Genome Sequencing of Omicron Variants of SARS-CoV-2 Circulating in Bangladesh during the Third Wave of the COVID-19 Pandemic.

The coding-complete genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was obtained from 39 nasopharyngeal swab samples collected in January 2022 from Dhaka, Bangladesh, during the 3rd wave of the COVID-19 pandemic, using Illumina MiniSeq sequencing technology. Sequence analysis showed that all of them belonged to the WHO-designated variant of concern (VOC) Omicron. The presence of different sublineages of Omicron was noted, among which sublineage BA.2 (Nextstrain clade 21L) was the most prevalent one.

Evaluation of plasma Epstein-Barr virus DNA as a biomarker for Epstein-Barr virus-associated Hodgkin lymphoma.

OBJECTIVES: Epstein-Barr virus is a tumorigenic virus and has been extensively studied as a causative agent for Hodgkin lymphoma. Although immunostaining of the tumor biopsy is the standard method for diagnosis of Epstein-Barr virus-driven Hodgkin lymphoma, the invasiveness of the procedure renders it difficult and less desirable for the patients. Therefore, we designed this study to evaluate the efficiency of plasma Epstein-Barr virus DNA detection as an alternative diagnostic and prognostic method for Epstein-Barr virus-associated Hodgkin lymphoma. METHODS: This analytical cross-sectional study was conducted during March 2017 to December 2018 including 43 Hodgkin lymphoma patients diagnosed histopathologically followed by the latent membrane protein-1 immunohistochemistry to determine their Epstein-Barr virus association. Plasma Epstein-Barr virus DNA in these samples was measured using quantitative polymerase chain reaction (qPCR). RESULTS: Of total, 29 (67.44%) patients tested positive for plasma Epstein-Barr virus DNA. On comparing results of latent membrane protein-1 immunohistochemistry (IHC) with plasma Epstein-Barr virus DNA, plasma Epstein-Barr virus DNA was found in 25 of 30 patients with latent membrane protein-1 expression and 4 of 13 patients without latent membrane protein-1 expression. The sensitivity and the specificity of plasma Epstein-Barr virus DNA detection with respect to latent membrane protein-1 IHC were found to be 83.33% and 69.23%, respectively (p = 0.0014). CONCLUSION: Determination of plasma Epstein-Barr virus DNA was found to be highly sensitive and specific in characterizing Epstein-Barr virus-associated Hodgkin lymphoma, suggesting that this diagnostic method holds promise as an alternative and more convenient method of diagnosis compared with tissue biopsy.

Persistence of SARS-CoV-2 RNA in a male with metabolic syndrome for 72 days: A case report.

Coronavirus disease-19 (COVID-19) was first identified in Wuhan, China, and spread gradually throughout the world. There are multiple reports of prolonged viral shedding in people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, such findings have not been documented in Bangladesh. Herein, we present a case of metabolic syndrome that remained positive for SARS-CoV-2 RNA over a prolonged period. On clinical and laboratory examination, the patient was diagnosed with obesity, raised blood pressure, dyslipidemia, and uncontrolled glycemia. However, upon taking appropriate measures and controlling the plasma sugar level, he tested negative for SARS-CoV-2 RNA on the 72nd day since illness onset. We observed that COVID-19 patients with several comorbidities, such as metabolic syndrome, may shed the virus over a prolonged period. Therefore, strict public health measures and isolation rules should be followed by a high-risk population.

Challenges in the establishment of a biosafety testing laboratory for COVID-19 in Bangladesh.

At the beginning of the coronavirus disease 2019 (COVID-19) pandemic in Bangladesh, there was a scarcity of ideal biocontainment facilities to detect the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a risk group of 3 organisms. Molecular detection of SARS-CoV-2 must be performed in a BSL-2 laboratory with BSL-3-equivalent infection prevention and control practices. Establishing these facilities within a short timeframe proved to be an enormous challenge, including locating a remote space distant from the university campus to establish a laboratory, motivating the laboratory staff to work with a novel pathogen without any prior experience, allocation of funds for essential equipment and accessories, and arrangement of a safe waste management system for environmental hazard reduction. This report also highlights several limitations, such as the facility's architectural design that did not follow the biosafety guidelines, lack of continuous flow of funds, and an inadequate number of laboratory personnel. This article describes various efforts taken to overcome the challenges during the establishment of this facility that may be adopted to create similar facilities in other regions of the country. Establishing a BSL-2 laboratory with BSL-3-equivalent infection prevention and control practices will aid in the early detection of a large number of cases, thereby isolating persons with COVID-19, limiting the transmission of SARS-CoV-2, and promoting a robust public health response to contain the pandemic.

Detection of SARS-CoV-2 RNA in conjunctival swab of a COVID-19 patient: The first report from Bangladesh.

Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 RNA (SARS-CoV-2 RNA). It usually manifests by fever and/or respiratory illness. Here, we present a case of COVID-19 patient who initially presented ocular symptoms like redness, itching, and watery discharge. Afterward, the patient developed fever and anosmia suggestive of COVID-19 disease. Nasopharyngeal swab and conjunctival swab test for SARS-CoV-2 RNA revealed positive by reverse-transcriptase real-time polymerase chain reaction. The patient was managed symptomatically at home and did not require any hospital admission. On day 12, the patient clinically recovered fully and his follow-up testing for SARS-CoV-2 RNA of both conjunctival swab and nasopharyngeal swab became undetected. This report emphasized that conjunctival mucosa may be considered as a portal of entrance for SARS-CoV-2 RNA in addition to the respiratory route. This study highlighted that any kind of ocular manifestations, such as conjunctival hyperemia, chemosis, watery discharge, periorbital erythema, and burning sensation should never be overlooked for probable COVID-19 in current pandemic settings. Moreover, strict eye protection using goggles/face shield should be used by all health care workers despite any working environment while caring for patients with or without COVID-19-related signs.