Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein

SARS-CoV-2 variants have become a major virological, epidemiological and clinical concern, particularly with regard to the risk of escape from vaccine-induced immunity. Here we describe the emergence of a new variant. For twelve SARS-CoV-positive patients living in the same geographical area of southeastern France, qPCR testing that screen for variant-associated mutations showed an atypical combination. The index case returned from a travel in Cameroon. The genomes were obtained by next-generation sequencing with Oxford Nanopore Technologies on GridION instruments within approximately 8 h. Their analysis revealed 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions. Fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions are located in the spike protein. This genotype pattern led to create a new Pangolin lineage named B.1.640.2, which is a phylogenetic sister group to the old B.1.640 lineage renamed B.1.640.1. Both lineages differ by 25 nucleotide substitutions and 33 deletions. The mutation set and phylogenetic position of the genomes obtained here indicate based on our previous definition a new variant we named 'IHU'. These data are another example of the unpredictability of the emergence of SARS-CoV-2 variants, and of their introduction in a given geographical area from abroad.

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The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh

10.1101/2020.07.29.226555 ◽

2020 ◽

Author(s):

Abu Sayeed Mohmmad Mahmud ◽

Tarannum Taznin ◽

Md. Murshed Hasan Sarkar ◽

Mohammad Samir Uzzaman ◽

Eshrar Osman ◽

...

Keyword(s):

Amino Acid ◽

Mutation Rate ◽

Local Environment ◽

Spike Protein ◽

Amino Acid Substitutions ◽

List Type ◽

Nucleotide Substitutions ◽

Disease Manifestation ◽

Entire Genome ◽

Nucleotide Mutation

AbstractGenomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions, especially in target proteins, mutation events per samples, mutation rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between the 10th of May 2020 and the 27th of June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in non-synonymous 274 amino acid substitutions in 22 different proteins were detected with nucleotide mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-like protease (nsp3). Although no mutations were found in nsp7, nsp9, nsp10, and nsp11, yet orf1ab accounts for 56% of total mutations. Among the structural proteins, the highest non-synonymous amino acid substitution (at 36 positions) observed in spike proteins, in which 9 unique locations were detected relative to the global strains, including 516E>Q in the boundary of the ACE2 binding region. The most dominated variant G614 (95%) based in spike protein is circulating across the country with co-evolving other variants including L323 (94%) in RNA dependent RNA polymerase (RdRp), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2. These variants are mostly seen as linked mutations and are part of a haplotype observed in Europe. Data suggest effective containment of clade G strains (4.8%) with sub-clusters GR 82.4%, and GH clade 6.4%.HighlightsWe have sequenced 137 and analyzed 184 whole-genomes sequences of SARS-CoV-2 strains from different divisions of Bangladesh.A total of 634 mutation sites across the SARS-CoV-2 genome and 274 non-synonymous amino acid substitutions were detected.The mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year.Nine unique variants were detected based on non-anonymous amino acid substitutions in spike protein relative to the global SARS-CoV-2 strains.

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Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells

PLoS ONE ◽

10.1371/journal.pone.0006130 ◽

2009 ◽

Vol 4 (7) ◽

pp. e6130 ◽

Cited By ~ 22

Author(s):

Yoshiyuki Yamada ◽

Xiao Bo Liu ◽

Shou Guo Fang ◽

Felicia P. L. Tay ◽

Ding Xiang Liu

Keyword(s):

Amino Acid ◽

Cell Fusion ◽

Cultured Cells ◽

Spike Protein ◽

Amino Acid Substitutions ◽

Fusion Activity ◽

Cell Cell

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In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2–Spike RBD Interface

International Journal of Molecular Sciences ◽

10.3390/ijms22041695 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1695

Author(s):

Bruno O. Villoutreix ◽

Vincent Calvez ◽

Anne-Geneviève Marcelin ◽

Abdel-Majid Khatib

Keyword(s):

