Understanding the possible origin and genotyping of the first Bangladeshi SARS‐CoV‐2 strain

Alam, A. S. M. Rubayet Ul; Islam, M. Rafiul; Rahman, M. Shaminur; Islam, Ovinu Kibria; Hossain, M. Anwar

doi:10.1002/jmv.26115

Cited by 28 publications

(28 citation statements)

References 14 publications

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“…The reduced efficacy of NPS in children underlines the difficulty in obtaining correct swabs from them, highlighting the potential of saliva collection particularly when diagnosing children. The overall performance of saliva was remarkable considering that we and others observed lower viral loads in saliva compared to NPS [ 22 , 41 ].…”

Section: Discussionmentioning

confidence: 84%

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

et al. 2021

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Rising demands for repetitive SARS-CoV-2 screens and mass testing necessitate additional test strategies. Saliva may serve as an alternative to nasopharyngeal swab (NPS) as its collection is simple, non-invasive and amenable for mass- and home testing, but its rigorous validation, particularly in children, is missing. We conducted a large-scale head-to-head comparison of SARS-CoV-2 detection by RT-PCR in saliva and NPS of 1270 adults and children reporting to outpatient test centers and an emergency unit. In total, 273 individuals were tested positive for SARS-CoV-2 in either NPS or saliva. SARS-CoV-2 RT-PCR results in the two specimens showed a high agreement (overall percent agreement = 97.8%). Despite lower viral loads in the saliva of both adults and children, detection of SARS-CoV-2 in saliva fared well compared to NPS (positive percent agreement = 92.5%). Importantly, in children, SARS-CoV-2 infections were more often detected in saliva than NPS (positive predictive value = 84.8%), underlining that NPS sampling in children can be challenging. The comprehensive parallel analysis reported here establishes saliva as a generally reliable specimen for the detection of SARS-CoV-2, with particular advantages for testing children, that is readily applicable to increase and facilitate repetitive and mass testing in adults and children.

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Section: Discussionmentioning

confidence: 84%

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

et al. 2021

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“…The sample size of the studies ranged from 134 to 79,381. The studies were conducted in Europe ( 14 , 20 – 25 ), America ( 26 , 27 ), and Asia ( 28 – 32 ). Moreover, the studies were cohort studies ( 14 , 22 , 25 , 27 , 30 ), case-control studies ( 20 , 21 , 26 , 31 , 32 ), cross-sectional studies ( 23 , 28 , 29 ) and interim audit ( 24 ) (see Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…A case-control study in Iran found that the level of serum 25(OH) vitamin D was significantly lower in COVID-19 positive patients ( p = 0.02) and it demonstrated that there was a significant relationship between the levels of serum 25(OH) vitamin D and the vulnerability to COVID-19 ( 32 ). Ye et al also revealed that VDD was a risk factor for COVID-19, especially for severe/critical cases ( 31 ).…”

Section: Resultsmentioning

confidence: 99%

The Impact of Vitamin D Level on COVID-19 Infection: Systematic Review and Meta-Analysis

