Whole Genome Comparison of Pakistani Corona Virus with Chinese and US Strains along with its Predictive Severity of COVID-19

Saif, Rashid; Mahmood, Tania; Ejaz, Aniqa; Zia, Saeeda; Qureshi, Abdul Rasheed

doi:10.1101/2020.05.01.072942

Cited by 4 publications

(8 citation statements)

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“…International travel has been considered as one of the potential risk factors for the transmission and circulation of different variants of SARS-CoV2 in Pakistan [ 31 – 34 ]. The initial-sequenced local SARS-CoV2 genomes (accession numbers: MT240479 and MT262993) are closely related to the Chinese SARS-CoV2 isolates [ 9 ], while the currently sequenced SARS-CoV2 isolate differs from that of the Chinese isolates (Fig. 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…Pakistan submitted its first coronavirus whole-genome sequence (SARS-CoV2/Gilgit1/human/2020/PAK; accession number: MT240479) to the GenBank on March 25, 2020. Following the first WGS of SARS-CoV2 from Pakistan, several WGS-based attempts were made and the sequencing data were submitted to the GenBank (SARS-CoV2/Manga1/human/2020/PAK; accession number: MT262993) [ 9 ]. The initial two sequenced strains of Pakistani coronavirus (accession numbers: MT240479 and MT262993) exhibited 99.98% and 100% sequence similarity to the Chinese SARS-CoV2 isolate [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

“…Following the first WGS of SARS-CoV2 from Pakistan, several WGS-based attempts were made and the sequencing data were submitted to the GenBank (SARS-CoV2/Manga1/human/2020/PAK; accession number: MT262993) [ 9 ]. The initial two sequenced strains of Pakistani coronavirus (accession numbers: MT240479 and MT262993) exhibited 99.98% and 100% sequence similarity to the Chinese SARS-CoV2 isolate [ 9 ]. During the COVID19 pandemic, the mortality pattern of SARS-CoV2 in Pakistan was found to be considerably different from the rest of the world.…”

Section: Introductionmentioning

confidence: 99%

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Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing

et al. 2022

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This study aimed to characterize the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) isolated from an oropharyngeal swab specimen of a Pashtun Pakistani patient using next-generation sequencing. Upon comparing the SARS-CoV2 genome to the reference genome, a total of 10 genetic variants were identified. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. Phylogenetic analysis ( n = 84) revealed that the current SARS-CoV2 genome was closely clustered with 8 Pakistani strains belonging to Punjab, Federal Capital, Azad Jammu and Kashmir (AJK), and Khyber Pakhtunkhwa (KP). In addition, the current SARS-CoV2 genome was very similar to the genome of SARS-CoV2 reported from Guam, Taiwan, India, the USA, and France. Overall, this study reports a slight mismatch in the SARS-CoV2 genome, indicating the presence of a single unique missense mutation. However, phylogenetic analysis revealed that the current SARS-CoV2 genome was closely clustered with 8 other Pakistani strains. Supplementary Information The online version contains supplementary material available at 10.1007/s00284-021-02743-y.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing

et al. 2022

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“…Only proper testing, tracing and treatment can minimize the loss due to this virus but still, there is a lack of testing kits and diagnostic facilities in many South Asian Countries. Already vaccines of SARS-CoV-2 are under investigation in 198 countries of the world, and of them, 42 have been going under clinical trials [21]. Bangladesh (BANCOVID vaccine) and India (COVAX vaccine) are two South Asian countries competing and their vaccines are still undergoing clinical trials where they are working with various national and international collaborators to develop a promising vaccine soon.…”

Section: Discussionmentioning

confidence: 99%

“…In another analysis of 4 whole genome sequences, 31 variants were identified including two causing alterations in ORF1ab gene, ORF1a and N genes with functional replication and translation. Mutations in N & ORF1a proteins showed alterations at the amino acid level [21].…”

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confidence: 99%

The COVID-19 pandemic: A Comprehensive Review of the Genomic variations, Epidemiological features, Diagnosis, Treatment and Intervention schemes in South Asia

Noman¹,

Ekra

Meem³

et al. 2021

Preprint

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The ongoing respiratory disease pandemic COVID-19 caused by a newly emerging highly infectious virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is aggravating the world’s health, economy and regular life. This unprecedented respiratory outbreak has already infected more than 43 million individuals and taken more than 1.1 million lives. The habitation of over 21% of the world’s population- the SAARC region is also susceptible to COVID-19 and comprises of more than 20% of the total infected cases. Demographic analysis showed that males and younger populations are mostly infected in South Asian countries. Similar genomic variations were observed in the countries such as variations in the ORF1ab, ORF1a, ORF3a and S genes were largely seen. As no effective treatment strategy hasn’t developed yet, only timely testing and tracing can mitigate the loss from the disease which led the way to the development of alternate screening methods with higher efficiency and timely results. Since no unanimously recognized treatment option is available, existing medicines and treatments are being utilized to treat the patients. Currently, a vaccine can be the ideal solution for this rapidly evolving disease and hence two South Asian country- Bangladesh and India has joined the race of vaccine development and one of them succeeded the phase II clinical trial. As the ‘Second Wave of COVID-19’ is approaching, it has become a matter of urgency to appraise the existing policies and strategies in order to ascertain and implement effective schemes that can mitigate the ramifications of the disease.

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Insect cell expression and purification of recombinant SARS‐COV‐2 spike proteins that demonstrate ACE2 binding

Struble¹,

Smith²,

Lutz³

et al. 2022

Protein Science

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The COVID-19 pandemic caused by SARS-CoV-2 infection has led to socioeconomic shutdowns and the loss of over 5 million lives worldwide. There is a need for the identification of therapeutic targets to treat COVID-19. SARS-CoV-2 spike is a target of interest for the development of therapeutic targets.We developed a robust SARS-CoV-2 S spike expression and purification protocol from insect cells and studied four recombinant SARS-CoV-2 spike protein constructs based on the original SARS-CoV-2 sequence using a baculovirus expression system: a spike protein receptor-binding domain that includes the SD1 domain (RBD) coupled to a fluorescent tag (S-RBD-eGFP), spike ectodomain coupled to a fluorescent tag (S-Ecto-eGFP), spike ectodomain with six proline mutations and a foldon domain (S-Ecto-HexaPro(+F)), and spike ectodomain with six proline mutations without the foldon domain (S-Ecto-HexaPro(-F)). We tested the yield of purified protein expressed from the insect cell lines Spodoptera frugiperda (Sf9) and Trichoplusia ni (Tni) and compared it to previous research using mammalian cell lines to determine changes in protein yield. We demonstrated quick and inexpensive production of functional glycosylated spike protein of high purity capable of recognizing and binding to the angiotensin converting enzyme 2 (ACE2) receptor. To further confirm functionality, we demonstrate binding of eGFP fused construct of the spike ectodomain (S-Ecto-eGFP) to surface ACE2 receptors on lung epithelial cells by flow cytometry analysis and show that it can be decreased by means of receptor manipulation (blockade or downregulation).

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Whole Genome Comparison of Pakistani Corona Virus with Chinese and US Strains along with its Predictive Severity of COVID-19

Cited by 4 publications

References 18 publications

Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing

Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing

The COVID-19 pandemic: A Comprehensive Review of the Genomic variations, Epidemiological features, Diagnosis, Treatment and Intervention schemes in South Asia

Insect cell expression and purification of recombinant SARS‐COV‐2 spike proteins that demonstrate ACE2 binding

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