¿Cuáles son las mutaciones observadas en el genoma del SARS-CoV-2 y con que frecuencia ocurren?

(What are the observed mutations in the sars-cov-2 genome and how often do the mutations occur?)

Primeras 5 respuestas:

Viruses with RdRp mutation have a median of 3 point mutations [range: 2-5],

Sequence substitutions were characterised by a preponderance of cytidine to uridine (C->U) transitions.

Viruses with RdRp mutation have a median of 3 point mutations [range: 2–5],

2152 mutation sites among different strains were detected which accounted for 7.36% of the complete genome.

Two mutations, 84S in orf8 protein and 251 V in orf3 protein, occurred coincidentally with human intervention.

Viruses with RdRp mutation have a median of 3 point mutations [range: 2-5],

... in RdRp changing its amino acid composition emerged on February 20th, 2020 in Italy (Lombardy). Viruses with RdRp mutation have a median of 3 point mutations [range: 2-5], otherwise they have a median of 1 mutation [range: 0-3] (p value < 0.001). CONCLUSIONS: ...

Ref: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant [J Transl Med, 2020]

Sequence substitutions were characterised by a preponderance of cytidine to uridine (C->U) transitions.

... mutational events within the short evolutionary period following the zoonotic transmission of SARS-CoV-2 into humans. Sequence substitutions were characterised by a preponderance of cytidine to uridine (C->U) transitions. The possibility that the initial diversity within a viral population was largely host-induced would have ...

Ref: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories [bioRxiv, 2020-05-01]

Viruses with RdRp mutation have a median of 3 point mutations [range: 2–5],

... in RdRp changing its amino acid composition emerged on February 20th, 2020 in Italy (Lombardy). Viruses with RdRp mutation have a median of 3 point mutations [range: 2–5], otherwise they have a median of 1 mutation [range: 0–3] (p value < 0.001). CONCLUSIONS: ...

Ref: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant [J Transl Med, 2020-04-22]

2152 mutation sites among different strains were detected which accounted for 7.36% of the complete genome.

... conducted high-resolution analysis of mutations within SARS-CoV-2 genome based on 3240 sequenced strains using BioAider. 2152 mutation sites among different strains were detected which accounted for 7.36% of the complete genome. These mutation sites included 1,335 non-synonymous substitution sites, implying abundant variations in the genome of ...

Ref: Characterization of the substitution hotspots in SARS-CoV-2 genome using BioAider and detection of a SR-rich region in N protein providing further evidence of its animal origin [bioRxiv, 2020-06-05]

Two mutations, 84S in orf8 protein and 251 V in orf3 protein, occurred coincidentally with human intervention.

... and ceased to increase afterwards, demonstrating the effectiveness of social distancing in preventing its spread. Two mutations, 84S in orf8 protein and 251 V in orf3 protein, occurred coincidentally with human intervention. The former first appeared on 1/5/2020 and plateaued around 1/23/2020. The latter rapidly increased in ...

Ref: The origin and underlying driving forces of the SARS-CoV-2 outbreak [J Biomed Sci, 2020-06-07]

The estimated mutation rate suggests that approximately 2 to 6 new mutations will occur each month in a virus assuming the overall uniform mutation rate.

... The estimated mutation rate suggests that approximately 2 to 6 new mutations will occur each month in a virus assuming the overall uniform mutation rate. However, the rate of the non-synonymous substitutions might vary during the course of the SARS-CoV evolution [25] . It was observed that there was an excess of mutations (and amino ...

Ref: Moderate mutation rate in the SARS coronavirus genome and its implications [BMC Evol Biol, 2004-06-28]

Two mutations, 84S in orf8 protein and 251V in orf3 protein, occurred coincidentally with human intervention.

... are needed to trace its evolutionary path and reveal critical steps required for effective spreading. Two mutations, 84S in orf8 protein and 251V in orf3 protein, occurred coincidentally with human intervention. The 84S first appeared on 1/5/2020 and reached a plateau around 1/23/2020, the lockdown of ...

Ref: The origin and underlying driving forces of the SARS-CoV-2 outbreak [bioRxiv, 2020-04-14]

These mutations have been spreading around the world and caused more than 2.5 million of infected cases and 170 thousands of deaths.

... we discovered that the genome of SARS-CoV-2 is changing rapidly from the originally isolated form. These mutations have been spreading around the world and caused more than 2.5 million of infected cases and 170 thousands of deaths. We found that fourteen frequent mutations identified in this study can characterize the six main ...

Ref: Genomic, geographic and temporal distributions of SARS-CoV-2 mutations [bioRxiv, 2020-04-24]

The mutation of C14408T at NSP12 in Indian isolates of SARS-CoV-2 lead to the substitution of proline with threonine.

... with the cofactors NSP7 and NSP8 to form the RNA dependent RNA polymerase (RdRP) complex. The mutation of C14408T at NSP12 in Indian isolates of SARS-CoV-2 lead to the substitution of proline with threonine. The proline residue at position 323 corresponding to the polyprotein results in an unusual turn ...

Ref: Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype [bioRxiv, 2020-06-07]

Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed.

... genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3" end of 4 primers aligned to the third codon position, showed high risk ...

Ref: Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia [Infect Genet Evol, 2020]

The mutations at the tips of the phylogeny were counted only once within each terminal branch.

... of the phylogeny, it is possible to infer the relative mutation stability of diagnostic sites. The mutations at the tips of the phylogeny were counted only once within each terminal branch. Table S1 reports the number of occurrences in both the tree branches and in the ...

Ref: The impact of super-spreaders in COVID-19: mapping genome variation worldwide [bioRxiv, 2020-06-12]

we observed 6,028 positions 78 with substitutions out 29,903 nucleotides in the genome (Fig. 2a ).

