Coding-complete genomes of 18 SARS-CoV-2 Omicron JN.1, JN.1.4, and JN.1.11 sub-lineages in Bangladesh.

We report 18 coding-complete genome sequences of emerging SARS-CoV-2 Omicron sub-lineages JN.1, JN.1.4, and JN.1.11 from Bangladesh. Nasopharyngeal swab samples were obtained from individuals with COVID-19 symptoms between December 2023 and January 2024. Whole genome sequencing was performed following the ARTIC Network-based protocol using Oxford Nanopore Technology.

Coding-complete genomes of XBB.1.16, XBB.2.3, FL.4 (alias of XBB.1.9.1.4), and XBB.3 of SARS-CoV-2 Omicron isolated from Bangladesh.

We announce the coding-complete genomes of four different strains of SARS-CoV-2 Omicron lineages, XBB.1.16, XBB.2.3, FL.4 (alias of XBB.1.9.1.4), and XBB.3. These strains were obtained between October 2022 and May 2023 from nasopharyngeal swabs of four Bangladeshi individuals, while one of them had a travel history. Genomic data were produced by implementing ARTIC Network-based amplicon sequencing using the Oxford Nanopore Technology.

Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to give rise to a highly transmissive and immune-escaping variant of concern, known as Omicron. Many aspects of the evolution of SARS-CoV-2 and the driving forces behind the ongoing Omicron outbreaks remain unclear. Substitution at the receptor-binding domain (RBD) in the spike protein is one of the primary strategies of SARS-CoV-2 Omicron to hinder recognition by the host angiotensin-converting enzyme 2 (ACE2) receptor and avoid antibody-dependent defense activation. Here, we scanned for adaptive evolution within the SARS-CoV-2 Omicron genomes reported from Bangladesh in the public database GISAID (www.gisaid.org; dated 2 April 2023). The ratio of the non-synonymous (Ka) to synonymous (Ks) nucleotide substitution rate, denoted as ω, is an indicator of the selection pressure acting on protein-coding genes. A higher proportion of non-synonymous to synonymous substitutions (Ka/Ks or ω > 1) indicates positive selection, while Ka/Ks or ω near zero indicates purifying selection. An equal amount of non-synonymous and synonymous substitutions (Ka/Ks or ω = 1) refers to neutrally evolving sites. We found evidence of adaptive evolution within the spike (S) gene of SARS-CoV-2 Omicron isolated from Bangladesh. In total, 22 codon sites of the S gene displayed a signature of positive selection. The data also highlighted that the receptor-binding motif within the RBD of the spike glycoprotein is a hotspot of adaptive evolution, where many of the codons had ω > 1. Some of these adaptive sites at the RBD of the spike protein are known to be associated with increased viral fitness. The M gene and ORF6 have also experienced positive selection. These results suggest that although purifying selection is the dominant evolutionary force, positive Darwinian selection also plays a vital role in shaping the evolution of SARS-CoV-2 Omicron in Bangladesh.

Oral cholera vaccine coverage evaluation survey: Forcibly Displaced Myanmar Nationals and host community in Cox's Bazar, Bangladesh.

Introduction: Cholera remains a significant public health concern in many parts of the world, particularly in areas with poor sanitation and hygiene. Bangladesh and other impoverished nations have been severely affected by cholera outbreaks, especially in areas with a high population density. In order to mitigate the spread of cholera, oral cholera vaccines (OCVs) are recommended as a prophylactic measure. In May 2018, 775,666 of the Forcibly Displaced Myanmar Nationals (FDMN) in the registered and makeshift camps and 103,605 of the residents in the host community received two doses of OCV ShancholTM in Cox's Bazar, Bangladesh, because the conditions in the area favored the transmission of cholera and other waterborne diseases. This study aimed to assess the coverage of OCV among the FDMN and the host community in Cox's Bazar. Methods: In August 2018, we enrolled 4,240 respondents for this study following the "World Health Organization (WHO) Vaccination Coverage Cluster Surveys: Reference Manual (2018)." The coverage survey was conducted with three strata of the population: the host community from the Teknaf Upazila, the registered camp, and the makeshift camp from the Ukhia Upazila. We collected information regarding OCV coverage, demographic characteristics, and knowledge and behaviors of people toward the vaccine. The data were analyzed using descriptive statistics. Results: According to our study, the overall OCV coverage was 85%, with 68% in the host community, 91% in the registered camp, and 98% in the makeshift camp. The lower coverage in the host community was due to residents unaware of the vaccination campaign, the unavailability of vaccines, and unaware where to go for vaccination. Discussion: Our findings demonstrate that the OCV campaign in the FDMN camps was successful, reaching over 90% coverage, while coverage in the host community was much lower. In order to make sure that OCV vaccination efforts are reaching the target population and having the desired impact, our study emphasizes the need to inform the target population of when and where to get vaccinated.

