An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020)

Holland, La Rinda A.; Kaelin, Emily A; Maqsood, Rabia; Estifanos, Bereket; Wu, Lily I.; Varsani, Arvind; Halden, Rolf U.; Hogue, Brenda G.; Scotch, Matthew; Lim, Efrem S.

doi:10.1128/jvi.00711-20

Cited by 137 publications

(122 citation statements)

References 18 publications

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“…To this regard, we note that the two common endemic human coronaviruses, HCoV-OC43 [33] and HCoV-299E [34], have extensive deletions in the C-terminal region of nsp1. Thought crystallization and biological data are needed to con rm our hypothesis, our observations, together with the recent ndings of two viral strains carrying in one case an extensive deletion in the orf7a gene [35] and in the other case a deletion in the nsp2 gene [36], indicate that SARS-CoV-2 genome may be undergoing a signi cant evolutionary process, which may result in virus -host adaptation [37]. Since the overwhelming majority of genomic sequences collected so far are from symptomatic subjects, it seems logical to characterize in detail SARS-CoV-2 genomes from the asymptomatic population.…”

Section: Discussionsupporting

confidence: 61%

Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1

Benedetti

Snyder²,

Giovanetti

et al. 2020

Preprint

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Background:The new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was ﬁrst detected in Wuhan (China) in December of 2019 is responsible for the current global pandemic.Phylogenetic analysis revealed that it is similar to other betacoronaviruses, such as SARS-CoV and Middle-Eastern Respiratory Syndrome, MERS-CoV. Its genome is ∼30 kb in length and contains two large overlapping polyproteins, ORF1a and ORF1ab that encode for several structural and non-structural proteins. The non-structural protein 1 (nsp1) is arguably the most important pathogenic determinant, and previous studies on SARS-CoV indicate that it is both involved in viral replication and hampering the innate immune system response. Detailed experiments of site-specific mutagenesis and in vitro reconstitution studies determined that the mechanisms of action are mediated by i) the presence of specific amino acid residues of nsp1 and b) the interaction between the protein and the host’s small ribosomal unit. In fact, substitution of certain amino acids resulted in reduction of its negative effects.Methods: A total of 17928 genome sequences were obtained from the GISAID database (December 2019 to July 2020) from patients infected by SARS-CoV-2 from different areas around the world. Genomes alignment was performed using MAFFT (REFF) and the nsp1 genomic regions were identified using BioEdit and verified using BLAST. Nsp1 protein of SARS-CoV-2 with and without deletion have been subsequently modelled using I-TASSER.Results: We identified SARS-CoV-2 genome sequences, from several Countries, carrying a previously unknown deletion of 9 nucleotides in position 686-694, corresponding to the AA position 241-243 (KSF). This deletion was found in different geographical areas. Structural prediction modelling suggests an effect on the C-terminal tail structure.Conclusions: Modelling analysis of a newly identified deletion of 3 amino acids (KSF) of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for regulation of viral replication and negative effect on host’s gene expression. In addition, substitution of the two amino acids (KS) from nsp1 of SARS-CoV was previously reported to revert loss of interferon-alpha expression. The deletion that we describe indicates that SARS-CoV-2 is undergoing profound genomic changes. It is important to: i) confirm the spreading of this particular viral strain, and potentially of strains with other deletions in the nsp1 protein, both in the population of asymptomatic and pauci-symptomatic subjects, and ii) correlate these changes in nsp1 with potential decreased viral pathogenicity.

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Section: Discussionsupporting

confidence: 61%

Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1

Benedetti

Snyder²,

Giovanetti

et al. 2020

Preprint

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“…Arizona State University genome sequencing. SARS-CoV-2 genomes were sequenced from nasopharyngeal swabs as previously described (35). Briefly, total nucleic acid was extracted using the bioMérieux eMAG platform.…”

Section: Methodsmentioning

confidence: 99%

An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona

Ladner

Larsen

Bowers

et al. 2020

mBio

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In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, the Arizona Department of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona. Phylogenetic analysis of 84 genomes from across Arizona revealed a minimum of 11 distinct introductions inferred to have occurred during February and March. We show that >80% of our sequences descend from strains that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related case in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020. IMPORTANCE As the COVID-19 pandemic swept across the United States, there was great differential impact on local and regional communities. One of the earliest and hardest hit regions was in New York, while at the same time Arizona (for example) had low incidence. That situation has changed dramatically, with Arizona now having the highest rate of disease increase in the country. Understanding the roots of the pandemic during the initial months is essential as the pandemic continues and reaches new heights. Genomic analysis and phylogenetic modeling of SARS-COV-2 in Arizona can help to reconstruct population composition and predict the earliest undetected introductions. This foundational work represents the basis for future analysis and understanding as the pandemic continues.

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“…SARS-CoV-2 WGS also allowed to explore lineage transmission and might be useful to assess the effectiveness of intervention measures (5)(6)(7)(8). Furthermore SARS-CoV-2 genomic surveillance allowed the characterization of some mutations for which the impact on virulence and transmissibility needs to be confirmed (9)(10)(11). SARS-CoV-2 WGS is performed at an unprecedented rate worldwide with the use of very diverse Next Generation Sequencing (NGS) methods.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

Charre¹,

Ginevra²,

Sabatier³

et al. 2020

Preprint

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Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialized kits including a hybridization capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP) and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples, with mNGS and RVOP producing the most complete genomes. For mid viral loads, 2/8 and 1/8 genomes were incomplete (<99%) with mNGS and both CleanPlex and RVOP, respectively. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques yielding complete genomes for 7/8 samples. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in two samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34-nt deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a default of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer annealing or probe-hybridizing regions and would require regular updates of the technique according to SARS-CoV-2 evolution.

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An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020)

Cited by 137 publications

References 18 publications

Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1

Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1

An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

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