Near coding-complete genome sequence of 12 dengue serotype 2 viruses from the 2023 outbreak in Bangladesh

We report the near coding-complete genomes of 12 DENV serotype 2 strains collected during the 2023 dengue outbreak in Bangladesh. Analyses showed that all 12 strains were closely related and belonged to genotype II-Cosmopolitan.

Emergence of SARS-CoV-2 Omicron sub-lineage JN.1 in Bangladesh

We report complete genome sequences of 14 severe acute respiratory syndrome coronavirus 2 Omicron sub-lineage JN.1 obtained from Bangladeshi individuals between 19 December 2023 and 21 January 2024. All sequence data were generated by Oxford Nanopore Sequencing Technology using the amplicon sequencing approach developed by the ARTIC network.

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.

Experience in establishing a high-risk biocontainment facility in response to COVID-19 pandemic under resource constrain settings

The health care systems in resource limited countries are facing major challenges in dealing with Coronavirus disease (COVID-19). In Bangladesh, a steady increase in the number of COVID-19 cases since its first report on March 8, 2020, has led to an increased demand for COVID-19 detection facilities throughout the country. The detection of severe acute respiratory syndrome (SARS-CoV-2), the causative organism of COVID-19 and a highly infectious group 3(three) organism, requires a high biocontainment laboratory with a certain standard prerequisite infrastructure. This study describes the necessary steps for establishing and running a COVID-19 laboratory under resource constraint settings. Our experience indicates that, with collaborative efforts, funding, and technical support from locally available expertise, it is feasible to set up an optimally functional biocontainment facility with an acceptable quality performance despite several short comings. BSMMU J 2021; 14 (COVID -19 Supplement): 45-50

Acceptance of a Symptom-Based Approach for COVID-19 rtRT-PCR Testing to Conserve Resources in a Lower Middle-Income Setting

SARS-CoV-2 initially emerged in Wuhan, China in late 2019. It has since been recognized as a pandemic and has led to great social and economic disruption globally. The Reverse Transcriptase Real-Time Polymerase Chain Reaction (rtRT-PCR) has become the primary method for COVID-19 testing worldwide. The method requires a specialized laboratory set up. Long-term persistence of SARS-CoV-2 RNA in nasopharyngeal secretion after full clinical recovery of the patient is regularly observed nowadays. This forces the patients to spend a longer period in isolation and test repeatedly to obtain evidence of viral clearance. Repeated COVID-19 testing in asymptomatic or mildly symptomatic cases often leads to extra workload for laboratories that are already struggling with a high specimen turnover. Here, we present 5 purposively selected cases with different patterns of clinical presentations in which nasopharyngeal shedding of SARS-CoV-2 RNA was observed in patients for a long time. From these case studies, we emphasized the adoption of a symptom-based approach for discontinuing transmission-based precautions over a test-based strategy to reduce the time spent by asymptomatic and mildly symptomatic COVID-19 patients in isolation. A symptom-based approach will also help reduce laboratory burden for COVID-19 testing as well as conserve valuable resources and supplies utilized for rtRT-PCR testing in an emerging lower-middle-income setting. Most importantly, it will also make room for critically ill COVID-19 patients to visit or avail COVID-19 testing at their convenience.

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.