Abstract：
:Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is recognized as one of the life-threatening viruses causing the most destructive pandemic in this century. The genesis of this virus is still unknown. To elucidate its molecular evolution and regulation of gene expression, the knowledge of codon usage is a pre-requisite. In this study, an attempt was made to document the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SARS-CoV-2 in human and dog. The SARS-CoV-2 genome showed relative abundance of A and U nucleotides and relative synonymous codon usage analysis revealed that the preferred synonymous codons mostly end with A/U. The analysis of ENc-GC3s, Neutrality and Parity rule 2 plots indicated that natural selection and other undefined factors dominate the overall codon usage bias in SARS-CoV-2 whereas the impact of mutation pressure is comparatively minor. The codon adaptation index and relative codon deoptimization index of SARS-CoV-2 deciphered that human is more favoured host for adaptation compared to dog. These results enhance our understanding of the factors involved in evolution of the novel human SARS-CoV-2 and its adaptability in dog.
journal_name
Virus Resjournal_title
Virus researchauthors
Dutta R,Buragohain L,Borah Pdoi
10.1016/j.virusres.2020.198113subject
Has Abstractpub_date
2020-10-15 00:00:00pages
198113eissn
0168-1702issn
1872-7492pii
S0168-1702(20)31020-0journal_volume
288pub_type
杂志文章相关文献
VIRUS RESEARCH文献大全abstract：:Numerous host factors are required for the efficient replication of rotavirus, including the activation and inactivation of several cell signaling pathways. One of the cellular structures that are reorganized during rotavirus infection is the actin cytoskeleton. In this work, we report that the dynamics of the actin m...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2019.01.003
更新日期：2019-04-02 00:00:00
abstract：:The hemagglutinin (HA) protein of influenza virus binds to terminal sialic acid residues present on cell surface glycoproteins and glycolipids. The specific amino acids involved in this interaction have been identified for a H3 subtype HA from the human non-pathogenic virus, A/Aichi/2/68, by both crystallographic and ...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/s0168-1702(01)00407-5
更新日期：2002-02-26 00:00:00
abstract：:Cells susceptible to persistent viral infections undergo important changes in their biological functions as a consequence of the expression of viral gene products that are capable of altering the gene expression profile of the host cell. Previously, we reported that persistence of the RSV genome in a mouse macrophage ...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2017.01.001
更新日期：2017-02-15 00:00:00
abstract：:Typically plasma viremia is controlled in macaques challenged with R5 tropic SHIV162P3 during the chronic phase of infection. However, in a few infected animals it sustains for a prolonged period. Persistent plasma viremia in two such macaques led to a rapid decline of CD4+ T-cells in blood leading to the induction of...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2010.04.006
更新日期：2010-08-01 00:00:00
abstract：:The core proteins of epizootic haemorrhagic disease virus (EHDV) have important roles to perform in maintaining the structure and function of the virus. A complete genetic and phylogenetic analysis was therefore performed on these proteins (and the genes that code for them) to allow comparison of the selective pressur...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2009.07.011
更新日期：2009-11-01 00:00:00
abstract：:Tick-borne encephalitis (TBE) is a serious human neurological disease caused by TBE virus (TBEV). However, the mechanisms of TBEV-caused pathogenesis remain unclear. The endoplasmic reticulum (ER) stress response, also defined as the unfolded protein response (UPR), is an important conserved molecular signaling pathwa...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2013.10.012
更新日期：2013-12-26 00:00:00
abstract：:Human adenoviruses have been used for mammalian expression vectors and recombinant vaccines for heterologous antigens. We constructed and characterized an infectious adenovirus recombinant containing core-E1-E2 genes of hepatitis C virus (HCV). The core protein was produced mainly during the early phase of viral infec...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/s0168-1702(98)00043-4
更新日期：1998-06-01 00:00:00
abstract：:Since wild ducks constitute a vital element in the epizootiology of avian influenza viruses (AIVs) as well as avian paramyxoviruses (APMVs) and play a key role in the ecology and inter-species transmission of these viruses, it is crucial to elucidate the diversity and prevalence of these viruses within these bird popu...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2009.02.018