... SARS-CoV-2 77 genome as it diversifies across many hosts. As shown in Figure 2 , we observed 6,028 positions 78 with substitutions out 29,903 nucleotides in the genome (Fig. 2a ). Of these, 2,070 positions had 79 more than one independent substitution, 1,858 of which were ...

Ref: SARS-CoV-2 genome evolution exposes early human adaptations [bioRxiv, 2020-05-26]

We found that most isolates reported from India have key mutations at 614th position of the S protein and 84th position of the ORF 8,

... of the world. Most ORFs are highly conserved; mutations were also detected in some ORFs. We found that most isolates reported from India have key mutations at 614th position of the S protein and 84th position of the ORF 8, which has been reported to be associated with high virulence and high transmission rate. Conclusion ...

Ref: Genome analysis of SARS-CoV-2 isolates occurring in India: Present scenario. [Indian journal of public health, 2020-06-01]

The estimated mutation rate is 1.87 x 10 -6 per nucleotide substitution per site per day (Figure 1 ),

... may be used as a proxy for the mutation rate per site and per day. The estimated mutation rate is 1.87 x 10 -6 per nucleotide substitution per site per day (Figure 1 ), which is expected and in concordance with what has been previously reported for SARS-CoV-1 (0.80 ...

Ref: Population genomics insights into the recent evolution of SARS-CoV-2 [bioRxiv, 2020-04-23]

This mutation rate is usually much higher than the corresponding one of any human host.

... RNA virus with an expected mutation rate similar to other RNA viruses, as discussed above. This mutation rate is usually much higher than the corresponding one of any human host. Therefore, as discussed in a recent paper [43] , any antiviral drug against SARS-CoV-2 would ...

Ref: Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes [Viruses, 2020-04-30]

The “major group” mutations fall in the A2a clade.

... “major group” (52.2%) and the “minor group” (30.4%), harboring four and five co-existing mutations, respectively. The “major group” mutations fall in the A2a clade. All the minor group mutations, except 11083G>T (L37F, NSP6) were unique to the Indian isolates. ...

Ref: The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020 [bioRxiv, 2020-05-26]

Such variants that are significantly high in number and have managed to survive the selection pressure might have important role in virus adaptation and evolution.

... identify possible mutations that might have emerged and propagated in the population in significant fractions. Such variants that are significantly high in number and have managed to survive the selection pressure might have important role in virus adaptation and evolution. Thus, such mutant proteins need to be characterized in depth to understand the role of ...

Ref: Two mutations P/L and Y/C in SARS-CoV-2 helicase domain exist together and influence helicase RNA binding [bioRxiv, 2020-05-15]

Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2.

... emerged independently multiple times (homoplasies), we identify 198 filtered recurrent mutations in the SARS-CoV-2 genome. Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2. Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the ...

Ref: Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 [Infect Genet Evol, 2020]

Mutation A404U introduces a premature stop codon in nsp1 , whereas the remainder are nonsynonymous.

... Histogram of the derived allele frequency of the four most common recurrent with-host protein-coding mutations across 401 samples (bin width=0.01). Mutation A404U introduces a premature stop codon in nsp1 , whereas the remainder are nonsynonymous. ...

Ref: A previously uncharacterized gene in SARS-CoV-2 illuminates the functional dynamics and evolutionary origins of the COVID-19 pandemic [bioRxiv, 2020-05-22]

The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations.

... serves an effective tool for monitoring and tracking the epidemic of pathogenic viruses in their global and local genetic variations. The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations. These mutations are critical for vaccine development in disease control. ...

Ref: Genotyping coronavirus SARS-CoV-2: methods and implications [Genomics, 2020]

Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level,

Ref: Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 [Infect Genet Evol, 2020]

One variant, y24034t, was the result of an ambiguous nucleotide in the reference sequence.

... observed in NR-52282 relative to the clinical isolate genome are shown in Table 2 . One variant, y24034t, was the result of an ambiguous nucleotide in the reference sequence. However, our variant calling methods report a T in this location with no minor variants ...

Ref: A Rare Deletion in SARS-CoV-2 ORF6 Dramatically Alters the Predicted Three-Dimensional Structure of the Resultant Protein [bioRxiv, 2020-06-10]

Altogether, 1,815 non-synonymous mutations were identified that belong to 1,176 genomes from 29 countries.

... Sprotein sequences translated from 2,954 SARS-CoV-2 genomes deposited in GISAID till 6 th April, 2020. Altogether, 1,815 non-synonymous mutations were identified that belong to 1,176 genomes from 29 countries. These mutations fall into 54 distinct types with 26 different amino acid substitutions present in ...

Ref: Structural and Functional Implications of Spike Protein Mutational Landscape in SARS-CoV-2 [bioRxiv, 2020-06-13]

The most abundant SNP mutation in SARS-CoV-2 isolates is (28144T>C) in nsp8 protein,

... Nsp8 has the primase capacity for de novo initiation RNA replication without primers [12] . The most abundant SNP mutation in SARS-CoV-2 isolates is (28144T>C) in nsp8 protein, in which amino acid leucine (L) is mutated to serine (S). Our result is consistent ...

Ref: Genotyping coronavirus SARS-CoV-2: Methods and implications [Genomics, 2020-04-27]

these mutations include 11829 synonymous mutations including 681 synonymous frameshifts and 21701 nonsynonymous mutations including 10 nonsynonymous frameshifts.

... regions. This database incorporated 39920 mutations over 3990 unique positions. According to the translational impact, these mutations include 11829 synonymous mutations including 681 synonymous frameshifts and 21701 nonsynonymous mutations including 10 nonsynonymous frameshifts. Development of SARS-CoV-2 mutation genome browsers is a fundamental step obliging towards the virus surveillance, ...

Ref: COVID-19 Variants Database: A repository for Human SARS-CoV-2 Polymorphism Data [bioRxiv, 2020-06-11]

We have noticed that the mutations 226 have accumulated at a relatively constant rate (Fig 4) .

