Bangladeshi Isolates Research Articles

Phylogenetic and Whole Genome Analysis of First Seven SARS-CoV-2 Isolates in Bangladesh

Aim: Whole genome and peptide mutation analysis can specify effective vaccine and therapeutics against severe acute respiratory coronavirus-2 (SARS-CoV-2). Materials & methods: Whole genome similarity for Bangladeshi SARS-CoV-2 was determined using ClustalW and BLASTn. Phylogenetic analysis was conducted using neighbor-joining method. Results: 100% of isolates in Bangladesh were in the G clade. We found 99.98–100% sequence similarity among Bangladeshi isolates and isolates of England, Greece, USA, Saudi Arabia and India. Deletion of bases at 5′ untranslated region and 3′ untranslated region was detected. Substitution 261 (E→D) at NSP13 and 1109 (F→L) at spike (S) protein were detected. Substitution 377 (D→G) at nucleocapsid with common substitution 614 (D→G) at S were also detected. Conclusion: This study will provide baseline data for development of an effective vaccine or therapeutics against SARS-CoV-2.

Molecular detection and identification of eight potato viruses in Gansu province of China

Potato (Solanum tuberosum), a major food crop in the world is commonly infected with viral diseases, causing a loss in both quality and quantity of this crop. To determine the prevalence of eight important potato viruses in Gansu province of China, tuber samples were collected from Weiheyuan potato seed industry development Co., Ltd., and nineteen different commercial potato production fields at different locations in October 2018. Viruses were identified by RT-PCR using coat protein (CP)-specific primers, and validated by cloning three PCR positive amplicons of each virus followed by sequencing of three positive clones from each plasmid. Sequences were deposited in the GenBank. RT-PCR results demonstrated that mixed infections were very common in the collected tuber samples. Mixed infection of Potato virus X (PVX) and Potato virus S (PVS) caused 12.5 %; PVX and Potato aucuba mosaic virus (PAMV) caused 20.83 %; PVX, PVS and PAMV caused 12.5 %; PVX, Potato virus H (PVH) and PAMV caused 8.33 %; Potato leafroll virus (PLRV), PVX, PVS and PAMV caused 8.33 %; PVX, PVS, PVH and PAMV caused 16.67 %; PLRV, PVX, PVS, PVH and PAMV caused 8.33 %; and PVX, PVS, PVH, PAMV and Potato virus M (PVM) caused 4.17 % tuber infection, respectively; whereas, Potato virus Y (PVY) and Potato virus A (PVA) were not detected. PVY and PVA requires further testing in the future, and the result for these two viruses in the current study cannot be validated due to the lack of positive controls. PVS and PVH were also confirmed by western blot analysis. Phylogenetic analysis further revealed that the PLRV from Gansu was closely related to a Guangdong isolate (GenBank accession no. MF062487), PVX was closely related to a Shandong isolate (GenBank accession no. AF628555), PVS was closely related to a Guangxi isolate (GenBank accession no. KF011279) and an Australi isolate (GenBank accession no. GU319949), PVH was closely related to a Yunnan isolate (GenBank accession no. JQ904630), PAMV was closely related to a Bangladeshi isolate (GenBank accession no. MF133526), and PVM was closely related to a Tanzania isolate (GenBank accession no. KC866622). These findings will provide a basis for control of potato viruses in this region in the future.

Effectiveness of the Wheat Blast Resistance Gene Rmg8 in Bangladesh Suggested by Distribution of an AVR-Rmg8 Allele in the Pyricularia oryzae Population.