Amino Acid ◽

South African ◽

In Silico ◽

Neutralizing Antibodies ◽

Viral Escape ◽

Spike Protein ◽

Amino Acid Substitutions ◽

The South ◽

African Strain ◽

The Uk

SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells. It has been reported that the UK and South African strains may have higher transmission capabilities, eventually in part due to amino acid substitutions on the SARS-CoV-2 Spike protein. The pathogenicity seems modified but is still under investigation. Here we used the experimental structure of the Spike RBD domain co-crystallized with part of the ACE2 receptor, several in silico methods and numerous experimental data reported recently to analyze the possible impacts of three amino acid replacements (Spike K417N, E484K, N501Y) with regard to ACE2 binding. We found that the N501Y replacement in this region of the interface (present in both the UK and South African strains) should be favorable for the interaction with ACE2, while the K417N and E484K substitutions (South African strain) would seem neutral or even unfavorable. It is unclear if the N501Y substitution in the South African strain could counterbalance the K417N and E484K Spike replacements with regard to ACE2 binding. Our finding suggests that the UK strain should have higher affinity toward ACE2 and therefore likely increased transmissibility and possibly pathogenicity. If indeed the South African strain has a high transmission level, this could be due to the N501Y replacement and/or to substitutions in regions located outside the direct Spike–ACE2 interface but not so much to the K417N and E484K replacements. Yet, it should be noted that amino acid changes at Spike position 484 can lead to viral escape from neutralizing antibodies. Further, these amino acid substitutions do not seem to induce major structural changes in this region of the Spike protein. This structure–function study allows us to rationalize some observations made for the UK strain but raises questions for the South African strain.

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Polymorphism in the coding sequence of the horse transferrin gene

Genome ◽

10.1139/g94-020 ◽

1994 ◽

Vol 37 (1) ◽

pp. 157-165 ◽

Cited By ~ 7

Author(s):

Margaret A. Carpenter ◽

Tom E. Broad

Keyword(s):

Amino Acid ◽

Iron Transport ◽

Nucleotide Substitution ◽

Three Dimensional ◽

Sequence Polymorphism ◽

Dimensional Structure ◽

Amino Acid Substitutions ◽

Nucleotide Substitutions ◽

Coding Sequence ◽

Transferrin Gene

Transferrin, the iron transport protein of the blood, is highly polymorphic in many species, including the horse. A number of sequence polymorphisms that distinguish several of the variants of horse transferrin are reported here. Previous studies indicated that exons 12 and 15 were likely to be polymorphic. Sequencing regions of exons 12 and 15 from D and R variants revealed 10 nucleotide substitutions that encoded six amino acid replacements. The F1, F2, H2, and * variants were identical to D, and the O variant was almost identical to R, in the regions studied. The data indicated that the horse transferrin variants make up two distinct groups. The positions of differences between the D and F1 alleles were determined by analyzing single-stranded conformation polymorphisms. Sequencing then revealed three nucleotide substitutions, two of which encoded amino acid substitutions. Location of the eight polymorphic residues on the three-dimensional structure of human lactoferrin revealed that all were clustered at one end of the C-lobe.Key words: sequence polymorphism, transferrin, horse, nucleotide substitution, allele.

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Phylogeny and Polymorphism in the Long Control Region, E6, and L1 of Human Papillomavirus Types 53, 56, and 66 in Central Brazil

International Journal of Gynecological Cancer ◽

10.1097/igc.0b013e318208c73d ◽

2011 ◽

Vol 21 (2) ◽

pp. 222-229 ◽

Cited By ~ 6

Author(s):

Patrícia Soares Wyant ◽

Daniela Marreco Cerqueira ◽

Daniella Sousa Moraes ◽

José Paulo Gagliardi Leite ◽

Cláudia Renata Fernandes Martins ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Genetic Variability ◽

