Insights into Omicron's Low Fusogenicity through In Silico Molecular Studies on Spike-Furin Interactions.

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we in silico targeted these mutations to find out which of the amino acids and interactions change plays the key role in fusion. To comprehend the epistatic effect of N679 K and P681 H mutations on the spike protein, we in silico constructed three types of spike protein sequences by changing the respective amino acids on 679 and 681 positions (P681 H, N679 K, K679 N-H681 P variants). We then analyzed the binding affinity of furin and spike (Furin-Wild, Furin-Omicron, Furin-P681 H, Furin-N679 K, and Furin-K679 N/H681 P) complexes. Omicron and P681 H variants showed a similar higher binding energy trend compared to the wild type and N679 K. The variation in hydrogen, hydrophobic, and salt bridge bonds between spike protein and furin provided an explanation for the observed low fusogenicity of Omicron. The fate of the epistasis in furin binding and possible cleavage depends on the efficient interaction between FCS in spike and furin catalytic triad, and in addition, the loss of the hydrogen bond between Arg 681 (spike) and Asn 295 (furin) along with inhibitor-like ineffective higher affinity plays an important role in the enzymatic activity.

Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been considered with great importance on correct screening procedure. The detection efficiency of recent variants of concern were observed by comparing 5 commercial RT-PCR kits and a SYBR-green method developed and validated in our laboratory. The RNA was extracted from nasopharyngeal samples from suspected COVID-19 patients and RT-PCR assay was performed according to the instruction of the respective manufacturers. The specificity and sensitivity of Maccura kit was 81.8% and 82.5%, A*Star kit was 100% and 75.4%, Da An Gene kit was 100% and 68.4%, Sansure kit was 54.5% and 91.2% and TaqPath kit was 100% and 70.2% respectively. Our in house SYBR-Green method showed a consistent detection result with 90.9% specificity and 91.2% sensitivity. We also found that detection kits targeting more genes showed better accuracy which facilitates less false positive results (< 20%). Our study found a significant difference (p < 0.005) in Ct value reported for common target genes shared by the RT-PCR kits in relation with different variants of COVID-19 infection. Recent variants of concerns contain more than 30 mutations in the spike proteins including 2 deletion and a unique insertion mutation by which makes detection of these variants difficult and these facilitates the variants to escape from being detected.

Genomic analysis and in vivo efficacy of Pediococcus acidilactici as a potential probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections.

Lactic acid bacteria are the well acknowledged probiotics that can cure a variety of diseases. In this study, we observed the in vivo potentials of Pediococcus to treat hyperglycemia, hypercholesterolemia and gastrointestinal infections. A total of 77 Lactobacillus were isolated from the milk of 10 cows and 10 goats, four of those strains inhibited both carbohydrates-hydrolyzing enzymes, α-glucosidase, and α-amylase. They all showed antagonistic effects on pathogenic E. coli and S. Typhimurium which were confirmed by performing pathogen challenge test and visualizing on Electron microscopy. 16S rRNA gene sequence identified that all four strains belong to Pediococcus genus which were further distinguished as Pediococcus acidilactici by pheS gene sequence. Whole genome sequence analysis revealed their non-pathogenic properties for human and the presence of probiotic genes responsible for stress resistance, immunomodulation, adhesion, metal and drug resistance. In vivo trial with diabetes-induced mice ascertained that all Pediococcus acidilactici had significant potentials to reduce elevated glucose and low-density lipoprotein level in blood. Interestingly, two out of four strains were significantly more effective (p < 0.0001 each) than metformin in reducing the blood glucose level. This in vivo study demonstrated that Pediococcus acidilactici might be a promising probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections.

Unique mutations in SARS-CoV-2 Omicron subvariants' non-spike proteins: Potential impacts on viral pathogenesis and host immune evasion.