... genomes of the SARS-CoV-2 virus during the first three months after the 225 emergence of this virus (December 24 to March 25). We have noticed that the mutations 226 have accumulated at a relatively constant rate (Fig 4) . The strains selected at the end of 227 ...

Ref: Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations [bioRxiv, 2020-05-21]

These mutations occur on all of SARS-CoV-2 genes and proteins,

... up to May 1, 2020, which have 5117 single mutations over about 29.8 kilobases (kb). These mutations occur on all of SARS-CoV-2 genes and proteins, indicating alarming impacts on the current efforts in the development of COVID-19 diagnostic tests, prevention ...

Ref: Mutations on COVID-19 diagnostic targets [bioRxiv, 2020-05-05]

Some of these mutations are predicted to have impact on viral and host factors, which might affect transmission and disease severity.

... in the important regions of the viral genome including Spike, RdRP and nucleocapsid coding genes. Some of these mutations are predicted to have impact on viral and host factors, which might affect transmission and disease severity. This preliminary evidence of emergence of multiple subclones of SARS-CoV-2, which might have altered phenotypes, ...

Ref: Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility [J Biosci, 2020-06-04]

Some of the observed AA substitutions in the S binding protein may serve as possible adaptation mutations in humans but more studies are needed to elucidate their function.

... relationship between SARS-CoV-2 and bat SARS-like strains. It also hypothesizes that pangolins might have been possible intermediate hosts of the infection. Some of the observed AA substitutions in the S binding protein may serve as possible adaptation mutations in humans but more studies are needed to elucidate their function. This article is protected by copyright. All rights reserved. ...

Ref: The Novel Coronavirus SARS-CoV-2: From a Zoonotic Infection to Coronavirus Disease-19 (COVID19) [J. med. virol, 2020]

G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein.

... the Spike glycoprotein. Further, our data revealed emergence of novel subclones harbouring nonsynonymous mutations, viz. G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. The N protein mutations reside in the SR-rich region involved in viral capsid formation and ...

Cys155Phe, Met195Val, Arg196Ser, Asp208Asn or Leu209-Pro) [21, 22] .

... mutants that lack sialic acid-binding activity contain single point mutations in the S protein ( Cys155Phe, Met195Val, Arg196Ser, Asp208Asn or Leu209-Pro) [21, 22] . Sialic acid-binding activity might help TGEV to resist detergent-like substances encountered during gastrointestinal passage and ...

Ref: Phylogenomics and bioinformatics of SARS-CoV [Trends Microbiol, 2004-02-04]

One of the two mutations, likely developed within the genome during virus spread, could affect virus intracellular survival.

... change stability analysis suggests both mutations could confer lower stability of the protein structures. INTERPRETATION: One of the two mutations, likely developed within the genome during virus spread, could affect virus intracellular survival. Genome follow-up of SARS-CoV-2 spread is urgently needed in order to identify mutations that could ...

Ref: Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy [J. infect, 2020]

We demonstrated that mutations were detected from samples with viral loads ranging from 8 to half a million copies.

... genome of SARS-CoV-2 can be enriched, sequenced and interrogated for the presence of any mutations. We demonstrated that mutations were detected from samples with viral loads ranging from 8 to half a million copies. For accurate sequencing and phylogenetic studies, a high-depth sequencing in the range of 300K reads ...

Ref: Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing [bioRxiv, 2020-05-18]

Analysis of SARS-WT identified two or three mutations in each genome.

... isolates each for S-ExoN1 and SARS-WT were determined from uncloned RT-PCR products (Table S1 ). Analysis of SARS-WT identified two or three mutations in each genome. In contrast, each of the 10 S-ExoN1 genome sequences contained 12 to 23 non-engineered (secondary) ...

Ref: Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing [PLoS Pathog, 2010-05-06]

A one-base deletion caused a frame-shift mutation in ORF10 of ZXC21 ( Fig. S1 ).

... protein sequence of SARS-CoV-2 ORF8 shared very low similarity with sequences in SARS-CoV and BM48-31, and ORF10 had a premature stop codon in both SARS-CoV and BM48-31 (Fig. S1) . A one-base deletion caused a frame-shift mutation in ORF10 of ZXC21 ( Fig. S1 ). ...

Ref: On the origin and continuing evolution of SARS-CoV-2 [Natl Sci Rev, 2020-03-03]

The trailing mutations never occur in the absence of the leading mutations.

... earlier time point and their presence is a pre-requisite for the development of trailing mutations. The trailing mutations never occur in the absence of the leading mutations. In view of possible sequencing errors, a maximum of 1 appearance of the trailing mutation(s) ...

Ref: Mutation landscape of SARS-CoV-2 reveals three mutually exclusive clusters of leading and trailing single nucleotide substitutions [bioRxiv, 2020-05-12]

Among these mutations, three changes the size of the gene ORF3a.

... to this date, among 2385 genomes, we see 118 different mutations in the ORF3a gene. Among these mutations, three changes the size of the gene ORF3a. Out of three changes, one is with deletion of one codon (MT358717-USA: WA), second with ...

Ref: Molecular conservation and Differential mutation on ORF3a gene in Indian SARS-CoV2 genomes [bioRxiv, 2020-05-17]

these mutations may affect the sensitivity of currently available real-time reverse transcription-polymerase chain reaction (RT-PCR) assays

... increasing number of SARS-CoV-2 viruses with mutations at the primer or probe binding sites, and these mutations may affect the sensitivity of currently available real-time reverse transcription-polymerase chain reaction (RT-PCR) assays targeting the N, E, and ORF1a/b genes. Using sequence-independent single-primer amplification (SISPA) and nanopore whole-genome ...

Ref: Identification of nsp1 gene as the target of SARS-CoV-2 real-time RT-PCR using nanopore whole genome sequencing. [Journal of medical virology, 2020-06-05]

There are 4459 single mutations in 6156 SARS-CoV-2 isolates.

