Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs

Kern, David; Sorum, Ben; Mali, Sonali; Hoel, Christopher; Sridharan, Savitha; Remis, Jonathan; Toso, Daniel B.; Kotecha, Abhay; Bautista, Diana M.; Brohawn, Stephen G.

doi:10.1101/2020.06.17.156554

Cited by 104 publications

(168 citation statements)

References 78 publications

Supporting

Mentioning

154

Contrasting

Order By: Relevance

“…However, a recent study showed that the mutation Gln57His does not affect the assembly or functional properties of this putative cation channel (Kern et al, 2020). SARS-CoV-2 N protein, a promising drug target for COVID-19, is a multifunctional RNA-binding protein required for RNA transcription and replication in virus.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations

Paul

Jani

Kumar

et al. 2020

Preprint

View full text Add to dashboard Cite

India has become the third worst-hit nation by the COVID-19 pandemic caused by the SARS-CoV-2 virus. Here, we investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in western India, the most affected region of the country. A total of 90 genomes were sequenced. Four nucleotide variants, namely C241T, C3037T, C14408T (Pro4715Leu), and A23403G (Asp614Gly), located at 5'UTR, Orf1a, Orf1b, and Spike protein regions of the genome, respectively, were predominant and ubiquitous (90%). Phylogenetic analysis of the genomes revealed four distinct clusters, formed owing to different variants. The major cluster (cluster 4) is distinguished by mutations C313T, C5700A, G28881A are unique patterns and observed in 45% of samples. We thus report a newly emerging pattern of linked mutations. The predominance of these linked mutations suggests that they are likely a part of the viral fitness landscape. A novel and distinct pattern of mutations in the viral strains of each of the districts was observed. The Satara district viral strains showed mutations primarily at the 3′ end of the genome, while Nashik district viral strains displayed mutations at the 5′ end of the genome. Characterization of Pune strains showed that a novel variant has overtaken the other strains. Examination of the frequency of three mutations i.e., C313T, C5700A, G28881A in symptomatic versus asymptomatic patients indicated an increased occurrence in symptomatic cases, which is more prominent in females. The age-wise specific pattern of mutation is observed. Mutations C18877T, G20326A, G24794T, G25563T, G26152T, and C26735T are found in more than 30% study samples in the age group of 10-25. Intriguingly, these mutations are not detected in the higher age range 61-80. These findings portray the prevalence of unique linked mutations in SARS-CoV-2 in western India and their prevalence in symptomatic patients.

show abstract

Section: Discussionmentioning

confidence: 99%

Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations

Paul

Jani

Kumar

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…ORF3a is an accessory protein of 275 amino acids long. It is a transmembrane protein which can exist in dimeric or tetrameric forms, and are shown to have ion channel activity [52][53][54] . While there are 23 new significant mutations emerged in the second phase, 12 mutations that are significant in the first phase are not seen in the second phase.…”

Section: Q57h and G251v Are Prominent In Orf3amentioning

confidence: 99%

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

Patro

Sathyaseelan

Uttamrao

et al. 2020

Preprint

View full text Add to dashboard Cite

To accelerate the drug and vaccine development against the severe acute respiratory syndrome virus 2 (SARS-CoV-2), a comparative analysis of SARS-CoV-2 proteome has been performed in two phases by considering manually curated 31389 whole genome sequences from 84 countries. Among the 9 mutations that occur at a high significance (T85I-NPS2, L37F-NSP6, P323L-NSP12, D614G-spike, Q57H-ORF3a, G251V-ORF3a, L84S-ORF8, R203K-nucleocapsid and G204R-nucleocapsid), R203K-nucleocapsid and G204R-nucleocapsid are co-occurring mutations and P323L-NSP12 and D614G-spike often appear simultaneously. Other notable variations that appear with a moderate to low significance are, M85-NSP1 deletion, D268-NSP2 deletion, 112 amino acids deletion in ORF8, a phenylalanine insertion amidst F34-F36 (NSP6) and several co-existing substitution/deletion (I559V & P585S in NSP2, P504L & Y541C in NSP13, G82 & H83 deletions in NSP1 and K141, S142 & F143 deletions in NSP2) mutations. P323L-NSP12, D614G-spike, L37F-NSP6, L84S-ORF8 and the sequences deficient of the high significant mutations has led to 4 major SARS-CoV-2 clades. The top 5 countries bearing all the high significant and majority of the moderate significant mutations are: USA, England, Wales, Australia and Scotland. Further, the majority of the significant mutations has evolved in the first phase and has already transmitted around the globe indicating the positive selection pressure. Among the 26 SARS-CoV-2 proteins, nucleocapsid protein, ORF3a, ORF8, RNA dependent RNA polymerase and spike exhibit a higher heterogeneity compared with the rest of the proteins. However, NSP9, NSP10, NSP8, the envelope protein and NSP4 are highly resistant to mutations and can be exploited for drug/vaccine development.

show abstract

“…1.A). All these mutations have been already identified in other studies 8,9,10 , although with different frequencies.…”

Section: Results and Discussion: Mutations Frequency Analysismentioning

confidence: 63%

“…Mutation G25563T produce a Q57H variant of Orf3a (Fig. 7.C) that did not show significant differences in expression, stability, conductance, selectivity or gating behavior 8 . We modelled Q57H mutation and we did not observe differences in the radius of constriction (Fig.…”

Section: G25563tmentioning

confidence: 95%

“…7.A) is required for efficient in vitro and in vivo replication in SARS-CoV 27 , has been implicated in inflammasome activation 28 , apoptosis 29 , necrotic cell death 30 and has been observed in Golgi membranes 31 where pH is slightly acidic 32 . Kern et al 2020 showed that Orf3a preferentially transports Ca +2 or K + ions through a pore (Fig 7.B) of in which one constriction is formed by the side chain of Q57 (Fig.7.C).…”

Section: G25563tmentioning

confidence: 99%

See 1 more Smart Citation

Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases during the Pandemic

Arévalo

Sifuentes

Robles

et al. 2020

Preprint

View full text Add to dashboard Cite

Since the identification of SARS-CoV-2 in December 2019 a large number of SARS-CoV-2 genomes has been sequenced with unprecedented speed around the world and deposited in several databases. This marks a unique opportunity to study how a virus spread and evolve in a worldwide context. However, currently there is not a useful haplotype classification system to help tracking the virus evolution. Here we identified eleven mutations with 10 % or more frequency in a data set of 7848 genomes. Using these mutations, we identified 6 SARS-CoV-2 haplotypes or OTUs (Operational Taxonomic Unit) that correlate well with a phylogenomic tree. After that, we analyzed the geographical and temporal distribution of these OTUs, as well as their correlation with patient status. Our geographical analysis showed different OTUs prevalence between continents and the temporal distribution analysis revealed an evolution-like pattern in SARS-CoV-2. Finally, we observed a homogenous distribution of OTUs in mild and severe patients and a great prevalence of OTU 2 in asymptomatic patients. However, genomes in the asymptomatic category, comes from isolates on three consecutive days in February (15 to 17), weakening this observation and highlighting the need to increase genomic analyzes in asymptomatic and severe patients. Our classification system is phylogenetically consistent and allows us to easily track geographic and temporal distribution of important mutations around the world. In the next months, it could be updated using similar steps that we used here.

show abstract

Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs

Cited by 104 publications

References 78 publications

Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations

Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases during the Pandemic

Contact Info

Product

Resources

About