The 2022 dengue outbreak in Bangladesh: hypotheses for the late resurgence of cases and fatalities.

Bangladesh reported the highest number of annual deaths (n = 281) related to dengue virus infection in 2022 since the virus reappeared in the country in 2000. Earlier studies showed that >92% of the annual cases occurred between the months of August and September. The 2022 outbreak is characterized by late onset of dengue cases with unusually higher deaths in colder months, that is, October-December. Here we present possible hypotheses and explanations for this late resurgence of dengue cases. First, in 2022, the rainfall started late in the season. Compared to the monthly average rainfall for September and October between 2003 and 2021, there was 137 mm of additional monthly rainfall recorded in September and October 2022. Furthermore, the year 2022 was relatively warmer with a 0.71°C increased temperature than the mean annual temperature of the past 20 yr. Second, a new dengue virus serotype, DENV-4, had recently reintroduced/reappeared in 2022 and become the dominant serotype in the country for a large naïve population. Third, the post-pandemic return of normalcy after 2 yr of nonpharmaceutical social measures facilitates extra mosquito breeding habitats, especially in construction sites. Community engagement and regular monitoring and destruction of Aedes mosquitoes' habitats should be prioritized to control dengue virus outbreaks in Bangladesh.

Coding-Complete Genome Sequences of 40 SARS-CoV-2 Omicron XBB, XBB.1, and XBB.2 Sublineage Strains in Bangladesh.

Here, we report the coding-complete genome sequences of 40 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains of the newly emerged recombinant Omicron variants XBB, XBB.1, and XBB.2. The strains were isolated from nasopharyngeal swab samples that had been collected from symptomatic patients in Bangladesh between September and October 2022 and were sequenced using an Oxford Nanopore Technologies (ONT) system.

Genome Sequences of 23 SARS-CoV-2 Omicron-Lineage Strains from Bangladesh.

We announce the coding-complete genome sequences of 23 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron strains obtained from Bangladeshi individuals. The Oxford Nanopore Technologies sequencing platform was utilized to generate the genomic data, deploying ARTIC Network-based amplicon sequencing.

Seroprevalence of SARS-CoV-2 antibodies among Forcibly Displaced Myanmar Nationals in Cox's Bazar, Bangladesh 2020: a population-based cross-sectional study.

OBJECTIVES: The study aimed to determine the seroprevalence, the fraction of asymptomatic infections, and risk factors of SARS-CoV-2 infections among the Forcibly Displaced Myanmar Nationals (FDMNs). DESIGN: It was a population-based two-stage cross-sectional study at the level of households. SETTING: The study was conducted in December 2020 among household members of the FDMN population living in the 34 camps of Ukhia and Teknaf Upazila of Cox's Bazar district in Bangladesh. PARTICIPANTS: Among 860 697 FDMNs residing in 187 517 households, 3446 were recruited for the study. One individual aged 1 year or older was randomly selected from each targeted household. PRIMARY AND SECONDARY OUTCOME MEASURES: Blood samples from respondents were tested for total antibodies for SARS-CoV-2 using Wantai ELISA kits, and later positive samples were validated by Kantaro kits. RESULTS: More than half (55.3%) of the respondents were females, aged 23 median (IQR 14-35) years and more than half (58.4%) had no formal education. Overall, 2090 of 3446 study participants tested positive for SARS-CoV-2 antibody. The weighted and test adjusted seroprevalence (95% CI) was 48.3% (45.3% to 51.4%), which did not differ by the sexes. Children (aged 1-17 years) had a significantly lower seroprevalence 38.6% (95% CI 33.8% to 43.4%) compared with adults (58.1%, 95% CI 55.2% to 61.1%). Almost half (45.7%, 95% CI 41.9% to 49.5%) of seropositive individuals reported no relevant symptoms since March 2020. Antibody seroprevalence was higher in those with any comorbidity (57.8%, 95% CI 50.4% to 64.5%) than those without (47.2%, 95% CI 43.9% to 50.4%). Multivariate logistic regression analysis of all subjects identified increasing age and education as risk factors for seropositivity. In children (≤17 years), only age was significantly associated with the infection. CONCLUSIONS: In December 2020, about half of the FDMNs had antibodies against SARS-CoV-2, including those who reported no history of symptoms. Periodic serosurveys are necessary to recommend appropriate public health measures to limit transmission.