Wheat blast caused by the Triticum pathotype of Pyricularia oryzae was first reported in 1985 in Brazil and recently spread to Bangladesh. We tested whether Rmg8 and RmgGR119, recently identified resistance genes, were effective against Bangladeshi isolates of the pathogen. Common wheat accessions carrying Rmg8 alone (IL191) or both Rmg8 and RmgGR119 (GR119) were inoculated with Brazilian isolates (Br48, Br5, and Br116.5) and Bangladeshi isolates (T-108 and T-109). Br48, T-108, and T-109 carried the eI type of AVR-Rmg8 (the avirulence gene corresponding to Rmg8) while Br5 and Br116.5 carried its variants, eII and eII' types, respectively. Detached primary leaves of IL191 and GR119 were resistant to all isolates at 25°C. At a higher temperature (28°C), their resistance was still effective against the eI carriers but was reduced to a low level against the eII/eII' carriers. A survey of databases and sequence analyses revealed that all Bangladeshi isolates carried the eI type which induced a higher level of resistance than the eII/eII' types. The resistance of IL191 (Rmg8/-) to the eI carriers was maintained even at the heading stage and at the higher temperature. In addition, GR119 (Rmg8/RmgGR119) displayed higher levels of resistance than IL191 at this stage. These results suggest that Rmg8 combined with RmgGR119 will be useful in breeding for resistance against wheat blast in Bangladesh.

RT-PCR Based Cloning and Sequencing of Potato Leaf Roll Virus-Coat Protein (PLRV-CP) Gene for Characterization as a Bangladeshi PLRV Isolate and Its Phylogenetic Analysis

An experiment was conducted in Molecular Biology and Plant Virology Laboratory under the Department of Plant Pathology, Sher-e-Bangla Agricultural University, Dhaka-1207, Bangladesh. Total RNA was extracted from Potato leaf roll virus (PLRV) positive leaves and complementary DNA (cDNA) were synthesized from total RNA. Reverse transcriptase polymerase chain reaction (RT-PCR) based detection conditions were optimized by using coat protein (CP) gene specific primers. In PCR amplification cDNA and in nucleotide sequencing PCR product was used as a template. A 346 bp amplicon of PLRV- CP gene was amplified and amplified gene region was sequenced. The expected nucleotide sequence of amplified PLRV-CP gene showed 95 to 98% homology when compared with the isolates sequences reported in Gene Bank database. This explored novel PLRV-CP gene was characterized as a PLRV Bangladeshi isolate (Accession number, Bankit 2274496, MN605963). PLRV-CP gene protein modeling was carried out using Expert Protein Analysis System (ExPaSy), DNASTAR’s protein tools server used for 3D protein modeling. Phylogenetic analysis was also carried out, the tree was made by using MEGA 4.0 software and maximum parsimony method was selected to construct phylogenetic tree. The RT-PCR based molecular technique optimized in this study, would be a useful for early detection, epidemiological studies of PLRV as well as in seed tubers certification program and the novel hyper variable sequenced region of PLRV-CP gene will be useful in pathogen derived resistance breeding program against the PLRV local strain.

Prediction of B-cell and T-cell epitopes in the spike glycoprotein of SARS-CoV-2 in Bangladesh: An in-silico approach

To combat highly infectious Severe Acute Respiratory SyndromeICLE Coronavirus 2 (SARS-CoV-2), scientists and researchers are toiling hard globally to develop effective drugs and vaccines. By exploring the structural proteins of SARS-CoV-2 can be a feasible way to find an effective vaccine. In this study by using in-silico tools, we recommended B-cell and T-cell epitopes of spike protein from a Bangladeshi isolate which can be considered for incorporation into a vaccine against the SARS-CoV-2. Homology modelling, energy minimization process, and finally Ramachandran model was used for the prediction of a more stable conformation of the spike protein. The most important peptides were screened through the VaxiJen server followed by the IEDB server and CTLPred Score predicted and analysed the desired epitopes. In the final analysis, the peptide EVRQIAPGQTGKIADY (starting from 91) showed the highest antigenicity score (1.3837) as a B-cell epitope although GSTPCNGVEGFNCYFP, starting at 161, showed highest score (0.91) in an initial analysis. On the contrary, as a T-cell epitope, 71 KLNDLCFTNV-80 was found with the highest antigenicity score (2.6927) which was also found as an epitope in further analysis. A combination of B-cell and T-cell epitopes may evoke a humoral and cell-mediated immune response which will possibly lead to an effective vaccine. Further, the various computational analyses will provide valuable information that will pave the way for modelling a novel vaccine against SARS-CoV-2. © 2020, Bangladesh Society for Microbiology, Immunology and Advanced Biotechnology. All rights reserved.

