Genomic Surveillance of SARS-CoV-2 Viruses Collected during the Ending Phase of the First Wave of the COVID-19 Pandemic in Bangladesh.

Mutations, deletions, and the emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may pose a serious health threat. Here, we report the genome sequences of SARS-CoV-2 viruses that were collected from SARS-CoV-2-infected patients during the end phase of the first wave of the COVID-19 pandemic in Dhaka, Bangladesh.

Coding-Complete Genome Sequence of SARS-CoV-2 Isolate from Bangladesh by Sanger Sequencing.

A coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate was revealed. The sample for the virus was isolated from a female patient from Dhaka, Bangladesh, suffering from coronavirus disease-2019 (COVID-19).

Complete Genome Sequence of a Circulating Hepatitis B Virus Genotype C Strain Isolated from a Chronically Infected Patient Identified at an Outdoor Hospital in Bangladesh.

Hepatitis B virus (HBV) causes significant global health problems despite the presence of a potential vaccine. HBV chronic cases are increasing rapidly in developing countries like Bangladesh. Here, we report the complete genome sequence of an HBV genotype C strain isolated from a chronic patient identified at an outdoor hospital section.

Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer.

BACKGROUND: The microarray has contributed to developing the omic analysis. However, as it depends basically on the surface reaction, it is hard to perform bulk reactions and sequential multistep reactions. On the other hand, the popular microplate technology, which has a great merit of being able to perform parallel multistep reactions, has come to its limit in increasing the number of wells (currently, up to 9600) and reducing the volume to deal with due to the difficulty in operations. RESULTS: Here, we report a novel microarray technology which enables us to explore advanced applications, termed microarray-with-manageable volumes (MMV). The technical essence is in the pipette-free direct parallel transfer from well to well performed by centrifugation, evading the evaporation and adsorption-losses during handling. By developing the MMV plate, accompanying devices and techniques, generation of multiple conditions (256 kinds) and performance of parallel multistep reactions, including PCR and in vitro translation reactions, have been made possible. These were demonstrated by applying the MMV technology to searching lysozyme-crystallizing conditions and selecting peptides aimed for Aß-binding or cathepsin E-inhibition. CONCLUSIONS: With the introduction of a novel concept microarray (MMV) technology, parallel and multistep reactions in sub-µL scale have become possible.

Importance of acetylator phenotype in the identity of Asian populations.

The Marma, Tripura, and Chakma are tribal populations of South Asian countries such as Bangladesh. The populations are thought to be immigrants who started moving from their original home in the Far East toward the west and south. We randomly selected 80 Marma, 53 Tripura, and 43 Chakma to determine acetylation capacity and acetylator phenotype. The mean acetylation capacities were 63% in the Marma, 65% in the Tripura, and 70% in the Chakma. The acetylator phenotype was bimodally distributed as fast and slow acetylator. The frequencies of fast acetylator were 83% in the Marma, 89% in the Tripura, and 88% in the Chakma. According to acetylation capacity, the tribes are different from the founder nontribal populations of Bangladesh. They identify themselves as having a separate single population origin. The frequency of fast acetylator predicted served as the acetylator status of the Far East Asian population. The segregation of populations by acetylator phenotype on geographic longitude might be appropriate for geonational identification of Asian populations.

Urinary iodine status and thyroid dysfunction: a Bangladesh perspective.