Seasonality of influenza and coseasonality with avian influenza in Bangladesh, 2010-19: a retrospective, time-series analysis.

BACKGROUND: Seasonal and avian influenza viruses circulate among human and poultry populations in Bangladesh. However, the epidemiology of influenza is not well defined in this setting. We aimed to characterise influenza seasonality, examine regional heterogeneity in transmission, and evaluate coseasonality between circulating influenza viruses in Bangladesh. METHODS: In this retrospective, time-series study, we used data collected between January, 2010, and December, 2019, from 32 hospital-based influenza surveillance sites across Bangladesh. We estimated influenza peak timing and intensity in ten regions using negative binomial harmonic regression models, and applied meta-analytic methods to determine whether seasonality differed across regions. Using live bird market surveillance data in Dhaka, Bangladesh, we estimated avian influenza seasonality and examined coseasonality between human and avian influenza viruses. FINDINGS: Over the 10-year study period, we included 8790 human influenza cases and identified a distinct influenza season, with an annual peak in June to July each year (peak calendar week 27·6, 95% CI 26·7-28·6). Epidemic timing varied by region (I2=93·9%; p<0·0001), with metropolitan regions peaking earlier and epidemic spread following a spatial diffusion pattern based on geographical proximity. Comparatively, avian influenza displayed weak seasonality, with moderate year-round transmission and a small peak in April (peak calendar week 14·9, 95% CI 13·2-17·0), which was out of phase with influenza peaks in humans. INTERPRETATION: In Bangladesh, influenza prevention and control activities could be timed with annual seasonality, and regional heterogeneity should be considered in health resource planning. Year-round avian influenza transmission poses a risk for viral spillover, and targeted efforts will be crucial for mitigating potential reassortment and future pandemic threats. FUNDING: Canadian Institute of Health Research Vanier Canada Graduate Scholarship.

Genome Sequences of 25 SARS-CoV-2 Sublineage B.1.1.529 Omicron Strains in Bangladesh.

We report the coding-complete genome sequences of 25 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineage B.1.1.529 Omicron strains obtained from Bangladeshi individuals in samples collected between December 2021 and January 2022. Genomic data were generated by Nanopore sequencing using the amplicon sequencing approach developed by the ARTIC Network.

Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh.

Genomics, combined with population mobility data, used to map importation and spatial spread of SARS-CoV-2 in high-income countries has enabled the implementation of local control measures. Here, to track the spread of SARS-CoV-2 lineages in Bangladesh at the national level, we analysed outbreak trajectory and variant emergence using genomics, Facebook 'Data for Good' and data from three mobile phone operators. We sequenced the complete genomes of 67 SARS-CoV-2 samples (collected by the IEDCR in Bangladesh between March and July 2020) and combined these data with 324 publicly available Global Initiative on Sharing All Influenza Data (GISAID) SARS-CoV-2 genomes from Bangladesh at that time. We found that most (85%) of the sequenced isolates were Pango lineage B.1.1.25 (58%), B.1.1 (19%) or B.1.36 (8%) in early-mid 2020. Bayesian time-scaled phylogenetic analysis predicted that SARS-CoV-2 first emerged during mid-February in Bangladesh, from abroad, with the first case of coronavirus disease 2019 (COVID-19) reported on 8 March 2020. At the end of March 2020, three discrete lineages expanded and spread clonally across Bangladesh. The shifting pattern of viral diversity in Bangladesh, combined with the mobility data, revealed that the mass migration of people from cities to rural areas at the end of March, followed by frequent travel between Dhaka (the capital of Bangladesh) and the rest of the country, disseminated three dominant viral lineages. Further analysis of an additional 85 genomes (November 2020 to April 2021) found that importation of variant of concern Beta (B.1.351) had occurred and that Beta had become dominant in Dhaka. Our interpretation that population mobility out of Dhaka, and travel from urban hotspots to rural areas, disseminated lineages in Bangladesh in the first wave continues to inform government policies to control national case numbers by limiting within-country travel.

Genome Sequences of 15 SARS-CoV-2 Sublineage B.1.617.2 Strains in Bangladesh.