... work, we retrieve and genotype 6156 SARS-CoV-2 isolates from word as of April 24, 2020. There are 4459 single mutations in 6156 SARS-CoV-2 isolates. Based on these mutations, we classify and track the geographical distributions of 6156 genoytype isolates ...

Ref: Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine [Journal of medical virology, 2020-04-29]

we identified a mutation that 25 leads to weaker receptor binding capability,

... the emergence of SARS- Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that 25 leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27 th January 2020 from 26 ...

Ref: Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity [bioRxiv, 2020-04-11]

three unique mutations that showed changes in the secondary structure of the RdRp protein at region of mutation.

... if any, variation between them. We report seven mutations observed in Indian SARS-CoV-2 isolates and three unique mutations that showed changes in the secondary structure of the RdRp protein at region of mutation. We also studied molecular dynamics using normal mode analyses and found that these mutations alter ...

Ref: Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure [bioRxiv, 2020-05-11]

6,028 positions 78 with substitutions out 29,903 nucleotides in the genome (Fig. 2a ).

... genome as it diversifies across many hosts. As shown in Figure 2 , we observed 6,028 positions 78 with substitutions out 29,903 nucleotides in the genome (Fig. 2a ). Of these, 2,070 positions had 79 more than one independent substitution, 1,858 of which were ...

Ref: SARS-CoV-2 genome evolution exposes early human adaptations [bioRxiv, 2020-05-26]

A total of 19 different non-synonymous amino acids substitutions were detected in ORF3a among 537 SARS-CoV-2 strains.

... presence of non-synonymous mutations and polyproline regions. Mutations were correlated with changes in epitope formation. A total of 19 different non-synonymous amino acids substitutions were detected in ORF3a among 537 SARS-CoV-2 strains. G251V was the most common and identified in 9.9% (n=53) of the strains and was ...

Ref: SARS-CoV-2 and ORF3a: Non-Synonymous Mutations and Polyproline Regions [bioRxiv, 2020-03-28]

Thirty-five specific gene mutations were identified by gene alignment.

... the underlying mechanisms, we isolated one strain of SARS-CoV-2 (ZJ01) from a mild COVID-19 patient. Thirty-five specific gene mutations were identified by gene alignment. Further phylogenetic analysis and relative synonymous codon usage heat map results suggested that ZJ01 may ...

Ref: Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site. [Emerging microbes & infections, 2020-06-16]

These mutations change or delete a putative ‘furin-like cleavage site’ in the region connecting the S1 and S2 domains

... E6 cells - SARS-CoV-2 apparently is under strong selection pressure to acquire adaptive mutations in its spike protein gene. These mutations change or delete a putative ‘furin-like cleavage site’ in the region connecting the S1 and S2 domains and result in a very prominent phenotypic change in plaque assays. ...

Ref: SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology [bioRxiv, 2020-04-20]

The mutation occurs due to some errors when copying RNA to a new cell. Mutations are mainly three kinds: Base substitution, Insertion, and Deletion.

... SARS-CoV-2 performs mutation during replication of genomic information [12] . The mutation occurs due to some errors when copying RNA to a new cell. Mutations are mainly three kinds: Base substitution, Insertion, and Deletion. Further, in base substitutions, there are some more divisions: silent, nonsense, missense, and frameshift [13] . Micro-level alteration of mutation ...

Ref: Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model [Chaos Solitons Fractals, 2020-06-13]

Prior mutation analysis has shown that mutating the packaging signals of one segment end leads to decreased packaging of other segments,

... Neuraminidase (NA), a viral surface protein essential for mediating budding of new virions 35 . Prior mutation analysis has shown that mutating the packaging signals of one segment end leads to decreased packaging of other segments, indicating that there is a cooperative mechanism for packaging the IAV genome 18 . Thus, ...

Ref: Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza [bioRxiv, 2020-03-14]

These additional mutations may cause changes in structural conformations and cause a higher binding affinity.

... receptors, there are several mutations that may have strengthened the binding affinity of the surface glycoprotein. Both the predictions and the 3D models reveal additional beta strands and hydrogen bonds. These additional mutations may cause changes in structural conformations and cause a higher binding affinity. ...

Ref: A comparative analysis for SARS-CoV-2 [bioRxiv, 2020-04-08]

The highly frequent SNP mutations might be associated with the changes in transmissibility and virulence of the virus.

... of SARS-CoV-2. This genotyping study discovers a few highly frequent mutations in the SARS-CoV-2 genomes. The highly frequent SNP mutations might be associated with the changes in transmissibility and virulence of the virus. The mutations are located in the S protein, RNA polymerase, RNA primase, and nucleoprotein, which ...

Ref: Genotyping coronavirus SARS-CoV-2: methods and implications [bioRxiv, 2020-03-24]

A hundred fifty-six total variants were found and 116 unique variants as shown in Tables 1 and 2.

... A hundred fifty-six total variants were found and 116 unique variants as shown in Tables 1 and 2. Among the 95 genomes we analyzed, 24 samples did not exhibit any variants except for missing starts and end base pairs. The distinct variants consist of 46 missense, 52 synonymous, ...

Ref: Genomic characterization of a novel SARS-CoV-2 [Gene Rep, 2020-04-16]

H93Y, L127I, W128L, L129F, and W131C.

... conserved (Fig. 2) . Several mutations were identified within this domain in SARS-CoV-2 and included H93Y, L127I, W128L, L129F, and W131C. The sequence alignment of 2,782 SARS-CoV-2 3a proteins revealed a 0.5% (n ϭ 14) prevalence ...

Ref: SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis [mSystems, 2020-05-05]

• Overwhelming mutations or SNPs of SARS-CoV-2 alerts drug treatment options.

