A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia

Fri, 01 Jan 2021 00:00:00 GMT

A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia Saha, Ayan Counts for SARS-CoV-2 associated infections and fatalities are on the rise globally even in regions which con- tained the spread momentarily. The pattern of infections has been found to be controlled by the distinctive selection pressures exerted by fluctuating environmental nature and hosts. A total of 410 whole-genome se- quences submitted by the South Asian countries were retrieved from the GISAID database and analyzed to assess the impact and pattern of mutations in this region. Most common and frequent mutations in the South Asian countries are 241C > T, 3037C > T, 14408C > T, and 23403A > G and about 85% SNPs are localized in ORF1ab, spike protein, and nucleocapsid. Among the identified mutations, the proportion of missense type (54.17%) was highest, followed by the synonymous (41.66%) and the non-coding types (4.17%). While analyzing transmission source in terms of geolocation, the largest clustered group from the South Asian countries was based on the G- clade (D614G) (81.7%; 335/410 samples), tracing the inception and transmission of SARS-CoV-2 infections in the South Asian countries from European regions. Phylogenetic analysis also revealed that the South Asian strains are highly related to the South American and European strains. We found that G-clade mutations are more prevalent (96.19%) in the samples of Bangladesh which were also prevalent in the European isolates. Surpris- ingly, one missense mutation (1163A > T) in ORF1ab gene became dominant only in Bangladesh (78.8%), which led to debates regarding effects on the pathogenicity and transmissibility of the virus. Overall, the findings of this study highlight the frequently mutated SARS-CoV-2 variants among the COVID-19 patients in the South Asian countries which might ease containment of the disease in this region through investigating the virulence reducing factors as the identified mutations are strongly correlated with low infection and mortality rate.

Characteristics, management and outcomes of critically ill COVID-19 patients admitted to ICU in hospitals in Bangladesh: a retrospective study

Fri, 01 Jan 2021 00:00:00 GMT

Characteristics, management and outcomes of critically ill COVID-19 patients admitted to ICU in hospitals in Bangladesh: a retrospective study SAHA, AYAN Objectives. This study aimed to analyze the epidemiological and clinical characteristics of COVID-19 cases and investigate risk factors including comorbidities and age in relation with the clinical aftermath of COVID-19 in ICU admitted cases in Bangladesh. Methods. In this retrospective study, epidemiological and clini- cal characteristics, complications, laboratory results, and clini- cal management of the patients were studied from data obtained from 168 individuals diagnosed with an advanced prognosis of COVID-19 admitted in two hospitals in Bangladesh. Results. Individuals in the study sample contracted COVID-19 through community transmission. 56.5% (n = 95) cases died in intensive care units (ICU) during the study period. The median age was 56 years and 79.2% (n = 134) were male. Typical clini- cal manifestation included Acute respiratory distress syndrome (ARDS) related complications (79.2%), fever (54.2%) and cough (25.6%) while diabetes mellitus (52.4%), hypertension (41.1%) and heart diseases (16.7%) were the conventional comorbidi- ties. Clinical outcomes were detrimental due to comorbidities rather than age and comorbid individuals over 50 were at more risk. In the sample, oxygen saturation was low (< 95% SpO2) in 135 patients (80.4%) and 158 (93.4%) patients received sup- plemental oxygen. Identical biochemical parameters were found in both deceased and surviving cases. Administration of anti- viral drug Remdesivir and the glucocorticoid, Dexamethasone increased the proportion of surviving patients slightly. Conclusions. Susceptibility to developing critical illness due to COVID-19 was found more in comorbid males. These atypical patients require more clinical attention from the prospect of con- trolling mortality rate in Bangladesh.