Binding Sites ◽

Long Control Region ◽

Amino Acid Substitutions ◽

Nucleotide Substitutions ◽

Central Brazil ◽

Hpv Types ◽

Genomic Regions

Introduction:Several studies related that different human papillomavirus (HPV) types and intratype variants can present different oncogenic potential. In opposite to HPVs 16 and 18 variants, information about variants of other carcinogenic HPV types is still scarce. The aim of this study was to investigate the genetic variability of HPVs 53, 56, and 66 from Central Brazil isolates.Methods:The long control region (LCR), E6, and L1 genomic regions were amplified and sequenced. We evaluate for nucleotide variations in relation to the reference sequence of each HPV type and also the conservation of physicochemical properties of the deduced amino acid substitutions. In silico analysis was performed to locate binding sites for transcriptional factors within the LCR. Moreover, we performed a phylogenetic analysis with the Central Brazilian and worldwide sequences available at genomic databases.Results:Gathering LCR, E6, and L1 genomic regions, the highest genetic variability was found among HPV-53 isolates with 52 nucleotide variations, followed by HPVs 56 and 66 with 24 and 16 nucleotide substitutions, respectively. The genetic analysis revealed 11 new molecular variants of all HPV types analyzed, totalizing 31 new nucleotide and 3 new amino acid variations. Eight nonconservative amino acid substitutions were detected, which may indicate a biological and pathogenic diversity among HPV types. Furthermore, 8 nucleotide substitutions were localized at putative binding sites for transcription factors in the LCR with a potential implication on viral oncogene expression. The HPVs 53, 56, and 66 phylogenetic analysis confirmed a dichotomic division only described to HPV subtypes and different from the patterns described for HPVs 16 and 18 variants.Conclusions:The high genetic variability observed emphasizes the importance of investigating polymorphisms in types other than HPVs 16 or 18 to better understand the molecular genomic profile of viral infection by different HPV types.

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CRISPR/Cas9-Mediated Multi-Allelic Gene Targeting in Sugarcane Confers Herbicide Tolerance

Frontiers in Genome Editing ◽

10.3389/fgeed.2021.673566 ◽

2021 ◽

Vol 3 ◽

Author(s):

Mehmet Tufan Oz ◽

Angelika Altpeter ◽

Ratna Karan ◽

Aldo Merotto ◽

Fredy Altpeter

Keyword(s):

Amino Acid ◽

Gene Targeting ◽

Crop Improvement ◽

Herbicide Tolerance ◽

Acetolactate Synthase ◽

Amino Acid Substitutions ◽

Dna Double Strand Breaks ◽

Nucleotide Substitutions ◽

Multiple Alleles ◽

Homology Directed Repair

Sugarcane is the source of 80% of the sugar and 26% of the bioethanol produced globally. However, its complex, highly polyploid genome (2n = 100 – 120) impedes crop improvement. Here, we report efficient and reproducible gene targeting (GT) in sugarcane, enabling precise co-editing of multiple alleles via template-mediated and homology-directed repair (HDR) of DNA double strand breaks induced by the programmable nuclease CRISPR/Cas9. The evaluation of 146 independently transformed plants from five independent experiments revealed a targeted nucleotide replacement that resulted in both targeted amino acid substitutions W574L and S653I in the acetolactate synthase (ALS) in 11 lines in addition to single, targeted amino acid substitutions W574L or S653I in 25 or 18 lines, respectively. Co-editing of up to three ALS copies/alleles that confer herbicide tolerance was confirmed by Sanger sequencing of cloned long polymerase chain reaction (PCR) amplicons. This work will enable crop improvement by conversion of inferior alleles to superior alleles through targeted nucleotide substitutions.

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Different Mutations in the Genome-Linked Protein VPg of Potato virus Y Confer Virulence on the pvr23 Resistance in Pepper

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-19-0557 ◽

2006 ◽

Vol 19 (5) ◽

pp. 557-563 ◽

Cited By ~ 86

Author(s):

Valérie Ayme ◽

Sylvie Souche ◽

Carole Caranta ◽

Mireille Jacquemond ◽

Joël Chadœuf ◽

...

Keyword(s):

Amino Acid ◽

Genetic Drift ◽

Potato Virus ◽

High Frequency ◽

Potato Virus Y ◽

Relative Fitness ◽

Amino Acid Substitutions ◽

Nucleotide Substitutions ◽

Single Nucleotide ◽

Pepper Plants

Five different amino acid substitutions in the VPg of Potato virus Y were shown to be independently responsible for virulence toward pvr23 resistance gene of pepper. A consequence of these multiple mutations toward virulence involving single nucleotide substitutions is a particularly high frequency of resistance breaking (37% of inoculated plants from the first inoculation) and suggests a potentially low durability of pvr23 resistance. These five mutants were observed with significantly different frequencies, one of them being overrepresented. Genetic drift alone could not explain the observed distribution of virulent mutants. More plausible scenarios were obtained by taking into account either the relative substitution rates, the relative fitness of the mutants in pvr23 pepper plants, or both.

