evolution at modifier sites impacts variation in mutation rates within and among populations. We then use simulations to study the effects of modifier sites under a plausible demographic model for Africans and Europeans. When comparing populations that evolve independently, weakly selected modifier sites (2Nes ≈ 1), which evolve slowly, contribute the most to variation in mutation rates. In contrast, when populations recently split from a common ancestral population, strongly selected modifier sites (2Nes ≫ 1), which evolve rapidly, contribute the most to variation between them. Moreover, a modest number of modifier sites (e.g., 10 per mutation type in the standard classification into 96 types) subject to moderate to strong selection (2Nes > 1) could account for the variation in mutation rates observed among human populations. If such modifier sites indeed underlie differences among populations, they should also cause variation in mutation rates within populations and their effects should be detectable in pedigree studies.

scholarly journals Molecular Evolution of SARS-CoV-2 Structural Genes: Evidence of Positive Selection in Spike Glycoprotein

2020 ◽  
Author(s):  
Xiao-Yong Zhan ◽  
Ying Zhang ◽  
Xuefu Zhou ◽  
Ke Huang ◽  
Yichao Qian ◽  
...  
Keyword(s):  
Positive Selection ◽  
Fixed Effects ◽  
Signal Sequence ◽  
Salt Bridge ◽  
Purifying Selection ◽  
Host Cells ◽  
Intragenic Recombination ◽  
S Protein ◽  
Codon Substitution ◽  
Global Pandemic

AbstractSARS-CoV-2 caused a global pandemic in early 2020 and has resulted in more than 8,000,000 infections as well as 430,000 deaths in the world so far. Four structural proteins, envelope (E), membrane (M), nucleocapsid (N) and spike (S) glycoprotein, play a key role in controlling the entry into human cells and virion assembly of SARS-CoV-2. However, how these genes evolve during its human to human transmission is largely unknown. In this study, we screened and analyzed roughly 3090 SARS-CoV-2 isolates from GenBank database. The distribution of the four gene alleles is determined:16 for E, 40 for M, 131 for N and 173 for S genes. Phylogenetic analysis shows that global SARS-CoV-2 isolates can be clustered into three to four major clades based on the protein sequences of these genes. Intragenic recombination event isn’t detected among different alleles. However, purifying selection has conducted on the evolution of these genes. By analyzing full genomic sequences of these alleles using codon-substitution models (M8, M3 and M2a) and likelihood ratio tests (LRTs) of codeML package, it reveals that codon 614 of S glycoprotein has subjected to strong positive selection pressure and a persistent D614G mutation is identified. The definitive positive selection of D614G mutation is further confirmed by internal fixed effects likelihood (IFEL) and Evolutionary Fingerprinting methods implemented in Hyphy package. In addition, another potential positive selection site at codon 5 in the signal sequence of the S protein is also identified. The allele containing D614G mutation has undergone significant expansion during SARS-CoV-2 global pandemic, implying a better adaptability of isolates with the mutation. However, L5F allele expansion is relatively restricted. The D614G mutation is located at the subdomain 2 (SD2) of C-terminal portion (CTP) of the S1 subunit. Protein structural modeling shows that the D614G mutation may cause the disruption of salt bridge among S protein monomers increase their flexibility, and in turn promote receptor binding domain (RBD) opening, virus attachment and entry into host cells. Located at the signal sequence of S protein as it is, L5F mutation may facilitate the protein folding, assembly, and secretion of the virus. This is the first evidence of positive Darwinian selection in the spike gene of SARS-CoV-2, which contributes to a better understanding of the adaptive mechanism of this virus and help to provide insights for developing novel therapeutic approaches as well as effective vaccines by targeting on mutation sites.

scholarly journals Estimating the viral loads of SARS-CoV-2 in the oral cavity when complicated with periapical lesions

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Alaa Muayad Altaie ◽  
Rania Hamdy ◽  
Thenmozhi Venkatachalam ◽  
Rifat Hamoudi ◽  
Sameh S. M. Soliman
Keyword(s):  
Gene Expression ◽  
Lactic Acid ◽  
Oral Cavity ◽  
Viral Infection ◽  
Mammalian Cells ◽  
Host Cells ◽  
Oral Lesions ◽  
Periapical Lesions ◽  
Viral Loads ◽  
The Impact

