Genomic and evolutionary study from SARS-CoV-2 virus isolates from Bangladesh during the early stage of pandemic strongly correlate with European origin and not with China.

The goal of this study was to identify the genomic variants and determine molecular epidemiology of SARS-CoV-2 virus during the early pandemic stage in Bangladesh. Viral RNA was extracted, converted to cDNA, and amplified using Ion AmpliSeq™ SARS-CoV-2 Research Panel. 413 unique mutants from 151 viral isolates were identified. 80% of cases belongs to 8 mutants: 241C toT, 1163A toT, 3037C toT, 14408C toT, 23403A toG, 28881G toA, 28,882 G toA, and 28883G toC. Observed dominance of GR clade variants that have strong presence in Europe, suggesting European channel a possible entry route. Among 37 genomic mutants significantly associated with clinical symptoms, 3916CtoT (associated with sore-throat), 14408C to T (associated with cough-protection), 28881G to A, 28882G to A, and 28883G to C (associated with chest pain) were notable. These findings may inform future research platforms for disease management and epidemiological study.

Genome Sequence of a SARS-CoV-2 P.1 Variant of Concern (20J/501Y.V3) from Bangladesh.

This study reports the coding-complete genome sequence, with variant identifications and phylogenetic analysis, of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) P.1 variant (20J/501Y.V3), obtained from an oropharyngeal swab specimen from a female Bangladeshi patient diagnosed with coronavirus disease 2019 (COVID-19) with no travel history.

Reports of Coding-Complete Genome Sequences of Five 2019 Novel Coronavirus (SARS-CoV-2) Strains Isolated in Bangladesh.

This study determined five coding-complete genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains isolated from oropharyngeal swab specimens of Bangladeshi patients who were diagnosed with coronavirus disease 2019 (COVID-19) and had no travel history.

Molecular analysis of hemagglutinin, neuraminidase, matrix genes provide insight into the genetic diversity of seasonal H3N2 human influenza a viruses in Bangladesh during July-August, 2012.

Influenza A virus subtype H3 is a threat to public health and it is important to understand the evolution of the viruses for the surveillance and the selection of vaccine strains. Comparative analysis of four Bangladeshi isolates with isolates circulating other parts of the world based on three candidate genes hemagglutinin (HA), neuraminidase (NA), matrix protein (MA) showed no evidence of significant distinct subclade of viruses circulating in the country over the period of study. Despite these findings, we found N161S substitution in all four H3N2 influenza stains resulting in the gain of NSS160-162 glycosylation site. All H3N2 Influenza subtypes in the study had amino acid substitution at position 31 on the M2 protein (Aspartic acid to Asparagine) which is known to be responsible for amantadine drug resistance.

PCR can help early diagnosis of pulmonary tuberculosis.

One hundred and fifty-one patients, clinically suspected for pulmonary tuberculosis (age: 31 +/- 13 years, male/female: 112/39), were investigated to evaluate the diagnostic potential of polymerase chain reaction (PCR) based detection of the Mycobacterium tuberculosis complex in sputum. The diagnostic efficacy of PCR was compared with culture of Mycobacterium tuberculosis on egg-based Lowenstein-Jensen modified medium. PCR detected 71.5% (108/151), whereas culture detected 66.2% (100/151) of the clinically suspected patients. There was a significant association between the results of PCR and culture (chi2 = 59.524, p < 0.001). However, 23.2% (35/151) samples were found negative in both culture and PCR. Considering culture as the gold standard, the sensitivity of the PCR was 92%. and its specificity 70%. This lower apparent specificity may be due to the higher sensitivity of PCR.

Effects of gamma irradiation on bacterial microflora associated with human amniotic membrane.

Human amniotic membrane is considered a promising allograft material for the treatment of ocular surface reconstruction, burns, and other skin defects. In order to avoid the transmission of any diseases, grafts should be perfectly sterile. Twenty-five amniotic sacs were collected to determine the microbiological quality of human amniotic membrane, to analyze the radiation sensitivity pattern of the microorganism, and to detect the radiation decimal reduction dose (D10) values. All the samples were found to be contaminated, and the bioburden was ranged from 3.4 × 10² to 1.2 × 105 cfu/g. Initially, a total fifty bacterial isolates were characterized according to their cultural, morphological, and biochemical characteristics and then tested for the radiation sensitivity in an incremental series of radiation doses from 1 to 10 KGy. The results depict gradual decline in bioburden with incline of radiation doses. Staphylococcus spp. were the most frequently isolated bacterial contaminant in tissue samples (44%). The D10 values of the bacterial isolates were ranged from 0.6 to 1.27 KGy. Streptococcus spp. were found to be the highest radioresistant strain with the radiation sterilization dose (RSD) of 11.4 KGy for a bioburden level of 1000. To compare the differences, D10 values were also calculated by graphical evaluations of the data with two of the representative isolates of each bacterial species which showed no significant variations. Findings of this study indicate that lower radiation dose is quite satisfactory for the sterilization of amniotic membrane grafts. Therefore, these findings would be helpful to predict the efficacy of radiation doses for the processing of amniotic membrane for various purposes.

PCR can help early diagnosis of pulmonary tuberculosis.

One hundred and fifty-one patients, clinically suspected for pulmonary tuberculosis (age: 31 +/- 13 years, male/female: 112/39), were investigated to evaluate the diagnostic potential of polymerase chain reaction (PCR) based detection of the Mycobacterium tuberculosis complex in sputum. The diagnostic efficacy of PCR was compared with culture of Mycobacterium tuberculosis on egg-based Lowenstein-Jensen modified medium. PCR detected 71.5% (108/151), whereas culture detected 66.2% (100/151) of the clinically suspected patients. There was a significant association between the results of PCR and culture (chi2 = 59.524, p < 0.001). However, 23.2% (35/151) samples were found negative in both culture and PCR. Considering culture as the gold standard, the sensitivity of the PCR was 92%. and its specificity 70%. This lower apparent specificity may be due to the higher sensitivity of PCR.