Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

Khan, Kashif Aziz; Cheung, Peter Pak-Hang

doi:10.1098/rsos.200636

Cited by 102 publications

(150 citation statements)

References 77 publications

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“…So diagnosis of the SARS-CoV-2 might be hampered by any kind of influential changes in targeted genes ( Khailany et al, 2020 ). In our study among all the studied genomic diagnostic assay, 5 sets of genomic diagnostic assay contain the mismatches in the targeted genomic portion which is partially supported by the study of Khan and Cheung (2020) who reported mismatches in 7 sets of genomic diagnostic assay out of 27 studied assays (Supplementary Table 2) which could affect the diagnostic procedure in Bangladesh. Therefore, mutation profiles of the circulating SARS-CoV-2 isolates in the country should be taken into account.…”

Section: Discussionsupporting

confidence: 70%

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: 70%

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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“…The latter is part of the China Centers for Disease Control and Prevention (CDC) protocol with variants in 1.117% in genomes from Kerala. We have earlier reported variants in this primer site in 39.5% of the genomes from India [11] and 18.8% [56] of global genomes. This information would be potentially valuable for laboratories in selecting reagents for screening and diagnosis.…”

Section: Discussionmentioning

confidence: 99%

Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions

Radhakrishnan

Divakar

Jain

et al. 2020

Preprint

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Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala.

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“…Next, we estimated the genetic complexity (S Finally, we analyzed the potential impact of iSNVs and SNPs on the probes and primers used for detection of SARS-CoV-2 (15,28). To evaluate this, we downloaded the set of probes and primers sequences available at the WHO website, as well as the Arctic primers.…”

Section: Intrahost Single Nucleotide Variant (Isnv) Landscapementioning

confidence: 99%

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

Sapoval¹,

Liu²,

Wang³

et al. 2020

Preprint

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The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.

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Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

Cited by 102 publications

References 77 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

Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

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