DNAStringSet alignments can be analysed as codon alignments to look for synonymous and nonsynonymous substitutions in a parallelised fashion. (gwdg.de)
Calculating synonymous (Ks) and nonsynonymous (Ka) substitutions from coding sequences and its ratio Ka/Ks can be used as an indicator of selective pressure acting on a protein. (gwdg.de)
Our findings demonstrate the coexistence of S- gene sequences with and without substitutions (compared to BJ01) in samples analyzed from some patients. (cdc.gov)
As a resource to the community, we provide a database of predictions for all possible human single amino acid substitutions and classify 89% of missense variants as either likely benign or likely pathogenic. (bvsalud.org)
Sequences2
One hundred thirteen sequence variations with nine recur- ples, and a TA-cloning assay was used with direct analysis rent variant sites were identified in analyzed S-gene of reverse transcriptase-polymerase chain reaction (RT- sequences compared with the BJ01 strain of SARS-CoV. (cdc.gov)
Among them, eight variant sites were, we think, the first doc- viously documented S-gene sequences of SARS-CoV. (cdc.gov)
Strain2
1). For the S-gene amplification, 18 pairs of primers were designed by using MacVactor computer software (Accelrys Inc, San Diego, CA) based on the BJ01 strain of SARS-CoV (GenBank accession no. (cdc.gov)
To overcome this barrier, we attempted to isolate the virus from NPMs infected with stHIV-1sv, search for a strain with an adaptive mutation in NPMs, and develop a more appropriate nonhuman primate model of HIV-1. (bvsalud.org)
Clinical2
Viral RNA templates for the S-gene amplifica- tion were directly extracted from raw clinical samples, virus-host interaction and is predicted to be the main target including plasma, throat swab, sputum, and stool, during the of immune response (14). (cdc.gov)
The vast majority of missense variants observed in the human genome are of unknown clinical significance. (bvsalud.org)
Variant1
We present AlphaMissense, an adaptation of AlphaFold fine-tuned on human and primate variant population frequency databases to predict missense variant pathogenicity. (bvsalud.org)
Infection4
Genetic variation in the ovine transmembrane 154 ( TMEM154 ) gene associates with infection susceptibility, and distinct SRLV genetic subgroups infect sheep in association with their TMEM154 diplotypes. (biomedcentral.com)
The past 2 years have witnessed remarkable advances in the development of antiretroviral therapy (ART) for human immunodeficiency virus (HIV) infection, as well as measurement of HIV plasma RNA (viral load) to guide the use of antiretroviral drugs. (cdc.gov)
Recent research advances have afforded substantially improved understanding of the biology of human immunodeficiency virus (HIV) infection and the pathogenesis of the acquired immunodeficiency syndrome (AIDS). (cdc.gov)
S-gene amplification, but only those that generated all six aviruses such as mouse hepatitis virus (MHV) (5,6). (cdc.gov)
1). For the S-gene amplification, 18 pairs of primers were designed by using MacVactor computer software (Accelrys Inc, San Diego, CA) based on the BJ01 strain of SARS-CoV (GenBank accession no. (cdc.gov)
METHODS: We performed single genome amplification of the env gene at three time points during six years in two EC with high intra-host HIV DNA diversity. (bvsalud.org)
Subgroups2
Occasionally, more than one RefSeq record is created in a species to represent different subgroups of the virus (e.g. (nih.gov)
It is also not known if genetic variation in proviral gag and/or env directly causes SRLV subgroups to associate with TMEM154 E35K genotypes, or is in linkage disequilibrium with causal alleles elsewhere in the SRLV genome. (biomedcentral.com)
Genome6
The National Center for Biotechnology Information ( NCBI ) Viral Genome Resource hosts all virus-related data and tools. (nih.gov)
A RefSeq record is created from one of the complete genome sequences for each virus species, and the others are tagged as neighbors to the RefSeq. (nih.gov)
Databases specific to viruses that have a large number of genome sequences generated from sequencing projects are created for easy data retrieval and analyses. (nih.gov)