... number of mutations and SNPs. • Mutations were found in the ACE2 binding region of SARS-CoV-2 spike glycoprotein. • ORF1ab, ORF8 and spike glycoprotein regions of SARS-CoV-2 are highly mutated. • Overwhelming mutations or SNPs of SARS-CoV-2 alerts drug treatment options. ...

Ref: Overwhelming Mutations or SNPs of SARS-CoV-2: A Point of Caution [Gene, 2020-05-20]

We observe less mutations than those in Fig. 4 due to the smaller database of sequences, but the results are qualitatively very similar.

... the sequences used. Fig. 4 , computed with the sequences submitted to GISAID by 2020-04-30. We observe less mutations than those in Fig. 4 due to the smaller database of sequences, but the results are qualitatively very similar. Figure SI. 3: All dinucleotide forces computed on the whole SARS-CoV-2 genome, without any codon ...

Ref: The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2 [bioRxiv, 2020-06-09]

We do not identify a single recurrent mutation convincingly associated with increased viral transmission.

... recurrent mutations identified within a dataset of over 15,000 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation convincingly associated with increased viral transmission. Instead, recurrent SARS-CoV-2 mutations currently in circulation appear to be either neutral or weakly deleterious. ...

Ref: No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2 [bioRxiv, 2020-05-21]

The mean differences in sidechain properties for observed M pro mutations are summarized in Table 1 .

... The mean differences in sidechain properties for observed M pro mutations are summarized in Table 1 . As observed in the network representation ( Figure 2 ), mutated residues are, on average, larger and more hydrophobic than those they replace. Although substituted residues are on average larger ...

Ref: Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease [bioRxiv, 2020-05-15]

Such mutations will not affect our analysis, provided that they occur outside of the identified epitope regions.

... and as more data is collected, it is expected that additional mutations will be observed. Such mutations will not affect our analysis, provided that they occur outside of the identified epitope regions. If mutations do occur within epitope regions, then these epitopes may be further screened in ...

Ref: Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies [bioRxiv, 2020-02-04]

The most frequent mutation detected so far 67 defines the G clade and causes an aminoacidic change, aspartate (D) or glycine (G),

... clade G, V, and S have emerged, showing 66 a different geographical prevalence [10] . The most frequent mutation detected so far 67 defines the G clade and causes an aminoacidic change, aspartate (D) or glycine (G), at 68 position 614 (D614G) of the viral Spike protein [11] . 69 Continual genomic ...

Ref: coronapp: A Web Application to Annotate and Monitor SARS-CoV-2 Mutations [bioRxiv, 2020-06-01]

Three AA substitutions localized in the S1 portion of the S gene were observed,

... genomes formed a monophyletic cluster, demonstrating that pangolins may be suggested as SARS‐CoV‐2 intermediate hosts. Three AA substitutions localized in the S1 portion of the S gene were observed, some of which have been correlated to structural modifications of the S protein which may ...

Ref: The Novel Coronavirus SARS‐CoV‐2: From a Zoonotic Infection to Coronavirus Disease‐19 (COVID19) [J Med Virol, 2020-05-29]

Potential adaptive mutations in the SARS-CoV-2 genome possibly made it highly pathogenic and difficult for drug and vaccine development [15] .

... newly identified SARS-CoV-2 infection causes severe respiratory illness and resulting in death in comorbid individuals. Potential adaptive mutations in the SARS-CoV-2 genome possibly made it highly pathogenic and difficult for drug and vaccine development [15] . This review provides comprehensive insights into the genome, proteome, structural features of potential drug targets, ...

Ref: Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach [Biochim Biophys Acta Mol Basis Dis, 2020-06-13]

four amino acid mutations are present in RaTG13.

... involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and SARS-CoV-2, but four amino acid mutations are present in RaTG13. Both Pangolin-CoV and RaTG13 lost the putative furin recognition sequence motif at S1/S2 cleavage site ...

Ref: Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak [Curr Biol, 2020]

Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan.

... cell cultures were confluent 3 days after the first blind passage of the sample. Coronavirus was confirmed with spherical particle having a fringe reminiscent of crown on transmission electron microscopy. Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan. ...

Ref: Virus Isolation from the First Patient with SARS-CoV-2 in Korea [J Korean Med Sci, 2020-02-18]

Of the 53 point mutations identified, 29 were missense that resulted in amino acid substitutions.

... insights into the mutant proteins, we characterized amino acid substitutions across the 104 viral genomes. Of the 53 point mutations identified, 29 were missense that resulted in amino acid substitutions. Figure 4 plots the occurrence of these mutations as a function of each viral protein. ...

Ref: Integrated genomic view of SARS-CoV-2 in India [bioRxiv, 2020-06-04]

Only 1,231 (4.19%) showed mutations in two or more sequences ( Figure 1B) .

... isolated from 68 countries ( Figure 1A ) (15) . There were 4,678 polymorphic sites. Only 1,231 (4.19%) showed mutations in two or more sequences ( Figure 1B) . The mean pairwise diversity across genomes was 0.08%, ranging between 0.01% for ORF7b to 0.11% ...

Ref: A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains [bioRxiv, 2020-04-27]

Some of these mutations can lead to novel virotypes, as strongly suggested by the results in Figure 3 .

... established population enlarges, due to the high error rates of viral polymerases [29; 30] . Some of these mutations can lead to novel virotypes, as strongly suggested by the results in Figure 3 . Based on these considerations, it is reasonable to hypothesize that longdistance dispersal constitutes an opportunity ...

Ref: Mega-phylogeny sheds light on SARS-CoV-2 spatial phylogenetic structure [bioRxiv, 2020-06-05]

The major mutations are in the critical proteins, including the S protein, RNA polymerase, RNA primase, and nucleoprotein.

... genotyping analysis provides insights on the frequent mutations that confer fast transmissibility of the virus. The major mutations are in the critical proteins, including the S protein, RNA polymerase, RNA primase, and nucleoprotein. Therefore, these high-frequency SNP mutation sites must be considered when designing a vaccine for preventing ...