SARS-CoV-2 is the causative agent behind the ongoing COVID-19 pandemic. This virus is a cumulative outcome of mutations, leading to frequent emergence of new variants and their subvariants. Some of them are a matter of high concern, while others are variants of interest for studying the mutational effect. The major five variants of concern (VOCs) are Alpha (B.1.1.7), Beta (B.1.315), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529.*/BA.*). Omicron itself has >100 subvariants at present, among which BA.1 (21K), BA.2 (21L), BA.4 (22A), BA.5 (22B), and BA.2.12.1 (22C) are the dominant ones. Undoubtedly, these variants and sometimes their progeny subvariants have significant differences in their spike region that impart them the unique properties they harbor. But alongside, the mutations in their non-spike regions could also be responsible elements behind their characteristics, such as replication time, virulence, survival, host immune evasion, and such. There exists a probability that these mutations of non-spike proteins may also impart epistatic effects that are yet to be brought to light. The focus of this review encompasses the non-spike mutations of Omicron, especially in its widely circulating subvariants (BA.1, BA.2, BA.4, BA.5, and BA.2.12.1). The mutations such as in NSP3, NSP6, NSP13, M protein, ORF7b, and ORF9b are mentioned few of all, which might have led to the varying properties, including growth advantages, higher transmission rate, lower infectivity, and most importantly better host immune evasion through natural killer cell inactivation, autophagosome-lysosome fusion prevention, host protein synthesis disruption, and so on. This aspect of Omicron subvariants has not yet been explored. Further study of alteration of expression or interaction profile of these non-spike mutations bearing proteins, if present, can add a great deal of knowledge to the current understanding of the viral properties and thus effective prevention strategies.

Development and validation of cost-effective one-step multiplex RT-PCR assay for detecting the SARS-CoV-2 infection using SYBR Green melting curve analysis.

TaqMan probe-based commercial real-time (RT) PCR kits are expensive but most frequently used in COVID-19 diagnosis. The unprecedented scale of SARS-CoV-2 infections needs to meet the challenge of testing more persons at a reasonable cost. This study developed a simple and cost-effective alternative diagnostic method based on melting curve analysis of SYBR green multiplex assay targeting two virus-specific genes along with a host-specific internal control. A total of 180 randomly selected samples portioning into two subsets based on crude and high-quality RNA extraction were used to compare this assay with a nationwide available commercial kit (Sansure Biotech Inc., (Hunan, China)), so that we could analyze the variation and validity of this in-house developed method. Our customized-designed primers can specifically detect the viral RNA likewise Sansure. We separately optimized SYBR Green RT-PCR reaction of N, E, S, and RdRp genes based on singleplex melting curve analysis at the initial stage. After several rounds of optimization on multiplex assays of different primer combinations, the optimized method finally targeted N and E genes of the SARS-CoV-2 virus, together with the ß-actin gene of the host as an internal control. Comparing with the Sansure commercial kit, our proposed assay provided up to 97% specificity and 93% sensitivity. The cost of each sample processing ranged between ~2 and ~6 USD depending on the purification level of extracted RNA template. Overall, this one-step and one-tube method can revolutionize the COVID-19 diagnosis in low-income countries.

Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into eight fundamental clades with four of these clades (G, GH, GR, and GV) globally prevalent in 2020. To explain plausible epistatic effects of the signature co-occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2. RdRp mutation p.P323L significantly increased genome-wide mutations (p < 0.0001), allowing for more flexible RdRp (mutated)-NSP8 interaction that may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact protein, RNA interactions, or both. Another silent 5'-UTR:C241T mutation might affect translational efficiency and viral packaging. These four G-clade-featured co-occurring mutations might increase viral replication. Sentinel GH-clade ORF3a:p.Q57H variants constricted the ion-channel through intertransmembrane-domain interaction of cysteine(C81)-histidine(H57). The GR-clade N:p.RG203-204KR would stabilize RNA interaction by a more flexible and hypo-phosphorylated SR-rich region. GV-clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. Our hypothetical model needs further retrospective and prospective studies to understand detailed molecular events and their relationship to the fitness of SARS-CoV-2.

Prevalence and stability of SARS-CoV-2 RNA on Bangladeshi banknotes.

