High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139.

Toxigenic Vibrio cholerae of the O139 serogroup have been responsible for several large cholera epidemics in South Asia, and continue to be of clinical and historical significance today. This serogroup was initially feared to represent a new, emerging V. cholerae clone that would lead to an eighth cholera pandemic. However, these concerns were ultimately unfounded. The majority of clinically relevant V. cholerae O139 isolates are closely related to serogroup O1, biotype El Tor V. cholerae, and comprise a single sublineage of the seventh pandemic El Tor lineage. Although related, these V. cholerae serogroups differ in several fundamental ways, in terms of their O-antigen, capsulation phenotype, and the genomic islands found on their chromosomes. Here, we present four complete, high-quality genomes for V. cholerae O139, obtained using long-read sequencing. Three of these sequences are from toxigenic V. cholerae, and one is from a bacterium which, although classified serologically as V. cholerae O139, lacks the CTXφ bacteriophage and the ability to produce cholera toxin. We highlight fundamental genomic differences between these isolates, the V. cholerae O1 reference strain N16961, and the prototypical O139 strain MO10. These sequences are an important resource for the scientific community, and will improve greatly our ability to perform genomic analyses of non-O1 V. cholerae in the future. These genomes also offer new insights into the biology of a V. cholerae serogroup that, from a genomic perspective, is poorly understood

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

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

Molecular dating of HIV-1 subtype C from Bangladesh.

Bangladesh has an overall low HIV prevalence of <0.1% in the general population and <1% among key affected populations, but it is one of few Asian countries that has yet to reverse the epidemic. In order to do this, it is important to understand the transmission dynamics in this country. The aim of this study was to investigate the phylogenetic relationships of HIV-1 subtype C strains from Bangladesh and related strains from other countries, and thereby clarify when and from where subtype C was introduced in the country and how it subsequently spread within Bangladesh. The phylogenetic analysis included 118 Bangladeshi gag sequences and 128 sequences from other countries and was performed using the BEAST package. Our analysis revealed that the vast majority of Bangladeshi sequences (97/118, 82%) fall into a large regional cluster of samples from Bangladesh, India, China and Myanmar, which dates back to the early 1960's. Following its establishment in the region, this strain has entered Bangladesh multiple times from around 1975 and onwards, but extensive in-country transmission could only be detected among drug users and not through sexual transmission. In addition, there have been multiple (at least ten) introductions of subtype C to Bangladesh from outside this region, but no extensive spread could be detected for any of these. Since many HIV-infections remain undetected while asymptomatic, the true extent of the transmission of each strain remains unknown, especially among hard to reach groups such as clients of sex workers and returning migrants with families

High incidence of reassortant G9P[4] rotavirus strain in Bangladesh: Fully heterotypic from vaccine strains

publisher: Elsevier articletitle: High incidence of reassortant G9P[4] rotavirus strain in Bangladesh: Fully heterotypic from vaccine strains journaltitle: Journal of Clinical Virology articlelink: http://dx.doi.org/10.1016/j.jcv.2013.09.024 content_type: simple-article copyright: Copyright © 2013 Elsevier B.V. All rights reserved.status: publishe

Peripheral blood buffy coat smear: a promising tool for diagnosis of visceral leishmaniasis

Confirmative diagnosis of visceral leishmaniasis (VL) is still a challenge at the primary health care facilities in most of the rural areas of endemicity in the Indian subcontinent. Conventional methods for parasitological confirmation are risky and require skilled personnel, and hence they are unavailable to the poor people in the regions of endemicity. Buffy coat smear microscopy, as a minimally invasive, simple alternative for the parasitological diagnosis of VL, was evaluated in this prospective study. One hundred twelve VL patients were enrolled in this study. The buffy coat was separated from peripheral blood of all enrolled subjects using Histopaque-1119 solution. Leishman-stained buffy coat smears were examined for Leishmania donovani bodies, and buffy coat was also utilized for detection of parasite DNA by Leishmania nested PCR (LnPCR) for all cases. Concomitant splenic smears could be examined for L. donovani bodies in 66 cases, and the parasite load was graded on a scale of 1 + to 6 + for L. donovani-positive smears. All splenic smear-positive cases were also found to be positive by LnPCR. Of 112 enrolled VL cases, 103 (92%) were found to be positive for L. donovani bodies in buffy coat smear microscopy, which is promising as a confirmative diagnosis tool. We have also found a significant association of the buffy coat smear positivity with parasitic burden in the spleen smear. In this preliminary observation in Bangladesh, buffy coat smear microscopy has been found to be very simple, minimally invasive, and risk-free method of parasitological diagnosis of VL with a good diagnostic accuracy and potential for field use