Ref: Genotyping coronavirus SARS-CoV-2: methods and implications [bioRxiv, 2020-03-24]

None.

Ref: Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 [J Infect, 2020-03-05]

Forty-two missense mutations were identified in all the major non-structural and structural proteins, except the envelope protein.

... It is interesting that our nucleotide sequence alignment also revealed ninety-three mutations over the entire genomes of SARS-CoV-2 (Table 1) . Forty-two missense mutations were identified in all the major non-structural and structural proteins, except the envelope protein. ...

Ref: Genetic diversity and evolution of SARS-CoV-2 [Infection, Genetics and Evolution, 2020-07-31]

We detected 17 high frequency (>6%) mutations in the 3050 sequences.

... database. After aligned by MAFFT, the mutation patterns were identified by phylogenetic tree analysis. Results: We detected 17 high frequency (>6%) mutations in the 3050 sequences. Based on these mutations, we classed the SARS-CoV-2 into four main groups and 10 subgroups. ...

Ref: Global genetic diversity patterns and transmissions of SARS-CoV-2 [Infection, Genetics and Evolution, 2020-05-08]

A total of 30 datasets (60%) contain at least a single founder mutation and most of the variants are missense (over 63%).

... 2020, we downloaded 50 illumina datasets, mostly from China, USA (WA State) and Australia (VIC). A total of 30 datasets (60%) contain at least a single founder mutation and most of the variants are missense (over 63%). Five-point mutations with clonal (founder) effect were found in USA next-generation sequencing samples. Sequencing samples ...

Ref: Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions [PeerJ, 2020-05-21]

a deletion mutation where Y (tyrosine) at position 144 was absent as compared with the Wuhan and Italian isolates.

... We observed that isolate 29 had two mutations, a deletion mutation where Y (tyrosine) at position 144 was absent as compared with the Wuhan and Italian isolates. Due to deletion of the amino acid residues in position 144 in the protein structure, there is a change in the β ...

Ref: A virus that has gone viral: amino acid mutation in S protein of Indian isolate of Coronavirus COVID-19 might impact receptor binding, and thus, infectivity [Biosci Rep, 2020-05-15]

Based on a systematic evaluation of all possible 3686 future mutations on the S protein receptor-binding domain (RBD),

... SARS-CoV-2 is slightly more infectious than SARS-CoV according to computed S protein-ACE2 binding affinity changes. Based on a systematic evaluation of all possible 3686 future mutations on the S protein receptor-binding domain (RBD), we show that most likely future mutations will make SARS-CoV-2 more infectious. Combining sequence alignment, ...

Ref: Mutations strengthened SARS-CoV-2 infectivity [Biosci Rep, 2020-05-27]

angiotensin converting enzyme-2 (ACE2) 33 polymorphisms and others.

... of these different COVID-19 clinical symptoms between 32 countries might be due to virus mutations, angiotensin converting enzyme-2 (ACE2) 33 polymorphisms and others. 1 In this paper, we will focus on the potential virus mutation 34 hypothesis through ...

Ref: cord_uid y5th0mrf Severe acute respiratory syndrome coronavirus ... y5th0mrf SARS-CoV-2: virus mutations in specific Europe... Name: title, dtype: object [Biosci Rep, cord_uid y5th0mrf 2020 y5th0mrf 2020-05-20 Name: publish_time, dtype: object]

Although eight mutations were detected in glutamate (2432 E), seven of them were synonymous mutations.

... as compared to the whole genome average mutation frequency (Fig. 5B, frequency = 3 .96). Although eight mutations were detected in glutamate (2432 E), seven of them were synonymous mutations. Next, we checked the electrostatic potential pattern in the SARS-CoV-2 SUDcore-like dimer structure. The SARS-CoV-2 ...

Ref: Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 [bioRxiv, 2020-06-05]

all identified mutations 359 are highlighted in red.

... pro template is 358 coloured cyan, the SARS-CoV-2 3CL pro structure is coloured grey, and all identified mutations 359 are highlighted in red. (E) Docking of 5,7,3",4"-tetrahydroxy-2"-(3,3-dimethylallyl) isoflavone 360 inside the receptor-binding site of SARS-CoV-2 3CL pro , ...

Ref: Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants [J Pharm Anal, 2020-03-26]

a 382-nucleotide deletion covering almost the entire ORF8 of SARS-CoV-2 was observed in eight hospitalized patients in Singapore;

... mutations can be interrogated for their effect on viral transmission and disease outcome. For example, a 382-nucleotide deletion covering almost the entire ORF8 of SARS-CoV-2 was observed in eight hospitalized patients in Singapore; virus isolation of the deletion strains has not been reported in the study (Su et ...

Ref: An Infectious cDNA Clone of SARS-CoV-2 [Cell Host Microbe, 2020-04-13]

Overwhelming mutations or SNPs of SARS-CoV-2 alerts drug treatment options.

... of mutations and SNPs. • Mutations were found in the ACE2 binding region of SARS-CoV-2 spike glycoprotein. • ORF1ab, ORF8 and spike glycoprotein regions of SARS-CoV-2 are highly mutated. • Overwhelming mutations or SNPs of SARS-CoV-2 alerts drug treatment options. ...

Ref: Overwhelming Mutations or SNPs of SARS-CoV-2: A Point of Caution [Gene, 2020-05-20]

In this population, the highest frequency variants were in known mutations in the 5'UTR, AA193 protein, RdRp and the spike glycoprotein.

... with confirmed SARS-CoV-2 infection. We identified and diagnosed 192 patients by our in-house qPCR assay. In this population, the highest frequency variants were in known mutations in the 5"UTR, AA193 protein, RdRp and the spike glycoprotein. SARS-CoV-2 transmission within the local community was tracked by integrating mutation data with patient postal ...