A new reassortant clade 2.3.2.1a H5N1 highly pathogenic avian influenza virus causing recent outbreaks in ducks, geese, chickens and turkeys in Bangladesh.

A total of 15 dead or sick birds from 13 clinical outbreaks of avian influenza in ducks, geese, chickens and turkeys in 2017 in Bangladesh were examined. The presence of H5N1 influenza A virus in the affected birds was detected by RT-PCR. Phylogenetic analysis based on full-length gene sequences of all eight gene segments revealed that these recent outbreaks were caused by a new reassortant of clade 2.3.2.1a H5N1 virus, which had been detected earlier in 2015 during surveillance in live bird markets (LBMs) and wet lands. This reassortant virus acquired PB2, PB1, PA, NP and NS genes from low pathogenic avian influenza viruses mostly of non-H9N2 subtypes but retained HA, NA and M genes of the old clade 2.3.2.1a viruses. Nevertheless, the HA gene of these new viruses was 2.7% divergent from that of the old clade 2.3.2.1a viruses circulated in Bangladesh. Interestingly, similar reassortment events could be traced back in four 2.3.2.1a virus isolates of 2013 from backyard ducks. It suggests that this reassortant virus emerged in 2013, which took two years to be detected at a broader scale (i.e. in LBMs), another two years until it became widely spread in poultry and fully replaced the old viruses. Several mutations were detected in the recent Bangladeshi isolates, which are likely to influence possible phenotypic alterations such as increased mammalian adaptation, reduced susceptibility to antiviral agents and reduced host antiviral response.

A novel multilocus sequence typing scheme identifying genetic diversity amongst Leishmania donovani isolates from a genetically homogeneous population in the Indian subcontinent

In the Indian subcontinent, infection with Leishmania donovani can cause fatal visceral leishmaniasis. Genetic variation in L. donovani is believed to occur rapidly from environmental changes and through selective drug pressures, thereby allowing continued disease occurrence in this region. All previous molecular markers that are commonly in use multilocus microsatellite typing and multilocus sequence typing, were monomorphic in L. donovani originating from the Indian subcontinent (with only a few exceptions) and hence are not suitable for this region. An multilocus sequence typing scheme consisting of a new set of seven housekeeping genes was developed in this study, based on recent findings from whole genome sequencing data. This new scheme was used to assess the genetic diversity amongst 22 autochthonous L. donovani isolates from Bangladesh. Nineteen additional isolates of the L. donovani complex (including sequences of L. donovani reference strain BPK282A1) from other countries were included for comparison. By using restriction fragment length polymorphism of the internal transcribed spacer 1 region (ITS1-RFLP) and ITS1 sequencing, all Bangladeshi isolates were confirmed to be L. donovani. Population genetic analyses of 41 isolates using the seven new MLST loci clearly separated L. donovani from Leishmania infantum. With this multilocus sequence typing scheme, seven genotypes were identified amongst Bangladeshi L. donovani isolates, and these isolates were found to be phylogenetically different compared with those from India, Nepal, Iraq and Africa. This novel multilocus sequence typing approach can detect intra- and inter-species variations within the L. donovani complex, but most importantly these molecular markers can be applied to resolve the phylogenetically very homogeneous L. donovani strains from the Indian subcontinent. Four of these markers were found suitable to differentiate strains originating from Bangladesh, with marker A2P being the most discriminative one.

Investigation on a Bangladeshi isolate Bacillus aryabhattai for promising biotechnological applications

A new isolate was investigated from soil sample collected from Shahrasti upazilla of Chandpur district of Bangladesh. Based on the physico-chemical studies the strain was identified as gram positive Bacilli. Moleculer characterization of the strain was identified as Bacillus aryabhattai which is the first report in Bangladesh. The strain can survive in extreme conditions of salt, temperature and pH. This strain was further characterized and screened for the ability to produce useful enzymes. The optimum temperature for growth and production of these enzymes was within the temperature range 35oC to 40oC. The pH was found to be 7 for its growth and production of different enzymes when investigated over 48 h of incubation. The isolate produced various extracellular enzymes such as α-amylases, cellulases, β-glucosidases, lipases and proteases. The findings of this study provide useful information of the new strain that has potential biotechnological applications.
 Jahangirnagar University J. Biol. Sci. 7(2): 33-45, 2018 (December)

Molecular analysis of hemagglutinin, neuraminidase, matrix genes provide insight into the genetic diversity of seasonal H3N2 human influenza a viruses in Bangladesh during July-August, 2012.