Originating in December 2019 in China, SARS-CoV-2 has emerged as the deadliest pandemic in humankind's history. Along with direct contact and droplet contaminations, the possibility of infections through contaminated surfaces and fomites is investigating. This study aims to assess SARS-CoV-2 viral RNA's prevalence by real-time one-step reverse transcriptase PCR on banknotes circulating in Bangladesh. We also evaluated the persistence of the virus on banknotes spiked with SARS-CoV-2 positive diluted human nasopharyngeal samples. Among the 425 banknote samples collected from different entities, 7.29% (n = 31) were tested positive for targeted genes. Twenty-four positive representative samples were assessed for n gene fragments by conventional PCR and sequenced. All the samples that carry viral RNA belonged to the GR clade, the predominantly circulating clade in Bangladesh. In the stability test, the n gene was detected for up to 72 h on banknotes spiked with nasopharyngeal samples, and CT values increase significantly with time (p < 0.05). orf1b gene was observed to be less stable, especially on old banknotes, and usually went beyond detectable limit within 8 to 10 h. The stability of virus RNA well fitted by the Weibull model and concave curve for new banknotes and convex curve for old banknotes revealed. Handling banknotes is unavoidable; hence, these findings imply that proper hygiene practice is needed to limit SARS-CoV-2 transmission through banknotes.

Evidence of combined effect of amino acid substitutions within G-H and B-C loops of VP1 conferring serological heterogeneity in foot-and-mouth disease virus serotype A.

Foot-and-mouth disease virus (FMDV) serotype A exhibits a higher degree of genetic and antigenic diversity resulting in frequent vaccine failure due to serological mismatch between the vaccine and heterologous strains. Currently, knowledge on the molecular basis of antigenic relationships among the FMDVs is limited; nevertheless, intratype antigenic variation due to mutation(s) is widely considered as the main hurdle to appropriate FMD vaccine development. Here, we studied genetic and antigenic variations of four FMDV serotype A isolates, BAN/GA/Sa-197/2013 (BAN-197), BAN/CH/Sa-304/2016 (BAN-304), BAN/DH/Sa-307/2016 (BAN-307) and BAN/DH/Sa-310/2017 (BAN-310) circulating in Bangladesh during 2013-2017. Initially, antigenic relationships (r1 -values) of the field isolates were evaluated by the two-dimensional microneutralization test (2D-MNT) using the hyperimmune antisera raised in cattle against the vaccine strain, BAN-304. Interesingly, the results showed protective serological cross-reactivity (r1 -values > 0.4) between the vaccine strain and the field isolates, BAN-307 and BAN-310, except BAN-197 that substantially mismatched (r1  = 0.129 ± 0.043) with the BAN-304. Although VP1-based phylogeny grouped all the isolates within the same sublineage C (a subgroup of VP3Δ59 variant) under the lineage A/ASIA/G-VII, strikingly, computational analyses of the viral capsid proteins demonstrated significant deviation at the VP1 G-H loop of BAN-197 from the vaccine strain, while VP(2-4) of both isolates were structurally conserved. To bridge the gap of how the distortion of the G-H loop and consequent antigenic hetergeneity occurred in BAN-197, we performed in silico combinatorial substitutions of the VP1 mutant amino acids (aa) of BAN-197 with the respective residues in BAN-304. Remarkably, our analyses revealed that two substitutions of distantly located aa at B-C (T48I:threonine â†’ isoleucine) and G-H (A143V:alanine â†’ valine) loops, in combination, distorted the VP1 G-H loop. Overall, this work contributes to understanding the molecular basis of antigenic relationships operating in serotype A FMDVs and the selection of suitable vaccine strain(s) for effective prophylaxis of FMD based on VP1-based analyses.

Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein and its consequences.