Ref: Analysis of SARS-CoV-2 Genomes from Southern California Reveals Community Transmission Pathways in the Early Stage of the US COVID-19 Pandemic [Gene, 2020-06-13]

one of which occurred at residue 501 (N501Y) of RBD in the S protein of SARS-CoV-2.

... sequencing of genes of this mouse-adapted SARS-CoV-2 showed five mutations absent in wild-type human SARS-CoV-2, one of which occurred at residue 501 (N501Y) of RBD in the S protein of SARS-CoV-2. This mutation was predicted to increase binding affinity to mACE2, potentially contributing to broad infectivity ...

Ref: Rapid adaptation of SARS-CoV-2 in BALB/c mice: Novel mouse model for vaccine efficacy [bioRxiv, 2020-05-02]

The analysis unravel various amino acid mutations in the viral proteins

... phylogenetic analysis of SARS-CoV2 isolates to understand discrete mutations that are occurring between patient samples. The analysis unravel various amino acid mutations in the viral proteins which may provide an explanation for varying treatment efficacies of different inhibitory drugs and a ...

Ref: Investigating the genomic landscape of novel coronavirus (2019-nCoV) to identify non-synonymous mutations for use in diagnosis and drug design [J Clin Virol, 2020]

11829 synonymous mutations including 681 synonymous frameshifts and 21701 nonsynonymous mutations including 10 nonsynonymous frameshifts.

... incorporated 39920 mutations over 3990 unique positions. According to the translational impact, these mutations include 11829 synonymous mutations including 681 synonymous frameshifts and 21701 nonsynonymous mutations including 10 nonsynonymous frameshifts. Development of SARS-CoV-2 mutation genome browsers is a fundamental step obliging towards the virus surveillance, ...

Ref: COVID-19 Variants Database: A repository for Human SARS-CoV-2 Polymorphism Data [bioRxiv, 2020-06-11]

We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades.

... we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades. Conclusion The worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment ...

Ref: Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world [bioRxiv, 2020-05-26]

A small number of mutations were observed to rise to high frequencies in both the Ebola and SARS-CoV-1 outbreaks.

... Examples from two previous viral outbreaks demonstrate these factors. A small number of mutations were observed to rise to high frequencies in both the Ebola and SARS-CoV-1 outbreaks. For both viruses, clearly demonstrating a functional effect of the mutations proved difficult, with some counterintuitive observations. The A82V amino acid ...

Ref: No evidence for distinct types in the evolution of SARS-CoV-2 [Virus Evol, 2020-04-30]

Mutations are mainly three kinds: Base substitution, Insertion, and Deletion.

... . The mutation occurs due to some errors when copying RNA to a new cell. Mutations are mainly three kinds: Base substitution, Insertion, and Deletion. Further, in base substitutions, there are some more divisions: silent, nonsense, missense, and frameshift [13] ...

Ref: Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model [Chaos Solitons Fractals, 2020-06-13]

The whole workflow can be completed in as short as 3.5 hours, and all reactions can be done in a simple heating block.

... at a time. NIRVANA uses a newly developed algorithm for on-the-fly data analysis during Nanopore sequencing. The whole workflow can be completed in as short as 3.5 hours, and all reactions can be done in a simple heating block. NIRVANA provides a rapid field-deployable solution of SARS-CoV-2 detection and surveillance of pandemic strains. ...

Ref: Multiplex Isothermal Amplification Coupled with Nanopore Sequencing for Rapid Detection and Mutation Surveillance of SARS-CoV-2 [Chaos Solitons Fractals, 2020-06-14]

At each bootstrap, m mutations were sampled with replacement from the the original set of mutations,

... quantify the uncertainty for the hypothesized transmission links, bootstrapping of the transmission networks was performed. At each bootstrap, m mutations were sampled with replacement from the the original set of mutations, and the mutation tree and the transmission network were constructed using the obtained mutation matrix ...

Ref: Global transmission network of SARS-CoV-2: from outbreak to pandemic [medRxiv, 2020-03-27]

We predicted the T cell epitopes and B cell epitopes that would be lost and gained due to the mutations in each strain.

... evolution. We examined individual mutations in each SARV-CoV-2 isolate with respect to the reference genome. We predicted the T cell epitopes and B cell epitopes that would be lost and gained due to the mutations in each strain. For T cell epitopes, we take a sum of the lost/gained epitopes weighted by the ...

Ref: The immune vulnerability landscape of the 2019 Novel Coronavirus, SARS-CoV-2 [bioRxiv, 2020-03-23]

A 29-nucleotide deletion characteristic of SARS-CoVs has been found in strains isolated at the beginning of the human epidemic.

... as SARS-CoV-related bat viruses were isolated but found to encode divergent ORF8 proteins [48] . A 29-nucleotide deletion characteristic of SARS-CoVs has been found in strains isolated at the beginning of the human epidemic. This deletion splits ORF8 into ORF8a and ORF8b and is thought to be an adaptive ...

Ref: Zoonotic origins of human coronaviruses [Int J Biol Sci, 2020-03-15]

The papain-like protease has the highest number of mutations of 599 while the envelope protein has the lowest number of mutations of 13.

... proteins that occurred in the recorded genomes between January 5, 2020, and April 24, 2020. The papain-like protease has the highest number of mutations of 599 while the envelope protein has the lowest number of mutations of 13. Since the sizes of proteins vary dramatically from 1945 for the papain-like protease to 75 ...

Ref: Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine [Int J Biol Sci, 2020-04-29]

Besides 614G, three more amino acid substitutions were identified in the 251 spike protein (Table 2) .

... illustrating a correlation between the mutation pattern and the phylogenetic tree clades. (Figure 4) . Besides 614G, three more amino acid substitutions were identified in the 251 spike protein (Table 2) . G206A, T951I, G227S, S911F, A1420V, A3995F in ORF1a 252 and V772I, T1238I in Spike protein, ...