Influenza A virus subtype H3 is a threat to public health and it is important to understand the evolution of the viruses for the surveillance and the selection of vaccine strains. Comparative analysis of four Bangladeshi isolates with isolates circulating other parts of the world based on three candidate genes hemagglutinin (HA), neuraminidase (NA), matrix protein (MA) showed no evidence of significant distinct subclade of viruses circulating in the country over the period of study. Despite these findings, we found N161S substitution in all four H3N2 influenza stains resulting in the gain of NSS160-162 glycosylation site. All H3N2 Influenza subtypes in the study had amino acid substitution at position 31 on the M2 protein (Aspartic acid to Asparagine) which is known to be responsible for amantadine drug resistance.

Introduction of Zika virus in Bangladesh: An impending public health threat.

To explore the presence of Zika virus (ZIKV) in Bangladesh and to understand the associated risk factors. A retrospective sero-surveillance was performed on stored serum samples of dengue surveillance conducted from 2013 to 2016. Real time RT-PCR was performed on randomly selected acute serum samples to detect the Zika virus nucleic acid. Of 200 samples screened, one was found positive for ZIKV by real time RT-PCR and further confirmed by genome sequencing. The case was a 65 years old male from a metropolitan city of Bangladesh who had no history of travel outside Bangladesh. Phylogenetic analysis of partial E gene sequences from Bangladeshi isolates demonstrated a close relationship with ZIKV from Brazil and current South American strains clustering within a monophyletic clade distinct from African lineage. Presence of ZIKV raises serious public health concerns in Bangladesh owing to its association with congenital anomalies/neurological-manifestations. We, therefore, recommend every suspected viral fever patient, particularly pregnant women be screened for ZIKV infection to rule out yet another emerging infection in Bangladesh.

Identification of Ribonuclease Z Gene from an Outbreak of Riemerella anatipestifer Infection in Ducks of Bangladesh

Duck septicemia is a deadly disease of duck causing huge economic losses in duck rearing areas. Despite its importance, no study was devoted to unravel the Riemerella (Pasteurella) anatepestifer in Bangladesh. Therefore, a systemic investigation was carried out to identify the isolate targeting ribonuclease Z gene from an outbreak in 2013-2014. Samples were collected from sixty randomly selected dead ducks from three outbreaks areas of North East Bangladesh (Netrokona district). Histopathological, cultural and sugar fermentation test of all samples revealed the infectivity with R. anatipestifer. Polymerase chain reaction specific to R. anatipestifer identified the 421 bp fragment of ribonuclease Z gene in thirty seven cases. Identified gene of the isolate was sequenced (Accession No. KU992381) and phylogenetic lineage was analyzed for the first time in Bangladesh. The phylogenetic analysis showed that Bangladeshi isolate R. anatipestifer BD 2014 resembles highest similarity with the R. anatipesrifer isolated from ducks of china. This study provide evidence that duck septicemia could be the main culprit of mortality in growing ducks in the duck rearing areas. Further investigation is needed to identify secondary or co-infection state as well as the prevalence of this infection including the economic burdens in duck industry in Bangladesh.

Species-Specific Immunodetection of an Entamoeba histolytica Cyst Wall Protein.