The genome organization and expression strategy can vary dramatically from virus to virus. (nih.gov)
All these factors contribute to sequence submission errors, such as wrong molecular information, incorrect/missing gene/protein annotation, and chaos of taxonomic assignment in some viral genome sequence records. (nih.gov)
From all complete viral genome sequences (including Viroids), one RefSeq record (or a set of RefSeq records for segmented viruses) is created for each species. (nih.gov)
Dengue3
Serologic evidence for an epizootic dengue virus infecting toque macaques (Macaca sinica) at Polonnaruwa, Sri Lanka. (lookformedical.com)
Humans are the principal reservoir of dengue viruses. (lookformedical.com)
It is unclear if nonhuman primates also serve as a reservoir of human dengue viruses under certain conditions. (lookformedical.com)
Antibodies2
HIV-1 env glycosylation pattern suggests that ancestral and evolving proviruses may display different phenotypes of resistance to broadly neutralising antibodies consistent with persistent immune pressure. (bvsalud.org)
The animal had been reared with her family, and her mother and 2 brothers had antibodies reactive to human T-cell leukemia virus. (lookformedical.com)
Biology1
The article will discuss the molecular biology of mRNA vaccines and underlying anti-virus and anti-tumor mechanisms, with an introduction of their immunological phenomena, delivery strategies, their importance on Corona Virus Disease 2019 (COVID-19) and related clinical trials against cancer and viral diseases. (biomedcentral.com)
Hepatitis2
Serum hepatitis B virus (HBV) RNA is a new serological indicator reflecting viral replication with good clinical application prospects. (bvsalud.org)
This study aimed to clarify the dynamic changes of serum HBV RNA levels and the quasispecies of HBV RNA virus-like particles in nucleos(t)ide analogues (NAs)-experienced chronic hepatitis B (CHB) patients harboring NAs-resistant mutations and their identifiable effects on NAs resistance. (bvsalud.org)
Viral5
Viral RNA templates for the S-gene amplifica- tion were directly extracted from raw clinical samples, virus-host interaction and is predicted to be the main target including plasma, throat swab, sputum, and stool, during the of immune response (14). (cdc.gov)
This overlapping fragments covering the full-length S-gene feature makes viruses highly adaptable and contributes to sequence (see Nested RT-PCR below and Figure 1) were difficulties in preventing and controlling viral disease. (cdc.gov)
BACKGROUND: Elite controllers (EC) are human immunodeficiency virus (HIV)-positive individuals who can maintain low viral loads for extended periods without antiretroviral therapy due to multifactorial and individual characteristics. (bvsalud.org)
FINDINGS: Both EC displayed quite diverse PBMCs-associated viral quasispecies (mean env diversity = 1.9-4.1%) across all time-points comprising both identical proviruses that are probably clonally expanded and unique proviruses with evidence of ongoing evolution. (bvsalud.org)
Multiple virus-oriented vaccines are currently used for routine vaccination, which gains significant progress in preventing and treating viral diseases. (biomedcentral.com)
Protein1
RefSeq records are subjected to curation procedures, which include automated gene locus_tag assignment, validation of molecule information and protein names, and annotation of novel proteins. (nih.gov)
Sequence1
To exclude culture- cloning assay with direct analysis of nested reverse tran- derived artifacts and estimate mutational heterogeneity, scription-polymerase chain reaction products in sequence. (cdc.gov)
Unique1
Viruses are unique compared to other organisms in that there is significant variability in the forms of their genomes-linear or circular, single-stranded or double-stranded, DNA or RNA. (nih.gov)
Analysis1
Specifically, we found that it is possible to identify transmission chains by limiting the analysis of iSNVs to only three well-conserved genes, namely nsp2, ORF3, and ORF7. (bvsalud.org)
History1
In 2006, the FDA approved the first cancer vaccine in human history: A vaccination against cervical cancer (Gardasil). (biomedcentral.com)