Ref: Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey [bioRxiv, 2020-06-10]

Two mutations at 241 and 29742, are in the 5' and 3' untranslated regions (UTRs).

... fact that Nsp14 (proof-reading) does not remove U (the product of cytosine deamination) [57] . Two mutations at 241 and 29742, are in the 5" and 3" untranslated regions (UTRs). Seven mutations are silent point mutations, including 313, 14805, 17247 and 28686, while the others ...

Ref: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting [bioRxiv, 2020-05-16]

C1-UY ancestor likely located in Australia presented one nonsynonymous mutation C3096T

... clusters and genetic differentiation. To further characterize Uruguayan SARS-CoV-2, we identified genetic differences among genomes. C1-UY ancestor likely located in Australia presented one nonsynonymous mutation C3096T which affected the ORF1ab protein (S955L) and genome UY-10 harbored one additional synonymous mutation A29731G. ...

Ref: Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay [bioRxiv, 2020-05-10]

Combined analysis with the frequently mutated residues identified 20 viral variants, among which 12 specific combinations comprised more than 97% of the isolates considered for the analysis.

... mutations across different proteins showed co-occurrence, suggesting their functional cooperation in stability, transmission and adaptability. Combined analysis with the frequently mutated residues identified 20 viral variants, among which 12 specific combinations comprised more than 97% of the isolates considered for the analysis. Analysis of protein structure stability of surface glycoprotein mutants indicated viability of specific variants and ...

Ref: Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission [bioRxiv, 2020-05-04]

The presence of 14 C to T mutations and 8 G to A mutation among the 37 mutations we report

... 2020) . Nonetheless, the specific motifs for APOBEC-mediated editing of virus genomes remain poorly understood. The presence of 14 C to T mutations and 8 G to A mutation among the 37 mutations we report gave us an opportunity to analyse preferences, if any for specific dinucleotide and trinucleotide motifs ...

Ref: Mutation landscape of SARS-CoV-2 reveals three mutually exclusive clusters of leading and trailing single nucleotide substitutions [bioRxiv, 2020-05-12]

All the minor group mutations, except 11083G>T (L37F, NSP6) were unique to the Indian isolates.

... four and five co-existing mutations, respectively. The “major group” mutations fall in the A2a clade. All the minor group mutations, except 11083G>T (L37F, NSP6) were unique to the Indian isolates. Conclusion The study highlights rapidly evolving SARS-CoV-2 virus and co-circulation of multiple clades and sub-clades, ...

Ref: The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020 [bioRxiv, 2020-05-26]

All were present in a small number of the viruses sequenced by us, as well as in a small number of viruses deposited in GISAID.

... oligos from the US CDC tests and two oligos from Corman et al. [9] . All were present in a small number of the viruses sequenced by us, as well as in a small number of viruses deposited in GISAID. In contrast, in the Nucleoprotein-protein assay from the Chinese CDC, we saw that 50 of ...

Ref: Failure of the cobas(R) SARS-CoV-2 (Roche) E-gene assay is associated with a C-to-T transition at position 26340 of the SARS-CoV-2 genome [bioRxiv, 2020-05-03]

These SNPs cause missense mutations in helicase, 3′-5′ exonuclease and ORF8 proteins.

... (22 April 2020) shows allele frequencies of 33-39% of these five SNPs across samples worldwide. These SNPs cause missense mutations in helicase, 3′-5′ exonuclease and ORF8 proteins. In the case of Victoria samples from Australia, founder variants from one up to eleven ...

Ref: Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions [PeerJ, 2020-05-21]

whereas a two-to six-fold increase in mutation frequency was sufficient to cause lethal mutagenesis of poliovirus in cell culture.

... whereas a two-to six-fold increase in mutation frequency was sufficient to cause lethal mutagenesis of poliovirus in cell culture. 7, 8, 16 Moreover, ribavirin is clearly ineffective against mouse-adapted SARS-CoV and appears to exacerbate disease, suggesting that the ExoN activity in wildtype viruses may reduce the efficacy of this ...

Ref: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity [RNA Biology, 2011-03-01]

Detailed investigation on nucleotide substitution unfolded 100 substitutions in the coding region of which 43 were synonymous and 57 were of non-synonymous type.

... clades from Group I to Group V revealed several mutations and concomitant amino acid changes. Detailed investigation on nucleotide substitution unfolded 100 substitutions in the coding region of which 43 were synonymous and 57 were of non-synonymous type. The non-synonymous substitutions resulting into 57 amino acid changes were found to be distributed over ...

Ref: Investigating the genomic landscape of novel coronavirus (2019-nCoV) to identify non-synonymous mutations for use in diagnosis and drug design [bioRxiv, 2020-05-01]

RNA sequencing using NGS in case 1 revealed mutations most consistent with Western European Clade A2a with ORF1a L3606F mutation.

... was detected in lungs, bronchi, lymph nodes, and spleen in both cases using qRT-PCR method. RNA sequencing using NGS in case 1 revealed mutations most consistent with Western European Clade A2a with ORF1a L3606F mutation. CONCLUSIONS: SARS-CoV-2 testing and viral sequencing can be performed from FFPE tissue. Detection and sequencing ...

Ref: Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases [Am. j. clin. pathol, 2020]

They can alter tissue tropism, cross the species barrier and adapt to different epidemiological situations [8] .

... ORF6, ORF7a, ORF7b, ORF8 and ORF10 [5, 6, 7] . SARS-CoV2 has been thought to be evolved due to rapid mutation, and recombination with existing other coronavirus in the body. They can alter tissue tropism, cross the species barrier and adapt to different epidemiological situations [8] . ...

Ref: Molecular conservation and differential mutation on ORF3a gene in Indian SARS-CoV2 genomes [Genomics, 2020-06-12]