更新日期：2009-07-01 00:00:00
abstract：:We selected Chinese hamster ovary (CHO) cell-adapted strains of human enterovirus 71 (HEV71) belonging to sub-genogroups B5 (HEV71-B5) and C2 (HEV71-C2) by serial passage in CHO cells at a high multiplicity of infection. During the course of CHO cell passage, virus growth improved significantly, with increasing virus ...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2012.02.009
更新日期：2012-05-01 00:00:00
abstract：:The genetic and antigenic characteristics of the Amur (AMR) and Far East (FE) virus lineages, which are both within the genus Hantavirus, were studied. Representative viruses, H5 and B78 for AMR and Bao 14 for FE, were used. The entire small (S) and medium (M) segments, except for the 3'- and 5'-ends, were sequenced. ...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2003.12.031
更新日期：2004-05-01 00:00:00
abstract：:Although African swine fever virus (ASFV) replicates in viral cytoplasmic factories, the presence of viral DNA within the host cell nucleus has been previously reported to be essential for productive infection. Herein, we described, for the first time, the intranuclear distribution patterns of viral DNA replication ev...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2015.07.006
更新日期：2015-12-02 00:00:00
abstract：:We have previously described the efficient homologous recombination system between 5' subgenomic RNA3a (sgRNA3a) and genomic RNA3 of Brome mosaic virus (BMV) in barley protoplasts (Sztuba-Solińska et al., 2011a). Here, we demonstrated that sequence alterations in the coat protein (CP)-binding cis-acting RNA motifs, th...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2012.10.001
更新日期：2012-12-01 00:00:00
abstract：:Transcription of human immunodeficiency virus (HIV-1) is activated by viral Tat protein which regulates HIV-long terminal repeat (LTR) transcription and elongation. HIV-1 Tat protein is a substrate for the deacetylase activity of sirtuin 1 (SIRT1). Here we investigate the signaling pathway involved in Tat-induced HIV-...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2009.08.005
更新日期：2009-12-01 00:00:00
abstract：:RNA-2 P75 open reading frame sequencing was conducted on BNYVV-infected sugar beet plants originating from 10 Belgian sources and was compared with sequences originating from France, Kazakhstan, Japan and China. This allowed the characterization of types A and B in Belgium. Sequence analysis confirmed that type A is i...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2004.07.007
更新日期：2005-03-01 00:00:00
abstract：:Transmissible spongiform encephalopathies (TSE) are a heterogeneous group of neurodegenerative disorders. The common feature of these diseases is the pathological conversion of the normal cellular prion protein (PrP(C)) into a β-structure-rich conformer-termed PrP(Sc). The latter can induce a self-perpetuating process...
journal_title：Virus research
pub_type： 杂志文章,评审
doi：10.1016/j.virusres.2014.10.020
更新日期：2015-09-02 00:00:00
abstract：:In the past few decades, dengue has spread rapidly and is an emerging disease in China. An unexpected dengue outbreak occurred in Xishuangbanna, Yunnan, China, resulting in 1331 patients in 2013. In order to obtain the complete genome information and perform mutation and evolutionary analysis of causative agent relate...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2017.06.015
更新日期：2017-06-15 00:00:00
abstract：:A comprehensive phylogenetic study based on the hemagglutinin (H) protein of all known African measles virus (MV) isolates is presented. The study includes 64 new H gene sequences from Ghana. Nigeria and South Africa as well as viruses from Zambia and The Gambia for which only incomplete sequencing data were available...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/s0168-1702(99)00072-6
更新日期：1999-07-01 00:00:00
abstract：:Human rabies cases have been on the rise during the past few years in China and a total of 2651 cases were reported in 2004. To better understand the current rabies epidemics in China, we isolated rabies viruses from dogs and humans from five provinces and characterized these isolates genetically by sequencing the ent...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2006.05.010
更新日期：2006-11-01 00:00:00
abstract：:Phylogenetic analysis has been extensively used as a tool for the reconstruction of epidemiological relations for research or for forensic purposes. It was our objective to assess the sensitivity of different phylogenetic methods and various phylogenetic programs to reconstruct epidemiological links among HIV-1 infect...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2012.03.002