Abstract Background The oral cavity represents a main entrance of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Angiotensin-converting enzyme 2 (ACE-2), neuropilin-1 (NRP-1), and transmembrane serine protease 2 (TMPRSS2) are essential for the entry of SARS-CoV-2 to the host cells. Both ACE-2 and NRP-1 receptors and TMPRSS2 have been identified in the oral cavity. However, there is limited knowledge about the impact of periapical lesions and their metabolites on the expression of these critical genes. This study aims to measure the impact of periapical lesions and their unique fatty acids (FAs) metabolites on the expression of the aforementioned genes, in addition to interleukin 6 (IL-6) gene and hence SARS-CoV-2 infection loads can be estimated. Methods Gene expression of ACE-2, NRP-1, TMPRSS2, and IL-6 was performed in periapical lesions in comparison to healthy oral cavity. Since FAs are important immunomodulators required for the lipid synthesis essential for receptors synthesis and viral replication, comparative FAs profiling was determined in oral lesions and healthy pulp tissues using gas chromatography–mass spectrometry (GC–MS). The effect of major identified and unique FAs was tested on mammalian cells known to express ACE-2, NRP-1, and TMPRSS2 genes. Results Gene expression analysis indicated that ACE-2, NRP-1, and TMPRSS2 were significantly upregulated in healthy clinical samples compared to oral lesions, while the reverse was true with IL-6 gene expression. Saturated and monounsaturated FAs were the major identified shared and unique FAs, respectively. Major shared FAs included palmitic, stearic and myristic acids with the highest percentage in the healthy oral cavity, while unique FAs included 17-octadecynoic acid in periapical abscess, petroselinic acid and l-lactic acid in periapical granuloma, and 1-nonadecene in the radicular cyst. Computational prediction showed that the binding affinity of identified FAs to ACE-2, TMPRSS2 and S protein were insignificant. Further, FA-treated mammalian cells showed significant overexpression of ACE-2, NRP-1 and TMPRSS2 genes except with l-lactic acid and oleic acid caused downregulation of NRP-1 gene, while 17-octadecynoic acid caused insignificant effect. Conclusion Collectively, a healthy oral cavity is more susceptible to viral infection when compared to that complicated with periapical lesions. FAs play important role in viral infection and their balance can affect the viral loads. Shifting the balance towards higher levels of palmitic, stearic and 1-nonadecene caused significant upregulation of the aforementioned genes and hence higher viral loads. On the other hand, there is a reverse correlation between inflammation and expression of SARS-CoV-2 receptors. Therefore, a mouth preparation that can reduce the levels of palmitic, stearic and 1-nonadecene, while maintaining an immunomodulatory effect can be employed as a future protection strategy against viral infection.

scholarly journals Multi-type branching and graph product theory of infectious disease outbreaks

2020 ◽  
Author(s):  
Alexei Vazquez
Keyword(s):  
Infectious Disease ◽  
Numerical Simulations ◽  
Disease Outbreaks ◽  
Single Equation ◽  
Reproductive Number ◽  
Human Populations ◽  
Crowd Management ◽  
Infectious Disease Outbreaks ◽  
Product Approach ◽  
The Impact

The heterogeneity of human populations is a major challenge to mathematical descriptions of infectious disease outbreaks. Numerical simulations are therefore deployed to account for the many factors influencing the disease spreading dynamics. Yet, the results from numerical simulations are often as complicated as the reality, leaving us with a sense of confusion about how the different factors account for the simulation results. Here, using a multi-type branching together with a graph tensor product approach, I derive a single equation for the effective reproductive number of an infectious disease outbreak. Using this equation I deconvolute the impact of crowd management, contact heterogeneity, testing, vaccination, mask use and smartphone tracing app use. This equation can be used to gain a basic understanding of infectious disease outbreaks and their simulations.

scholarly journals Proteolytic activation of SARS-CoV-2 spike at the S1/S2 boundary: potential role of proteases beyond furin

2020 ◽  
Author(s):  
Tiffany Tang ◽  
Javier A. Jaimes ◽  
Miya K. Bidon ◽  
Marco R. Straus ◽  
Susan Daniel ◽  
...  
Keyword(s):  
Cell Line ◽  
Viral Entry ◽  
Receptor Expression ◽  
Host Cells ◽  
Epithelial Cell Line ◽  
Proteolytic Activation ◽  
S Protein ◽  
Endosomal Membrane ◽  
Bioinformatic Tools ◽  
The Impact

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses its spike (S) protein to mediate viral entry into host cells. Cleavage of the S protein at the S1/S2 and/or S2’ site(s) is associated with viral entry, which can occur at either the cell plasma membrane (early pathway) or the endosomal membrane (late pathway), depending on the cell type. Previous studies show that SARS-CoV-2 has a unique insert at the S1/S2 site that can be cleaved by furin, which appears to expand viral tropism to cells with suitable protease and receptor expression. Here, we utilize viral pseudoparticles and protease inhibitors to study the impact of the S1/S2 cleavage on infectivity. Our results demonstrate that S1/S2 pre-cleavage is essential for early pathway entry into Calu-3 cells, a model lung epithelial cell line, but not for late pathway entry into Vero E6 cells, a model cell line. The S1/S2 cleavage was found to be processed by other proteases beyond furin. Using bioinformatic tools, we also analyze the presence of a furin S1/S2 site in related CoVs and offer thoughts on the origin of the insertion of the furin-like cleavage site in SARS-CoV-2.

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