Genotyping coronavirus SARS-CoV-2: methods and implications

Yin, Changchuan

doi:10.1016/j.ygeno.2020.04.016

Cited by 296 publications

(406 citation statements)

References 44 publications

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“…This diversity can be associated with fitness or transmission 209 by viral genome. Among the 5 frequent mutations observed in these strains, 2 were 210 reported mutation (11083G>T and 1397G>A, [20]. Divergence from the main strain 211 can be easily pointed out in the constructed phylogenetic tree ( Figure 2) with additional 212 root node.…”

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confidence: 93%

“…The most common 67 SNP's that were observed in this analysis includes the previously reported mutation in 68 leader sequence (241C>T), Coronaviruses includes subgenomic identical 5 Leader 69 sequence which plays role in viral replication process. This mutation was seen to suggested to increase the transmission [20].…”

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confidence: 93%

“…Rahila et al [16] studied impact of the 13 mutations in the spike glycoprotein function and stability in the novel virus. 14 Changchuan [20] presented a method for effectively genotyping SARS-CoV-2 viruses 15 using complete genomes. 16 In this report, an analysis of 468 novel and early virus genome is presented.…”

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confidence: 99%

“…19 The data was downloaded from GenBank, GISAID, and SRA. Data was collected for 20 this study last as of 9th April 2020, with 440 genome sequence of the novel and early 21 strains from the world along with 28 sequences from India. The MEGAX tool [11] has 22 been used to perform the analysis.…”

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confidence: 99%

“…There has been a report on SNP mutations in SARS-CoV2 genome which majorly 63 demonstrated mutations frequent in European strains [20]. These mutations were 64 analysed in 28 submitted sequences from India.…”

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confidence: 99%

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Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

Joshi

Paul

2020

Preprint

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Recently classified as a pandemic by WHO, novel Corononavirus 2019 has affected almost every corner of the globe causing human deaths in a range of hundred thousands. The virus having its roots in Wuhan (China) has been spread over the world by its own property to change itself accordingly. These changes correspond to its transmission and pathogenicity due to which the concept of social distancing appeared into the picture.

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confidence: 93%

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confidence: 93%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

Joshi

Paul

2020

Preprint

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Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic

et al. 2020

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IMPORTANCE In late December 2019, an outbreak of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Data on the routes of transmission to Los Angeles, California, the US West Coast epicenter for coronavirus disease 2019 (COVID-19), and subsequent community spread are limited. OBJECTIVE To determine the transmission routes of SARS-CoV-2 to Southern California and elucidate local community spread within the Los Angeles metropolitan area. DESIGN, SETTING, AND PARTICIPANTS This case series included 192 consecutive patients with reverse transcription-polymerase chain reaction (RT-PCR) test results positive for SARS-CoV-2 who were evaluated at Cedars-Sinai Medical Center in Los Angeles, California, from March 22 to April 15, 2020. Data analysis was performed from April to May 2020. MAIN OUTCOMES AND MEASURES SARS-CoV-2 viral genomes were sequenced. Los Angeles isolates were compared with genomes from global subsampling and from New York, New York; Washington state; and China to determine potential sources of viral dissemination. Demographic data and outcomes were collected. RESULTS The cohort included 192 patients (median [interquartile range] age, 59.5 [43-75] years; 110 [57.3%] men). The genetic characterization of SARS-CoV-2 isolates in the Los Angeles population pinpointed community transmission of 13 patients within a 3.81 km 2 radius. Variation landscapes of this case series also revealed a cluster of 10 patients that contained 5 residents at a skilled nursing facility, 1 resident of a nearby skilled nursing facility, 3 health care workers, and a family member of a resident of one of the skilled nursing facilities. Person-to-person transmission was detected in a cluster of 5 patients who shared the same single-nucleotide variation in their SARS-CoV-2 genomes. High viral genomic diversity was identified: 20 Los Angeles isolates (15.0%) resembled SARS-CoV-2 genomes from Asia, while 109 Los Angeles isolates (82.0%) were similar to isolates originating from Europe. Analysis of other common respiratory viral pathogens did not reveal coinfection in the cohort. CONCLUSIONS AND RELEVANCE These findings highlight the precision of detecting person-toperson transmission and accurate contact tracing directly through SARS-CoV-2 genome isolation and sequencing. Development and application of phylogenetic analyses from the Los Angeles population established connections between COVID-19 clusters locally and throughout the US.

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Role of hemagglutinin‐esterase protein in SARS‐CoV‐2 infection?

Zandi

Soltani

2021

Cell Biology International

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In a published mini-review article in Cell Biology International, the authors considered hemagglutinin-esterase (HE) as a structural protein of SARS-CoV-2 which has roles in the entry and release processes of virus (Tantuoyir & Rezaei, 2020). Coronaviruses are divided in four genera including alpha-, beta-, gamma-, and delta-coronavirus (Yang & Leibowitz, 2015). The five subgenera are recognized within the genus betacoronavirus (Yang & Leibowitz, 2015). SARS-CoV-2 as a beta-coronavirus in lineage B causes COVID-19 (Letko et al., 2020). It encodes four structural proteins: (1) the spike-surface glycoprotein, (2) the small envelope protein, (3) the membrane glycoprotein, and (4) the nucleocapsid protein, also several nonstructural proteins (Yin, 2020); however, other betacoronaviruses in lineage A such as HCoV-OC43, HCoV-HKU1, BCoV, and MHV encode HE (Yang & Leibowitz, 2015). As a result, according to evidence, the genome of SARS-CoV-2 lacks the HE gene, therefore, HE cannot have a role in SARS-CoV-2 replication.

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Genotyping coronavirus SARS-CoV-2: methods and implications

Cited by 296 publications

References 44 publications

Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic

Role of hemagglutinin‐esterase protein in SARS‐CoV‐2 infection?

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