High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139

Abstract Toxigenic Vibrio cholerae of the O139 serogroup have been responsible for several large cholera epidemics in South Asia, and continue to be of clinical and historical significance today. This serogroup was initially feared to represent a new, emerging V. cholerae clone that would lead to an eighth cholera pandemic. However, these concerns were ultimately unfounded. The majority of clinically relevant V. cholerae O139 isolates are closely related to serogroup O1, biotype El Tor V. cholerae, and comprise a single sublineage of the seventh pandemic El Tor lineage. Although related, these V. cholerae serogroups differ in several fundamental ways, in terms of their O-antigen, capsulation phenotype, and the genomic islands found on their chromosomes. Here, we present four complete, high-quality genomes for V. cholerae O139, obtained using long-read sequencing. Three of these sequences are from toxigenic V. cholerae, and one is from a bacterium which, although classified serologically as V. cholerae O139, lacks the CTXφ bacteriophage and the ability to produce cholera toxin. We highlight fundamental genomic differences between these isolates, the V. cholerae O1 reference strain N16961, and the prototypical O139 strain MO10. These sequences are an important resource for the scientific community, and will improve greatly our ability to perform genomic analyses of non-O1 V. cholerae in the future. These genomes also offer new insights into the biology of a V. cholerae serogroup that, from a genomic perspective, is poorly understood

Phylogenetic tree of 246 <i>gag</i>-sequences, including 118 Bangladeshi HIV-1 C strains in green.

<p>The HIV1-C strains found in Bangladesh do not fall into a country specific clade, instead our results point to repeated introductions with substantial in-country transmission only among PWIDs. Four clades with ≥3 BD strains had a posterior probability of around 0.7 or higher, and are shown in the figure. <b><i>Clade</i><i> 1</i></b> is a monophyletic clade of 47 BD strains, of which 43 originate from PWIDs in Dhaka. The tMRCA of this clade is around 1975. It is a subset of the large regional <b><i>Clade</i><i> 2</i></b>, which is dominated by strains from Bangladesh, Myanmar, India and China. Over 80% of all BD strains can be found within this clade, which appears to have been introduced to this region around 1962. The intermixing of sequences collected from different countries indicates frequent cross-border transmission in this region. In addition to the 47 strains in Clade 1, the BD strains in Clade 2 includes sequences from returning migrants from Nepal, India and the Middle East as well as some weakly supported clades of strains from sex workers and VCT/STI patients. <b><i>Clade</i><i> 3</i></b> consists of seven PWID strains from Dhaka, and the short branches in this clade reveal rapid transmission (and detection) within this group. <b><i>Clade</i><i> 4</i></b> contains five strains from VCT visitors in Dhaka and Chittagong, at least 3 of whom had a history of migrant work in the Middle East. The long branches show that they are not very close genetically and it is possible that they represent separate introductions of related strains. Most of the BD strains found outside these clades appear to represent separate introductions.</p

Genomic epidemiology of Vibrio cholerae during a mass vaccination campaign of displaced communities in Bangladesh

Abstract Ongoing diarrheal disease surveillance throughout Bangladesh over the last decade has revealed seasonal localised cholera outbreaks in Cox’s Bazar, where both Bangladeshi Nationals and Forcibly Displaced Myanmar Nationals (FDMNs) reside in densely populated settlements. FDMNs were recently targeted for the largest cholera vaccination campaign in decades. We aimed to infer the epidemic risk of circulating Vibrio cholerae strains by determining if isolates linked to the ongoing global cholera pandemic (“7PET” lineage) were responsible for outbreaks in Cox’s Bazar. We found two sublineages of 7PET in this setting during the study period; one with global distribution, and a second lineage restricted to Asia and the Middle East. These subclades were associated with different disease patterns that could be partially explained by genomic differences. Here we show that as the pandemic V. cholerae lineage circulates in this vulnerable population, without a vaccine intervention, the risk of an epidemic was very high