Entamoeba histolytica causes intestinal disease in endemic settings throughout the world. Diagnosis of E. histolytica infection would be improved by the identification of biomarkers that are expressed by cysts of E. histolytica, but not by cysts of closely related commensal species of Entamoeba. Herein, we describe two novel monoclonal antibodies (1A4 and 1D3) produced against a spacer region of the E. histolytica Jacob2 lectin, an outer cyst wall protein. These reagents demonstrated no cross-reaction to E. dispar recombinant antigen and low picomolar molecular detection limits when paired in ELISA sandwich assays. In an immunofluorescence microscopy assay, the α-Jacob2 murine antibodies labeled cysts of three xenically cultured E. histolytica isolates but did not label cysts of three E. bangladeshi isolates. Monoclonal antibody 1A4 did not cross-react with xenic cultures of three E. dispar isolates, demonstrating specificity to E. histolytica, while monoclonal antibody 1D3 cross-reacted with two out of three E. dispar isolates. Both antibodies labeled cysts in formalin-fixed slides, a potential logistical advantage in some settings. The monoclonal antibody 1A4 was also used in an immunofluorescence microscopy assay with formalin-fixed stool specimens. Seven out of ten ELISA-positive stool specimens exhibited 1A4-labeled cyst-like objects, compared to one out of seven ELISA-negative specimens. These results demonstrate that antibodies generated against the flexible spacer of E. histolytica Jacob2 lectin recognize and bind to Jacob2 protein in whole cysts and are capable of differentiating Entamoeba species in fixed specimens. Thus, Jacob2 is a promising biomarker for use in diagnosing E. histolytica infection.

Isolation, identification and molecular characterization of contagious ecthyma virus from goat and sheep

Contagious ecthyma (CE) is one of the most widespread viral diseases; primarily affect goat and sheep but also reported from human, reindeer, musk ox, dog, cat, red squirrel etc. The disease is caused by contagious ecthyma virus (CEV) and he virus is circulating in Bangladesh. Present study was aimed at isolation, identification and molecular characterization of the CEV circulating in Bangladesh. A total of 13 samples (scab materials; 11 from goat and 2 from sheep) were collected from three different farms of Sylhet and Dhaka divisions followed by processing for virus detection by PCR and isolation in Vero cell. Four different sets of primers were used targeting four different genes of CEV. Of these samples, 10 (8 from goat and 2 from sheep) were found positive by PCR. From these positive samples three viruses were isolated. Sequencing of different genes of several CEV isolates has been done directly from PCR product using automated DNA sequencer 3010 Genetic Analyzer available at the National Reference Laboratory for Avian Influenza (NRL-AI), Bangladesh. Bangladeshi isolates were found to have 95-99% identity to each other. When compared to viruses from other countries, high homology (92-96%) was observed to viruses from New Zealand and India, and phylogenetically clustered with them. This is the first report of molecular characterization, though partial, of CEV in Bangladesh.Bangladesh J. of Livestock Res. 19(1-2): 97-106, Jan-Dec 2012

Phylogeny and synonymous codon usage pattern ofPapaya ringspot viruscoat protein gene in the sub-Himalayan region of north-east India

Sub-Himalayan West Bengal is favorable for the production of several fruits and vegetables. Papaya is one of the common plants cultivated in the area. Most of the papaya plants of the area are susceptible to Papaya ringspot virus (PRSV). Coat protein genes of 6 PRSV isolates of the area were sequenced following RT-PCR. Phylogenetic study of the PRSV isolates showed about 80%-90% similarity with Cuban isolates. The codon usage pattern of our isolates was also analyzed, along with several other isolates. PRSV isolates of our study showed a preference for 8 putative optimal codons. Correspondence analysis of the genes of different isolates along the first 2 major axes were done, as the first 2 axes contributed more in shaping codon usage pattern. In the phylogenetic tree constructed by the neighbour-joining method, our isolates clustered together with the east Indian, north Indian, and Bangladeshi isolates. The diversity and codon usage pattern of the PRSV isolates of different regions were studied, and it was observed that the codon usage pattern of PRSV isolates is probably influenced by translational selection along with mutational bias.