更新日期：2012-06-01 00:00:00
abstract：:Reovirus is a gastroenteric virus with a genome that consists of ten segments of double-stranded RNA. The segmented nature of the genome allows for genetic mixing when cells are simultaneously infected with two different viral serotypes. The ability of viral reassortment to take place in asynchronous infections has no...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/s0168-1702(98)00023-9
更新日期：1998-04-01 00:00:00
abstract：:The fidelity of poliovirus RNA-dependent RNA polymerase (3D(pol)) was determined using a system based on the fidelity of synthesis of the alpha-lac gene which codes for a subunit of beta-galactosidase. Synthesis products are screened for mutations by an alpha-complementation assay, in which the protein product from al...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/s0168-1702(00)00256-2
更新日期：2001-04-01 00:00:00
abstract：:The interaction between UV-B irradiation and cutaneous human papillomaviruses (HPV) has been suggested to be of relevance for the development of non-melanoma skin cancers. We investigated the activity within the upstream regulatory region (URR) of the HPV types 8, 38, 92, 93 and 96, as well as their responsiveness to ...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2008.07.013
更新日期：2008-11-01 00:00:00
abstract：:This study reports the detection by RT-PCR and molecular characterization of partial RdRp gene of picobirnavirus (PBV) dsRNA in fecal samples (n = 100) from a meat sheep flock in southern Brazil. The analysis of the results allowed the identification of two important characteristics of PBV infection. The first was the...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2018.06.016
更新日期：2018-08-15 00:00:00
abstract：:We performed phylogenetic and cluster analysis of human rhinovirus species A (HRV-A) isolated from 76 children with acute respiratory infection in Yamagata prefecture, Japan during the period 2003-2007. Phylogenetic trees based on the nucleotide and amino acid sequences of the VP4/VP2 coding region showed that the pre...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2009.11.011
更新日期：2010-02-01 00:00:00
abstract：:The interaction of human adenovirus type 12 (Ad12) with Syrian hamster cells is remarkable in that there is a block of viral DNA replication and late gene transcription. We have screened several cellular factors known to play a role in adenovirus replication for their possible contributions to the interactions of Ad12...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/s0168-1702(01)00242-8
更新日期：2001-12-04 00:00:00
abstract：:PCR amplification of proviral DNA extracted from peripheral blood lymphocytes of three Chinese pigs (Banna minipig inbreed (BMI), Wu-Zhi-Shan pig (WZSP) and Neijiang pig (NJP)), using primers corresponding to highly conserved regions of reverse transcriptase (RT) of pol gene and nucleocapsid sequence of gag gene. PCR ...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2004.05.007
更新日期：2004-10-01 00:00:00
abstract：:Viruses are most frequently discovered because they cause disease. To expand knowledge of plant-associated viruses beyond these narrow constraints, non-cultivated plants of the Tallgrass Prairie of the United States were systematically surveyed for evidence of viruses. This report discusses putative viruses of the fam...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2012.03.016
更新日期：2012-07-01 00:00:00
abstract：:In present study, we report the first complete genomic sequence of pig bovine viral diarrhea (BVD) virus, that of strain ZM-95, which is 12,220 nucleotides long and contains short 5' and 3' non-coding regions and one open reading frame encoding a large polyprotein with 28 potential N-glycosylation sites (Asn-X-Ser or ...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2006.05.005
更新日期：2006-12-01 00:00:00
abstract：:Herein we describe the construction of recombinant human rhinoviruses (rHRVs) encoding HIV Gag or Tat by inserting the full length tat gene or regions of the gag gene flanked by sequences encoding the HRV 2A protease cleavage site into the junction between HRV genes encoding structural (P1) and non-structural (P2) pro...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/j.virusres.2015.04.002
更新日期：2015-05-04 00:00:00
abstract：:The capsid structures of the 7 serotypes of foot-and-mouth disease virus have been compared utilizing a series of neutralizing monoclonal antibodies which were previously shown to recognize at least 4 distinct epitopes on type A12 virus. A radioimmune binding assay using radioactively labeled antigens and the monoclon...
journal_title：Virus research
pub_type： 杂志文章
doi：10.1016/0168-1702(86)90055-9
更新日期：1986-10-01 00:00:00