Teshome

Adane

Girma

et al. 2021

Front. Public Health

112

101

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Background: Coronavirus disease (COVID-19) is a respiratory and systemic disorder caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or novel Coronavirus (nCoV). To date, there is no proven curative treatment for this virus; as a result, prevention remains to be the best strategy to combat coronavirus infection (COVID-19). Vitamin D deficiency (VDD) has been proposed to play a role in coronavirus infection (COVID-19). However, there is no conclusive evidence on its impact on COVID-19 infection. Therefore, the present review aimed to summarize the available evidence regarding the association between Vitamin D levels and the risk of COVID-19 infection.Methods: A systematic literature search of databases (PUBMED/MEDLINE, Cochrane/Wiley library, Scopus, and SciELO) were conducted from May 15, 2020, to December 20, 2020. Studies that assessed the effect of vitamin D level on COVID-19/SARS-2 infection were considered for the review. The qualities of the included studies were evaluated using the JBI tools. Meta-analysis with a random-effects model was conducted and odds ratio with their 95%CI were reported. This systematic review and meta-analysis are reported according to the preferred reporting items for systematic review and meta-analysis (PRISMA) guideline.Results: The electronic and supplementary searches for this review yielded 318 records from which, only 14 of them met the inclusion criteria. The qualitative synthesis indicated that vitamin D deficient individuals were at higher risk of COVID-19 infection as compared to vitamin D sufficient patients. The pooled analysis showed that individuals with Vitamin-D deficiency were 80% more likely to acquire COVID-19 infection as compared to those who have sufficient Vitamin D levels (OR = 1.80; 95%CI: 1.72, 1.88). Begg's test also revealed that there was no significant publication bias between the studies (P = 0.764). The subgroup analysis revealed that the risk of acquiring COVID-19 infection was relatively higher in the case-control study design (OR = 1.81).Conclusions: In conclusion, low serum 25 (OH) Vitamin-D level was significantly associated with a higher risk of COVID-19 infection. The limited currently available data suggest that sufficient Vitamin D level in serum is associated with a significantly decreased risk of COVID-19 infection.

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“…The I300F mutation (occurred in 78% isolates) was predicted to reduce the stability of NSP2 protein the function of which is not yet confirmed. One study suggested that the amino acid is positioned within the internal groove of the protein and less likely to interact with host factors (55). There two other functionally significant mutations which are Q57H in ORF3a and S194L in N protein.…”

Section: Discussionmentioning

confidence: 99%

Molecular characterization of SARS-CoV-2 from Bangladesh: Implications in genetic diversity, possible origin of the virus, and functional significance of the mutations

Rahman

Kader

Rizvi

2020

Preprint

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In a try to understand the pathogenesis, evolution, and epidemiology of the SARS-CoV-2 virus, scientists from all over the world are tracking its genomic changes in real-time. Genomic studies can be helpful in understanding the disease dynamics. We have downloaded 324 complete and near-complete SARS-CoV-2 genomes submitted in the GISAID database from Bangladesh which were isolated between 30 March to 7 September 2020. We then compared these genomes with the Wuhan reference sequence and found 4160 mutation events including 2253 missense single nucleotide variations, 38 deletions, and 10 insertions. The C>T nucleotide change was most prevalent possibly due to selective mutation pressure to reduce CpG sites to evade CpG targeted host immune response. The most frequent mutation that occurred in 98% of the isolates was 3037C>T which is a synonymous change that almost always accompanied 3 other mutations that include 241C>T, 14408C>T (P323L in RdRp), and 23403A>G (D614G in spike protein). The P323L was reported to increase mutation rate and D614G is associated with increased viral replication and currently the most prevalent variant circulating all over the world. We identified multiple missense mutations in B-cell and T-cell predicted epitope regions and/or PCR target regions (including R203K and G204R that occurred in 86% of the isolates) that may impact immunogenicity and/or RT-PCR based diagnosis. Our analysis revealed 5 large deletion events in ORF7a and ORF8 gene products that may be associated with less severity of the disease and increased viral clearance. Our phylogeny analysis identified most of the isolates belonged to the Nextstrain clade 20B (86%) and GISAID clade GR (88%). Most of our isolates shared common ancestors either directly with European countries or jointly with middle eastern countries as well as Australia and India. Interestingly, the 19B clade (GISAID S clade) was unique to Chittagong which was originally prevalent in China. This reveals possible multiple introductions of the virus in Bangladesh via different routes. Hence more genome sequencing and analysis with related clinical data are needed to interpret the functional significance and better predict the disease dynamics that may be helpful for policymakers to control the COVID-19 pandemic in Bangladesh.

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Understanding the possible origin and genotyping of the first Bangladeshi SARS‐CoV‐2 strain

Cited by 28 publications

References 14 publications

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

The Impact of Vitamin D Level on COVID-19 Infection: Systematic Review and Meta-Analysis

Molecular characterization of SARS-CoV-2 from Bangladesh: Implications in genetic diversity, possible origin of the virus, and functional significance of the mutations

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