Iodine deficiency is endemic in Bangladesh. Compulsory iodization of table salt was introduced since 1993 to prevent and improve thyroid disorders in the country. Urinary iodine status, thyroid function and antithyroid antibodies were studied in 397 newly diagnosed thyroid patients and 94 age-sex matched controls. Among thyroid patients, 96 were hyperthyroid, 185 euthyroid and 116 hypothyroid. Mean and median urinary iodine were higher (p=0.075) in thyroid patients (26.13+/-0.91 and 23.03) than controls (22.65+/-1.47 and 18.59); in hyperthyroid and euthyroid than hypothyroid (p=0.020); in multinodular (28.08+/-2.80 and 26.94) and diffuse (27.35+/-1.19 and 26.71) goitre than uninodular (23.91+/-2.37 and 19.14) and nongoitrous (NG, 21.5+/-2.05 and 18.27) (p=0.098) patients but no sex difference (p=0.466). Antimicrosomal (26.7%) and antithyroglobulin (34%) antibodies were more frequently positive among thyroid patients than controls (6.4% and 12.8% respectively) (p=0.00002 and p=0.00005 respectively). Antibody positivity was higher in diffuse (82/228) and multinodular (20/47) goitre than nongoitrous (20/56) and uninodular (13/66) goitre (p=0.046) as well as in hypothyroid (55.2%) and hyperthyroid (36.5%) than euthyroid (19.5%) patients (P<0.001). Urinary iodine correlated neither with antimicrosomal (thyroid patients: p=0.597 and control: p=0.112) nor with antithyroglobulin (thyroid patients: p=0.388 and control: p=0.195) antibody. Thyroid autoimmunity and dysfunction seems common; and interaction of salt iodization with iodine status and thyroid disorders may be important in Bangladesh.

Dust-lower-hybrid drift instabilities with dust charge fluctuations in an inhomogeneous dusty magnetoplasma.

Effects of a uniform magnetic field, the plasma inhomogeneity, and dust charge fluctuations on low-frequency dust-lower-hybrid drift waves have been investigated. Charging currents of electrons and ions to a spherical dust grain in a nonuniform magnetized dusty plasma have been calculated to study the charge fluctuation induced damping or growth of low-frequency drift waves. It is found that for strongly magnetized electrons and ions, the charge fluctuation damping is reduced significantly from that of an unmagnetized plasma. For sufficiently hot electrons, the drift wave exhibits instability in the absence of dust charge fluctuation damping.

Dust charge fluctuations in a magnetized dusty plasma.

Charging currents of electrons and ions to a spherical dust grain in a uniform magnetized dusty plasma have been examined. It is found that the external magnetic field reduces the charging currents, thereby decreasing the dust charge fluctuation damping of a low-frequency electrostatic wave in a dusty plasma.

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.

Predominance of the DEN-3 genotype during the recent dengue outbreak in Bangladesh.

A recent outbreak of dengue in Bangladesh was marked by many fatal complications. As clinical virulence varies among the genotypes of dengue virus, a study was conducted to investigate the molecular genotypes of dengue in Bangladesh. Reverse transcription polymerase chain reaction was used to determine viral genotypes using oligonucleotide generic primers that produce a 511 bp product. The resulting product was typed by nested PCR with strain-specific primers, yielding 482 (DEN-1), 119 (DEN-2), 290 (DEN-3) and 392 (DEN-4), visualized on UV transilluminator after electrophoresis on 2% agarose gel stained with ethidium bromide. Of 45 clinically diagnosed dengue patients (mean age 28 years; male/female 30/15), 19 (42.2%) had detectable viral RNA in their blood. However, during the first 5 days of fever in 30 patients, the frequency was 60% (18/30), implying that the sooner serum is drawn after the fever, the greater the chances of detecting viral RNA. DEN-3 was detected in all except 2 patients who were infected with DEN-2. DEN-2 (two cases) and DEN-4 (one case) were present as co-infections with DEN-3. All of the patients presented with fever, anorexia and vomiting; many had headache and general body ache; a few had a rash. About a quarter had suffered episodes of bleeding, while ascites, pleural effusion and CNS symptoms were found in a few patients Patients positive for viral RNA were also positive for anti-dengue IgM (p=0.007) in subsequent sampling. The study suggests the predominance of DEN-3 infection with occasional co-infection with other types, during the recent outbreak of dengue in Bangladesh.

Effect of a magnetic field on the wake potential in a dusty plasma with streaming ions.

The wake potential of a test dust particulate due to an ion cyclotron wave in a dusty plasma with streaming ions is calculated. The role of the external magnetic field on the periodic attractive forces is clarified. The amplitude of wake potential is reduced because the overshielding by streaming ions is inhibited in the presence of the external magnetic field.