We report the coding-complete genome sequences of 15 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineage B.1.617.2 strains that were obtained from Bangladeshi individuals with a history of recent travel to India and from the Bangladeshi community. Genomic data were generated by Nanopore sequencing using the amplicon sequencing approach developed by the ARTIC Network.

Antibody responses after COVID-19 infection in patients who are mildly symptomatic or asymptomatic in Bangladesh.

OBJECTIVES: Studies on serological responses following coronavirus disease-2019 (COVID-19) have been published primarily in individuals who are moderately or severely symptomatic, but there are few data from individuals who are mildly symptomatic or asymptomatic. METHODS: We measured IgG, IgM, and IgA to the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by using enzyme-linked immunosorbent assay in mildly symptomatic (n = 108) and asymptomatic (n = 63) on days 1, 7, 14, and 30 following RT-PCR confirmation in Bangladesh and when compared with pre-pandemic samples, including healthy controls (n = 73) and individuals infected with other viruses (n = 79). RESULTS: Mildly symptomatic individuals developed IgM and IgA responses by day 14 in 72% and 83% of individuals, respectively, while 95% of individuals developed IgG response, and rose to 100% by day 30. In contrast, individuals infected with SARS-CoV-2 but who remained asymptomatic developed antibody responses significantly less frequently, with only 20% positive for IgA and 22% positive for IgM by day 14, and 45% positive for IgG by day 30 after infection. CONCLUSIONS: These results confirm immune responses are generated following COVID-19 who develop mildly symptomatic illness. However, those with asymptomatic infection do not respond or have lower antibody levels. These results will impact modeling needed for determining herd immunity generated by natural infection or vaccination.

Circulating dengue virus serotypes in Bangladesh from 2013 to 2016.

To identify the circulating serotype(s) of dengue viruses in Bangladesh, a retrospective molecular identification was performed on stored serum samples of dengue surveillance during the period of 2013-2016. Real time RT-PCR was performed on serum samples collected from the patients with less than 5 days fever for detection of dengue virus nucleic acid. The samples, positive for dengue PCR were further analyzed for serotypes by real time RT-PCR. The overall prevalence of dengue virus infection was varied among 13-42% in study years with a single peak flanked by April to September. Among the four dengue serotypes DEN1 and DEN2 were in the circulation in three metropolitan cities with sequential emergence of DEN1 where DEN2 was persisted constantly during the study period. Persistence of all four serotypes in the neighboring country makes Bangladesh vulnerable for devastating secondary infection by introduction of new serotype(s) other than currently circulating viruses in the country. Thus continuous virological surveillance is crucial for early warning of emergence of new serotype in the circulation and public health preparedness.

Event based surveillance of Middle East Respiratory Syndrome Coronavirus (MERS- CoV) in Bangladesh among pilgrims and travelers from the Middle East: An update for the period 2013-2016.

INTRODUCTION: Every year around 150,000 pilgrims from Bangladesh perform Umrah and Hajj. Emergence and continuous reporting of MERS-CoV infection in Saudi Arabia emphasize the need for surveillance of MERS-CoV in returning pilgrims or travelers from the Middle East and capacity building of health care providers for disease containment. The Institute of Epidemiology, Disease Control & Research (IEDCR) under the Bangladesh Ministry of Health and Family welfare (MoHFW), is responsible for MERS-CoV screening of pilgrims/ travelers returning from the Middle East with respiratory illness as part of its outbreak investigation and surveillance activities. METHODS: Bangladeshi travelers/pilgrims who returned from the Middle East and presented with fever and respiratory symptoms were studied over the period from October 2013 to June 2016. Patients with respiratory symptoms that fulfilled the WHO MERS-CoV case algorithm were tested for MERS-CoV and other respiratory tract viruses. Beside surveillance, case recognition training was conducted at multiple levels of health care facilities across the country in support of early detection and containment of the disease. RESULTS: Eighty one suspected cases tested by real time PCR resulted in zero detection of MERS-CoV infection. Viral etiology detected in 29.6% of the cases was predominantly influenza A (H1N1 and H3N2), and influenza B infection (22%). Peak testing occurred mostly following the annual Hajj season. CONCLUSIONS: Respiratory tract infections in travelers/pilgrims returning to Bangladesh from the Middle East are mainly due to influenza A and influenza B. Though MERS-CoV was not detected in the 81 patients tested, continuous screening and surveillance are essential for early detection of MERS-CoV infection and other respiratory pathogens to prevent transmissions in hospital settings and within communities. Awareness building among healthcare providers will help identify suspected cases.