An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)

Holland, LaRinda 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:10.1101/2020.04.17.20069641

Cited by 32 publications

(26 citation statements)

References 15 publications

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“…Furthermore, several deletion mutations in ORF7a and ORF8 have also been observed in the analysis which have greater impact on viral host adaptation followed by transmission and replication ( Su et al, 2020 ). A recent study by Holland et al (2020) has also found this type of mutation in the circulating strain in Arizona which is also supported by another study conducted by Su et al in 2020 and Parvez et al in 2020. In addition, the 382-nucleotide deletion was also reported spanning from downstream of ORF7b to the ORF8 region by Liu et al in 2020 which have an impact of enhanced transcription of the subsequent N protein ( Su et al, 2020 ).…”

Section: Discussionsupporting

confidence: 71%

Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh

Saha

Hossain

2020

Gene Reports

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new strain of beta coronavirus that has spread worldwide within a short period of time and has been responsible for the current COVID-19 pandemic. This novel virus shows high transmission and adaptability frequency into the host with rapid changes in genomic sequences. In this study, we analyzed the complete genome of 41 strains isolated in Bangladesh to understand the evolutionary route and genetic variations of this rapidly evolving virus. The phylogenetics, parsimony informative sites and mutation analyses were performed using MEGA X, Multiple sequence alignment program (MAFFT), and Virus Pathogen Resource. The phylogenetic analysis of the studied genomes along with the reference genome suggested that the viral strains found in Bangladesh might be coming from multiple countries such as France, Germany, India, the USA, and Brazil. After entering into the country, intra-cluster and inter-cluster began to circulate in the 8 individual divisions of Bangladesh. We also identified 26 parsimony-informative sites along with the 9 most important sites for virus evolution. Genome-wide annotations revealed 256 mutations, of which 10 were novel (NSP3, RdRp, Spike) in Bangladeshi strains where I120F(NSP2), P323L(RdRp), D614G (Spike), R203K, G204R(N) are the most prominent. Most importantly, numerous mutations were flourishing in the N protein gene (67) followed by S (45), RdRp (38), NSP2 (34), NSP3 (20), and ORF8 (6) gene. Moreover, nucleotide deletion analysis found nine deletions throughout the genomes including in ORF7a (8), ORF8 (1) with one insertion (G) at 265 positions in only one genome. The underlying mechanism of disease severity, molecular evolution, and epidemiology lie in genomic sequences that are not fully understood yet. Identification of the evolutionary history, parsimony-informative sites and others genetic variations of this deadly virus will facilitate the development of new strategies to control the local transmission and provide deep insight in the identification of potential therapeutic targets for controlling COVID-19.

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Section: Discussionsupporting

confidence: 71%

Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh

Saha

Hossain

2020

Gene Reports

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“…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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“…Three deletion events in the SARS-CoV-2 genome have been reported so far. Deletions in the region spanning ORFs 7a and 7b were detected during a surveillance program in Arizona, USA from among the samples screened in the week of 16–19 March 2020 [ 45 ]. This 81 nucleotide deletion, leading to a 27 amino-acid in-frame deletion in one of the genomes AZ-ASU2923, maps to the putative signal peptide and first two beta strands in the protein structure [ 45 ].…”

Section: Orf8 Subgenomic Mrna8 Stabilitymentioning

confidence: 99%

SARS-CoV-2 ORF8 and SARS-CoV ORF8ab: Genomic Divergence and Functional Convergence

et al. 2020

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The COVID-19 pandemic, in the first seven months, has led to more than 15 million confirmed infected cases and 600,000 deaths. SARS-CoV-2, the causative agent for COVID-19, has proved to be a great challenge for its ability to spread in asymptomatic stages and the diverse disease spectrum it has generated. This has created a challenge of unimaginable magnitude, not only affecting human health and life but also potentially generating a long-lasting socioeconomic impact. Both medical sciences and biomedical research have also been challenged, consequently leading to a large number of clinical trials and vaccine initiatives. While known proteins of pathobiological importance are targets for these therapeutic approaches, it is imperative to explore other factors of viral significance. Accessory proteins are one such trait that have diverse roles in coronavirus pathobiology. Here, we analyze certain genomic characteristics of SARS-CoV-2 accessory protein ORF8 and predict its protein features. We have further reviewed current available literature regarding its function and comparatively evaluated these and other features of ORF8 and ORF8ab, its homolog from SARS-CoV. Because coronaviruses have been infecting humans repeatedly and might continue to do so, we therefore expect this study to aid in the development of holistic understanding of these proteins. Despite low nucleotide and protein identity and differentiating genome level characteristics, there appears to be significant structural integrity and functional proximity between these proteins pointing towards their high significance. There is further need for comprehensive genomics and structural-functional studies to lead towards definitive conclusions regarding their criticality and that can eventually define their relevance to therapeutics development.

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An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)

Cited by 32 publications

References 15 publications

Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh

Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh

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

SARS-CoV-2 ORF8 and SARS-CoV ORF8ab: Genomic Divergence and Functional Convergence

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