Status of antithyroid antibodies in Bangladesh.

To study autoimmunity among thyroid diseases, 397 thyroid patients (age 30 (13) years; M/F 75/322) from two referral centres in Bangladesh and 94 healthy controls (age 30 (13) years; M/F 24/70) were studied for antimicrosomal and antithyroglobulin antibodies. Thyroid patients were clinically grouped as suspected autoimmune thyroid disease (AITD), non-autoimmune, or indeterminate groups (where no decision could be reached). Antimicrosomal antibody was strongly positive in 19.4% and weakly positive in 7.3% of patients but only 4.3% and 2.1% respectively in the controls (chi(2) = 17.852; p = 0.000) whereas strong and weak positivity were 27.2% and 6. 8% in patients compared with 8.5% and 4.3% respectively in the controls (chi(2) = 16.916; p = 0.000) for antithyroglobulin antibody. Antibodies were positive in 63.0% with Hashimoto's thyroiditis, 36.4% with Graves' disease, and 44.7% with atrophic thyroiditis among the autoimmune group. In the non-autoimmune group antibodies were positive in 100% with multinodular hypothyroidism, 46.7% with subacute thyroiditis, 40.0% with suspected iodine deficiency goitre, 31.3% with toxic multinodular goitre, 30.8% with non-toxic solitary nodules, and 19.4% with simple diffuse goitre. None was positive for antimicrosomal antibody without being positive for antithyroglobulin antibody. The two antibodies strongly correlated in both patients (r = 0.977, p = 0.000) and controls (r = 0.986, p = 0.000). About 9% (36/397) of patients were mismatched with the final diagnosis on antibody measurement; most of them had Hashimoto's thyroiditis (33/36). Prevalence of AITD among thyroid patients was 48.36%. Specificity of antimicrosomal and antithyroglobulin antibodies were 93% and 87%. It was concluded that AITD is not uncommon in Bangladesh; antimicrosomal antibody is a useful marker for AITD and unless antibodies are checked, an appreciable number of patients with AITDs will remain undetected.

Genetic background of diabetic and nondiabetic sibs in young Bangladeshis.

The prevalence of diabetes mellitus in the young is higher in Bangladesh like other Asian developing nations. Albeit, undernutrition has been shown to be associated with diabetes in the young, not all such individuals are diabetic. Diabetes Mellitus is a multigenic disease. In IDDM, DR3/4 heterozygotes were shown to have a greatly increased risk of developing the disease, suggesting the concept of genetic factor(s) being involved in the development of diabetes. Therefore, this study was undertaken to determine the distribution of HLA class II alleles (DRB) and to identify the HLA associated risk for developing diabetes mellitus in the young Bangladeshis. A total of fifty individuals were investigated. Half of them (n=25) were diabetic patients, registered in BIRDEM and half the participants were their non-diabetic sibs. A genomic DNA PCR and Enzyme Linked Probe Hybridization Assay (ELPHA, Bio-test, Germany) was used to determine HLA class II alleles (DRB1, DRB 3, 4, 5) by in vitro amplification of DRB gene. Among all the sero-equivalent antigens found in the study subjects, the prevalence of DR15 (DR2) was overrepresented, both in the diabetic subjects and in their non-diabetic sibs. Moreover, compared with the non-diabetic group the diabetic patients showed higher frequency of DR15 alleles (39 and 25%) though the difference was not significant (chisq. 1.7, p>0.05). Next to DR15, DR4 was the most prevalent HLA-DRB gene found in the study population. Interestingly, the frequency of DR4 was higher in the diabetic than in the non-diabetic group (20 vs. 14%). The study showed that the DR15 and DR4 were the most prevalent in the study population. Moreover, DR7 though not very significant, was higher in non-diabetic compared to their diabetic sibs. Comparison between the diabetic and non-diabetic sibs could have been interesting and significant but we could not confirm our findings, possibly, due to small sample size. A study in a larger paired sample of unrelated population is also needed to substantiate our findings, and also to prove the susceptibility or resistant haplotype in the young diabetic subjects.