The establishment of reference sequence for SARS‐CoV‐2 and variation analysis

Wang, Changtai; Liu, Zhongping; Chen, Zixiang; Huang, Xin; Xu, Mengyuan; He, Tao; Zhang, Zhenhua

doi:10.1002/jmv.25762

Cited by 469 publications

(513 citation statements)

References 24 publications

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“…These results demonstrate the existence of several mutated positions across the genome leading to relatively low percentage of identical sites (62 to 64%). However, the level of genetic diversity is relatively low, as shown by the high percentage of pairwise identity (>99%), suggesting that most mutations only occur in a few genomes, in line with other studies[18][19][20].…”

supporting

confidence: 88%

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CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2

Carneiro¹,

Pereira

2020

Preprint

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The ability to detect the SARS-CoV-2 in a widespread epidemic is crucial for screening of carriers and for the success of quarantine efforts. Methods based on real-time reverse transcription polymerase chain reaction (RT-qPCR) and sequencing are being used for virus detection and characterization. However, RNA viruses are known for their high genetic diversity which poses a challenge for the design of efficient nucleic acid-based assays. The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics.Here we describe the CoV2ID(http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19.The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Updated sequences alignments are used to constantly verify the theoretical efficiency of available testing methods. Detailed information on available detection protocols are also available to help laboratories implementing SARS-CoV-2 testing.

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supporting

confidence: 88%

“…The primer NIID_WH-1_Seq_F519 has a PIS of only 15%, meaning that only 15% of its positions are conserved across all sequences in the alignments. Previous works have already detected polymorphisms in primers and probes that may cause problem when performing the testing [20,21].…”

Section: For Example Primers Niid_wh-1_f24381 and Niid_wh-1_seq_f243mentioning

confidence: 99%

CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2

Carneiro¹,

Pereira

2020

Preprint

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“…Later submissions or the sequences with many undetermined nucleotides (denoted as N) were not considered. 15 Countries those had multiple entries, highest number of entries with whole genome sequence were matched for identifying representative sequence to consider (e.g. for USA, out of 44 submitted complete genomic sequences, the sequence with 29 submissions were of complete genomic sequence with 100% identity and thus one representative sequence was considered for the present study).…”

Section: Methodsologymentioning

confidence: 99%

Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence

Banerjee

Dhar

Bhattacharjee

et al. 2020

Preprint

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Background COVID-19 is a disease with global public health emergency that have shook the world since its' first detection in China in December, 2019. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is the pathogen responsible behind this pandemic. The lethality of different viral strains is found to vary in different geographical locations but the molecular mechanism is yet to be known.Methods Available data of whole genome sequencing of different viral strains published by different countries were retrieved and then analysed using Multiple Sequence Alignment and Pair-wise Sequence Alignment leading to Phylogenetic tree construction. Each location and the corresponding genetic variations were screened in depth. Then the variations are analysed at protein level giving special emphasis on Non Synonymous amino acid substitutions. The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination. FindingsAll the viral strains have been found to evolve from the viral strain of Taiwan (MT192759) which is 100% identical with the ancestor SARS-CoV-2 sequences of Wuhan (NC 045512.2; submitted on 5 th Jan, 2020). Transition from C to T (C>T) is the most frequent mutation in this viral genome and mutations A>T, G>A, T>A are the rarest ones, found in countries with maximum fatality rate i.e Italy, Spain and Sweden. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. The functional effect on the structure and function of the protein can favourably or unfavourably interact with the host body.

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“…This amino acid replacement is present in genomes from the A2a clade, and distinguishes the A2a clade from other SARS-CoV-2 clades. The other amino acid changes in nsp12 were mainly present in single isolates from individual Houston strains, and some have been identified in other strains in the global GISAID collection (23,24). A prominent exception was the identification of 29 strains with a Met600Ile polymorphism.…”

Section: Machine Learning Analysismentioning

confidence: 99%

Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas

Long

Olsen

Christensen

et al. 2020

Preprint

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We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. These genomes were from the viruses causing infections in the earliest recognized phase of the pandemic affecting Houston. Substantial viral genomic diversity was identified, which we interpret to mean that the virus was introduced into Houston many times independently by individuals who had traveled from different parts of the country and the world. The majority of viruses are apparent progeny of strains derived from Europe and Asia. We found no significant evidence of more virulent viral types, stressing the linkage between severe disease, underlying medical conditions, and perhaps host genetics. We discovered a signal of selection acting on the spike protein, the primary target of massive vaccine efforts worldwide. The data provide a critical resource for assessing virus evolution, the origin of new outbreaks, and the effect of host immune response.SignificanceCOVID-19, the disease caused by the SARS-CoV-2 virus, is a global pandemic. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. We identified no evidence that a particular strain or its progeny causes more severe disease, underscoring the connection between severe disease, underlying health conditions, and host genetics. Some amino acid replacements in the spike protein suggest positive immune selection is at work in shaping variation in this protein. Our analysis traces the early molecular architecture of SARS-CoV-2 in Houston, and will help us to understand the origin and trajectory of future infection spikes.

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The establishment of reference sequence for SARS‐CoV‐2 and variation analysis

Cited by 469 publications

References 24 publications

CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2

CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2

Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence

Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas

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