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.

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.

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.

Whole genome sequencing data of Chromobacterium amazonense BASUSDA_45 isolated from soil in Bangladesh capable of degrading pesticide.

This article reports the Chromobacterium amazonense BASUSDA_45 strain's draft genomic sequence. The bacterium was isolated from cypermethrin pesticide contaminated soil and then the sequencing was carried out. Initially de novo assembly of the raw sequences, trimming and quality check generates 125 contigs having N50 of 78,923. Further mapping of the contigs generated scaffolds. The genome contains 53 scaffolds with a total length of 4,295,151 bp having 62.30% GC content and N50 of 3,726,017. Annotation using Prokaryotic Genome Annotation Pipeline (PGAP) reveals 4181 genes among which 4096 were coding sequences, 76 tRNAs, 3 rRNAs, 4 noncoding RNAs. The raw sequence reads and annotated genome were uploaded to NCBI's Bioproject repository with the accession number PRJNA686506.

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.

The Sporisorium reilianum Effector Vag2 Promotes Head Smut Disease via Suppression of Plant Defense Responses.

Genome comparison between the maize pathogens Ustilago maydis and Sporisorium reilianum revealed a large diversity region (19-1) containing nearly 30 effector gene candidates, whose deletion severely hampers virulence of both fungi. Dissection of the S. reilianum gene cluster resulted in the identification of one major contributor to virulence, virulence-associated gene 2 (vag2; sr10050). Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) experiments revealed high expression of vag2 during biotrophic growth of S. reilianum. Using the yeast secretion trap assay, we confirmed the existence of a functional signal peptide allowing protein secretion via the conventional secretory pathway. We identified the cytoplasmic maize chorismate mutase ZmCM2 by yeast two-hybrid screening as a possible interaction partner of Vag2. Interaction of the two proteins in planta was confirmed by bimolecular fluorescence complementation. qRT-PCR experiments revealed vag2-dependent downregulation of salicylic acid (SA)-induced genes, which correlated with higher SA levels in plant tissues colonized by Δvag2 deletion strains relative to S. reilianum wildtype strains. Metabolite analysis suggested rewiring of pathogen-induced SA biosynthesis by preferential conversion of the SA precursor chorismate into the aromatic amino acid precursor prephenate by ZmCM2 in the presence of Vag2. Possibly, the binding of Vag2 to ZmCM2 inhibits the back reaction of the ZmCM2-catalyzed interconversion of chorismate and prephenate, thus contributing to fungal virulence by lowering the plant SA-induced defenses.

Whole-Genome Sequencing of Klebsiella pneumoniae BASUSDALSc45PDB48, a Unique Strain Capable of Growing in Pesticide-Containing Medium, Isolated from Soil in Bangladesh.

We report the draft genome sequence of Klebsiella pneumoniae strain BASUSDALSc45PDB48, isolated from pesticide-contaminated soil; this strain showed the ability to grow in a medium with cypermethrin as the only carbon source. The genome assembly comprised 5,249,704 bp, with 128.17 Ns per 100 kbp, an N50 value of 5,035,968 bp, a GC content of 57.57%, and 5,349 annotated genes.