Isolation and Molecular Characterization of Vp2 Gene of Infectious Bursal Disease: Demonstrated No Predominant New Strains Circulating in Bangladesh

The present study was conducted for molecular characterization of Bangladeshi isolates of Infectious Bursal Disease virus to establish genetic diversity with other European and Asian strains. A total of 129 bursa of Fabricius were collected after post mortem from IBD infected chicken. Only 30 samples were confirmed for IBDV by amplification of a 729-bp fragment of the VP2 gene hyper variable region using RT-PCR. The hyper variable region (aa 184-426) of amplified VP2 fragments of the 30 IBDV isolates were sequenced and compared with 10 strains published in Gene Bank and their phylogenic relationship were analyzed. Amino acid sequences analysis of the hyper variable region of the VP2 gene revealed that 27 isolates were 99% identical with European and Asian vvIBDV strains and 3 isolates showed close relationship with classical strains of IBDV. Twenty seven Bangladeshi vvIBDV isolates encode amino acids 222A, 2421, 2561, 294I, and 299S, which are conserved among other vvIBDV strains. The 3 Classical isolates showed amino acid substitutions at 222A→P, 256I→V, and 299 S→N positions. All isolates had the same heptapeptide 279D, S-W-S-A-S-G-S (326→332), and 284A. Phylogenetic analysis based on the nucleotide sequence revealed that the Bangladeshi isolates were closely related to European and Asian vvIBDV. Taken together, there was no predominant new strain circulating in Bangladesh during June 2009-May 2011. Moreover, in order to protect birds from the sudden emergence of new predominant strains, continuing surveillance of IBDV strains circulating in the field is of utmost importance.

Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh

Babesia gibsoni is a tick-borne hemoprotozoan parasite of dogs that often causes fever and hemolytic illness. Detection of B. gibsoni has been predominantly reported in Asian countries, including Japan, Korea, Taiwan, Malaysia, Bangladesh and India. The present study shows the first molecular characterization of B. gibsoni detected from dogs in Bangladesh. Blood samples were collected on FTA® Elute cards from 50 stray dogs in Mymensingh District in Bangladesh. DNA eluted from the cards was subjected to nested PCR for the 18S rRNA gene of Babesia species. Approximately 800bp PCR products were detected in 15 of 50 dogs (30%). Based on restriction fragment length polymorphism (RFLP) and direct sequencing of the PCR products, all parasite isolates were identified as B. gibsoni. Furthermore, the BgTRAP (B. gibsoni thrombospondin-related adhesive protein) gene fragments were detected in 13 of 15 18S rRNA gene PCR positive blood samples. Phylogenetic analysis of the BgTRAP gene revealed that B. gibsoni parasites in Bangladesh formed a cluster, which was genetically different from other Asian B. gibsoni isolates. In addition, tandem repeat analysis of the BgTRAP gene clearly showed considerable genetic variation among Bangladeshi isolates. These results suggested that B. gibsoni parasites in a different genetic clade are endemic in dogs in Bangladesh. Further studies are required to elucidate the origin, distribution, vector and pathogenesis of B. gibsoni parasites circulating in dogs in Bangladesh.

Molecular characterization of Duck Plague virus isolated from Bangladesh

Duck plague (DP) is the most feared duck disease in the world. For isolation, identification, molecular detection and characterization of DP virus (DPV), a total of 94 samples were collected from commercial farms (n=6) and households (n=13) from Rajshahi (n=37), Netrokona (n=35) and Mymensingh (n=22) districts of Bangladesh. The samples were processed and inoculated into 11-13 days old embryonated duck eggs for virus propagation. Virus was identified using agar gel immunodiffusion test (AGIT) and passive hemagglutination (PHA) test, and was confirmed by polymerase chain reaction (PCR) targeting DNA polymerase and gC genes, followed by sequencing. Pathogenicity tests were performed using duck embryos, ducklings and ducks. Among the 94 samples, 17 isolates were confirmed as DPV by PCR amplification of partial DNA polymerase (446-bp) and gC genes (78-bp), respectively. One of the isolates (Anatid herpes 1 BAU DMH) was sequenced and found to be closely related with a Chinese variant of DPV (GenBank: JQ647509.1). Thus, we assume that both Bangladeshi and Chinese isolates of DPV may have a common ancestor. http://dx.doi.org/10.5455/javar.2015.b90

