Emergence of European and North American mutant variants of SARS‐CoV‐2 in South‐East Asia

Islam, Ovinu Kibria; Al‐Emran, Hassan M.; Hasan, Md. Shazid; Anwar, Azraf; Jahid, Iqbal Kabir; Hossain, M. Anwar

doi:10.1111/tbed.13748

Cited by 53 publications

(62 citation statements)

References 32 publications

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“…The SARS-CoV-2 genome identified among the study enrolled patients belonged to G, GR and GH phylogenetic clades. These three clades cover more than 85% of the strains worldwide 26 . Our study also analyzed various alpha (α) and beta (β) diversity indexes to observe metagenomic variations in all samples.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic diagnosis and pathogenic network profile of SARS-CoV-2 in patients co-morbidly affected by type 2 diabetes

Al‐Emran¹,

Rahman

Hasan³

et al. 2021

Preprint

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Background: The mortality of COVID-19 disease is very high among males or elderly or individuals having comorbidities with obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic feature of SARS-CoV-2 infected patients with or without type 2 diabetes to identify the microbial interactions associated with its fatal consequences. Method: This study compared the baseline nasopharyngeal microbiome of SARS-CoV-2 infected diabetic and non-diabetic patients with controls adjusted with age and gender. The mNGS were performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan-package in R. Results: All three groups possessed significant bacterial diversity and dissimilarity indexes (p<0.05). Spearmans correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r=0.6-1.0, p<0.05), and 109 positive correlations among normal-flora and probiotic bacteria (r>0.6, p<0.05). The SARS-CoV-2 diabetic group exhibited a significant increase of pathogens (p<0.05) and opportunistic pathogens (p<0.05) with a simultaneous decrease of normal-flora (p<0.05). The molecular docking analysis of Salivaricin, KLD4 (alpha), and enterocin produced by several enriched probiotic strains presented strong binding affinity with Shiga toxin, outer membrane proteins (ompA, omp33) or hemolysin. Conclusion: The dysbiosis of the bacterial community might be linked with severe consequences of COVID-19 infected diabetic patients, although few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal-flora and probiotics through dietary changes and reduction of excessive pro-inflammatory states by preventing pathogenic environment might lead to a better outcome for those co-morbid patients.

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Section: Discussionmentioning

confidence: 99%

Metagenomic diagnosis and pathogenic network profile of SARS-CoV-2 in patients co-morbidly affected by type 2 diabetes

Al‐Emran¹,

Rahman

Hasan³

et al. 2021

Preprint

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“…In our case, potentially disadvantageous mutations (present in strain 1, which decreased its abundance over time) include Q57H in NS3 protein, T85I in NSP2 protein, and T1482I in NSP3 protein. NS3_Q57H demarcates GH clade [25]. As of 11.11.2020, it occurs in 4.6 % (40 out of 874) of Russian SARS-CoV-2 sequences.…”

Section: Discussionmentioning

confidence: 99%

“…These mutations occur together as a result of the substitution of three consecutive nucleotides. The presence of these mutations demarcates clade GR [25]. Over 85% of Russian SARS-CoV-2 genomes submitted to GISAID (11.11.2020) belong to the GR clade and possess both of these mutations.…”

Section: Discussionmentioning

confidence: 99%

“…Spike_D614G is one of the most widely discussed mutations. Its presence defines G clade [25], it increases infectivity [32][33][34], mortality [35,36], alters viral fitness [37], and, according to protein modeling, strengthens the folding stability of the spike protein [28]. It is present in 99.2 % of SARS-CoV-2 genomes obtained from Russia (as of 11.11.2020).…”

Section: Discussionmentioning

confidence: 99%

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Change of dominant strain during dual SARS-CoV-2 infection

Samoilov

Kaptelova

Bukharina

et al. 2020

Preprint

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Background: The effect of SARS-CoV-2 mutations and viral load on the severity of COVID-19 is not well understood. The possibility of reinfection with SARS-CoV-2 has already been reported, but dual infection with SARS-CoV-2 is poorly described and is currently under discussion. We describe a study of two strains of SARS-CoV-2 detected in the same patient during the same disease presentation. Methods: Two nasopharyngeal swabs were obtained eight days apart from the patient in their 90s, diagnosed with lobar pneumonia (J18.1). Both tests were positive for SARS-CoV-2 with high viral load (Ct = 13). We have performed high-throughput sequencing of SARS-CoV-2 genomes from both swabs. Findings: Genomic analysis of SARS-CoV-2 revealed the presence of two genetically distant strains in both swabs. Detected strains belong to different phylogenetic clades (GH and GR) and differ in the seven nucleotide positions. The relative abundance of strains was 70% (GH) and 30% (GR) in the first swab, and 3% (GH) and 97% (GR). Interpretation: Our findings suggest that the patient was infected by two genetically distinct SARS-CoV-2 strains at the same time. One of the possible explanations is that the second infection occurred in the hospital. Change of the dominant strain ratio during disease manifestation could be explained by the advantage or higher virulence of the strain belonging to the clade GR.

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“…An early examination revealed several mutations in the S protein gene in circulating viral strains [48,49], including the D614G substitution now found in most of the global SARS-CoV-2 strains [48,[56][57][58][59][60][61][62]. The D614G mutation lies in the S1 subunit of the protein, just downstream of the receptor binding domain, and is proposed to play a critical role in receptor binding by alteration of the positioning of the receptor binding domain.…”

Section: Effect Of Circulating S Mutations On Protein Stability Cleamentioning

confidence: 99%

Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

Barrett

Neal

Edmonds

et al. 2021

Preprint

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The SARS-CoV-2 spike protein (S) is the sole viral protein responsible for both viral binding to a host cell and the membrane fusion event needed for cell entry. In addition to facilitating fusion needed for viral entry, S can also drive cell-cell fusion, a pathogenic effect observed in the lungs of SARS-CoV-2 infected patients. While several studies have investigated S requirements involved in viral particle entry, examination of S stability and factors involved in S cell-cell fusion remain limited. We demonstrate that S must be processed at the S1/S2 border in order to mediate cell-cell fusion, and that mutations at potential cleavage sites within the S2 subunit alter S processing at the S1/S2 border, thus preventing cell-cell fusion. We also identify residues within the internal fusion peptide and the cytoplasmic tail that modulate S cell-cell fusion. Additionally, we examine S stability and protein cleavage kinetics in a variety of mammalian cell lines, including a bat cell line related to the likely reservoir species for SARS-CoV-2, and provide evidence that proteolytic processing alters the stability of the S trimer. This work therefore offers insight into S stability, proteolytic processing, and factors that mediate S cell-cell fusion, all of which help give a more comprehensive understanding of this highly sought-after therapeutic target.

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Emergence of European and North American mutant variants of SARS‐CoV‐2 in South‐East Asia

Cited by 53 publications

References 32 publications

Metagenomic diagnosis and pathogenic network profile of SARS-CoV-2 in patients co-morbidly affected by type 2 diabetes

Metagenomic diagnosis and pathogenic network profile of SARS-CoV-2 in patients co-morbidly affected by type 2 diabetes

Change of dominant strain during dual SARS-CoV-2 infection

Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

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