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Characterization of Chromosome-Mediated BlaOXA-894 in Shewanella xiamenensis Isolated from Pig Wastewater

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph16193768 ◽

2019 ◽

Vol 16 (19) ◽

pp. 3768

Author(s):

Huiyun Zou ◽

Ziyu Zhou ◽

Huiyu Xia ◽

Qian Zhao ◽

Xuewen Li

Keyword(s):

Amino Acid ◽

Rural China ◽

Water Environment ◽

Amino Acid Substitutions ◽

Gene Encoding ◽

Potential Health ◽

Carbapenem Resistant ◽

Gene Environment ◽

New Variant ◽

Its Gene

A new variant of the blaOXA-546 gene, namely blaOXA-894, was identified on the chromosome of Shewanella xiamenensis isolated from pig wastewater in rural China. OXA-894 differs from OXA-546 (A46V, I219del) and OXA-48 (T167I, I219del) with two amino acid substitutions, respectively. The isolate was resistant to ampicillin, aztreonam, imipenem, meropenem and fosfomycin. Carba NP test confirmed S. xiamenensis strain sx20 as a carbapenemase-producer. The blaOXA-894 gene was located between the gene encoding a LysR family transcriptional regulator and the C15 gene. Its gene environment was similar to other S. xiamenensis with chromosome-located blaOXA-48-like genes. The T24H and T94V amino acid substitutions of LuxS protein were predicted to be deleterious, which may affect the virulence phenotype. The occurrence and potential health risk of carbapenem-resistant S. xiamenensis in a water environment is of concern.

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Analysis of the ARTIC version 3 and version 4 SARS-CoV-2 primers and their impact on the detection of the G142D amino acid substitution in the spike protein

10.1101/2021.09.27.461949 ◽

2021 ◽

Author(s):

James Davis ◽

Scott Wesley Long ◽

Paul Christensen ◽

Randall J Olsen ◽

Robert Olson ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Substitution ◽

Drop Out ◽

Spike Protein ◽

Clinical Samples ◽

New Variant ◽

Common Resource ◽

Improved Performance ◽

Primer Sets ◽

Public Repositories

The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses.

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Inactivation of the ampD Gene inPseudomonas aeruginosa Leads to Moderate-Basal-Level and Hyperinducible AmpC β-Lactamase Expression

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.44.3.583-589.2000 ◽

2000 ◽

Vol 44 (3) ◽

pp. 583-589 ◽

Cited By ~ 58

Author(s):

Taimour Yousef Langaee ◽

Luc Gagnon ◽

Ann Huletsky

Keyword(s):

Escherichia Coli ◽

Pseudomonas Aeruginosa ◽

Amino Acid ◽

Genetic Locus ◽

Gene Replacement ◽

Complementation Analysis ◽

Amino Acid Substitutions ◽

Wild Type ◽

Promoter Regions ◽

Nucleotide Substitutions

ABSTRACT It has been shown in enterobacteria that mutations inampD provoke hyperproduction of chromosomal β-lactamase, which confers to these organisms high levels of resistance to β-lactam antibiotics. In this study, we investigated whether this genetic locus was implicated in the altered AmpC β-lactamase expression of selected clinical isolates and laboratory mutants ofPseudomonas aeruginosa. The sequences of theampD genes and promoter regions from these strains were determined and compared to that of wild-type ampD fromP. aeruginosa PAO1. Although we identified numerous nucleotide substitutions, they resulted in few amino acid changes. The phenotypes produced by these mutations were ascertained by complementation analysis. The data revealed that the ampDgenes of the P. aeruginosa mutants transcomplementedEscherichia coli ampD mutants to the same levels of β-lactam resistance and β-lactamase expression as wild-typeampD. Furthermore, complementation of the P. aeruginosa mutants with wild-type ampD did not restore the inducibility of β-lactamase to wild-type levels. This shows that the amino acid substitutions identified in AmpD do not cause the altered phenotype of AmpC β-lactamase expression in the P. aeruginosa mutants. The effects of AmpD inactivation in P. aeruginosa PAO1 were further investigated by gene replacement. This resulted in moderate-basal-level and hyperinducible expression of β-lactamase accompanied by high levels of β-lactam resistance. This differs from the stably derepressed phenotype reported in AmpD-defective enterobacteria and suggests that further change at another unknown genetic locus may be causing total derepressed AmpC production. This genetic locus could also be altered in the P. aeruginosa mutants studied in this work.

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