Genetic characterization of highly pathogenic H5N1 avian influenza virus from live migratory birds in Bangladesh

Since the first outbreak of highly pathogenic avian influenza virus (HPAIV) subtype H5N1 in Bangladesh in 2007, the virus has been circulating among domestic poultry causing severe economic losses. To investigate the presence of HPAIV H5N1 in migratory birds and their potential role in virus spread, 205 pools of fecal samples from live migratory birds were analyzed. Here, the first virus isolation and genome characterization of two HPAIV H5N1 isolates from migratory birds (A/migratory bird/Bangladesh/P18/2010 and A/migratory bird/Bangladesh/P29/2010)are described. Full-length amplification, sequencing, and a comprehensive phylogenetic analysis were performed for HA, NA, M, NS, NP, PA, PB1, and PB2 gene segments. The selected migratory bird isolates belong to clade 2.3.2.1 along with recent Bangladeshi isolates from chickens, ducks, and crows which grouped in the same cluster with contemporary South and South-East Asian isolates. The studied isolates were genetically similar to other H5N1 isolates from different species within the respective clade although some unique amino acid substitutions were observed among them. Migratory birds remain a real threat for spreading pathogenic avian influenza viruses across the continent and introduction of new strains into Bangladesh.

Genomic Variability of Corchorus Golden Mosaic Virus Originating from Bangladesh

Yellow mosaic disease of jute (Corchorus capsularis) was observed on several plants in different jute growing region (Bangladesh) in April 2013. PCR assays and BLAST analysis of the DNA sequences were performed. We have cloned and sequenced eleven isolates of Corchorus golden mosaic virus (CoGMV) collected from eleven different regions in Bangladesh. DNA A sequence of CoGMV Bangladeshi (BD) isolates shared highest identity 97.3-99.1% with the Indian isolates and 93.9-94.3% with the Vietnamese isolate of CoGMV, whereas DNA B shared sequence identity 93.9-94.3% with the CoGMV isolates reported from Vietnam and India. Genetic analysis revealed that CoGMV isolates originating from Bangladesh possessed greater genetic variability than the Indian and Vietnamese isolates. This is thought to be the first report of Corchorus golden mosaic virus (CoGMV) associated with yellow mosaic disease of jute from Bangladesh

Deciphering the origin of the 2012 cholera epidemic in Guinea by integrating epidemiological and molecular analyses.

Cholera is typically considered endemic in West Africa, especially in the Republic of Guinea. However, a three-year lull period was observed from 2009 to 2011, before a new epidemic struck the country in 2012, which was officially responsible for 7,350 suspected cases and 133 deaths. To determine whether cholera re-emerged from the aquatic environment or was rather imported due to human migration, a comprehensive epidemiological and molecular survey was conducted. A spatiotemporal analysis of the national case databases established Kaback Island, located off the southern coast of Guinea, as the initial focus of the epidemic in early February. According to the field investigations, the index case was found to be a fisherman who had recently arrived from a coastal district of neighboring Sierra Leone, where a cholera outbreak had recently occurred. MLVA-based genotype mapping of 38 clinical Vibrio cholerae O1 El Tor isolates sampled throughout the epidemic demonstrated a progressive genetic diversification of the strains from a single genotype isolated on Kaback Island in February, which correlated with spatial epidemic spread. Whole-genome sequencing characterized this strain as an “atypical” El Tor variant. Furthermore, genome-wide SNP-based phylogeny analysis grouped the Guinean strain into a new clade of the third wave of the seventh pandemic, distinct from previously analyzed African strains and directly related to a Bangladeshi isolate. Overall, these results highly suggest that the Guinean 2012 epidemic was caused by a V. cholerae clone that was likely imported from Sierra Leone by an infected individual. These results indicate the importance of promoting the cross-border identification and surveillance of mobile and vulnerable populations, including fishermen, to prevent, detect and control future epidemics in the region. Comprehensive epidemiological investigations should be expanded to better understand cholera dynamics and improve disease control strategies throughout the African continent.