The emerged novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a global health crisis that warrants an accurate and detailed characterization of the rapidly evolving viral genome for understanding its epidemiology, pathogenesis, and containment. Here, we explored 61,485 sequences of the nucleocapsid (N) protein, a potent diagnostic and prophylactic target, for identifying the mutations to review their roles in real-time polymerase chain reaction based diagnosis and observe consequent impacts. Compared to the Wuhan reference strain, a total of 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n = 30,221) globally. Of these mutations, 367 occupy primer binding sites including the 3'-end mismatch to the primer-pair of 11 well-characterized primer sets. Noteworthily, CDC (USA) recommended the N2 primer set contained a lower mismatch than the other primer sets. Moreover, 684 amino acid (aa) substitutions were located across 317 (75.66% of total aa) unique positions including 82, 21, and 83 of those in the RNA binding N-terminal domain (NTD), SR-rich region, and C-terminal dimerization domain, respectively. Moreover, 11 in-frame deletions, mostly (n = 10) within the highly flexible linker region, were revealed, and the rest was within the NTD region. Furthermore, we predicted the possible consequence of high-frequency mutations (≥20) and deletions on the tertiary structure of the N protein. Remarkably, we observed that a high frequency (67.94% of mutated sequences) co-occuring mutations (R203K and G204R) destabilized and decreased overall structural flexibility. The N protein of SARS-CoV-2 comprises an average of 1.2 mutations per strain compared to 4.4 and 0.4 in Middle East respiratory syndrome-related coronavirus and SARS-CoV, respectively. Despite being proposed as the alternative target to spike protein for vaccine and therapeutics, the ongoing evolution of the N protein may challenge these endeavors, thus needing further immunoinformatics analyses. Therefore, continuous monitoring is required for tracing the ongoing evolution of the SARS-CoV-2 N protein in prophylactic and diagnostic interventions.

Comparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study.

Recent outbreak of novel coronavirus and its rapid pandemic escalation in all over the world has drawn the attention to urgent need for effective drug development. However, due to prolonged vaccine and drug development procedure against a newly emerged devastating SARS-CoV-2 virus pathogen, repurposing of existing potential pertinent drug molecules would be preferable strategy to reduce mortality immediately and further development of new drugs to combat overall global Covid-19 crisis in all over the world. Herein, we have filtered 23 prospective drug candidates through literature review. Assessing evidences from molecular docking studies, it was clearly seen that, Epirubicin, Vapreotida, and Saquinavir exhibited better binding affinity against SARS-CoV-2 Main Protease than other drug molecules among the 23 potential inhibitors. However, 50 ns molecular dynamics simulation indicated the less mobile nature of the docked complex maintaining structural integrity. Our overall prediction findings indicate that Epirubicin, Vapreotida, and Saquinavir may inhibit COVID-19 by synergistic interactions in the active cavity and those results can pave the way in drug discovery although it has to be further validated by in-vitro and in-vivo investigations.Communicated by Ramaswamy H. Sarma.

Understanding the possible origin and genotyping of the first Bangladeshi SARS-CoV-2 strain.

The novel coronavirus, SARS-CoV-2, has caused the most unfathomable pandemic in the history of humankind. Bangladesh is also a victim of this critical situation. To investigate the genomic features of the pathogen from Bangladesh, the first complete genome of the virus has very recently been published. Therefore, long-awaited questions regarding the possible origin and typing of the strain(s) can now be answered. Here, we endeavor to mainly discuss the published reports or online-accessed data (results) regarding those issues and present a comprehensive picture of the typing of the virus alongside the probable origin of the subclade containing the Bangladeshi strain. Our observation suggested that this strain might have originated from the United Kingdom or the other European countries epidemiologically linked to the United Kingdom. According to different genotyping classification schemes, this strain belongs to the A2a clade under the G major clade, is of B and/or L type, and is a SARS-CoV-2a substrain. In the future, randomized genomic data will certainly increase in Bangladesh, however because of globalization and immigrant movement, we urgently need a mass regional sequencing approach targeting the partial or complete genome that can link the epidemiological data and may help in further clinical intervention.

In silico Evolutionary Divergence Analysis Suggests the Potentiality of Capsid Protein VP2 in Serotype-Independent Foot-and-Mouth Disease Virus Detection.

Foot-and-mouth disease (FMD) is an economically devastating disease of the livestock worldwide and caused by the FMD virus (FMDV), which has seven immunologically distinct serotypes (O, A, Asia1, C, and SAT1-SAT3). Studies suggest that VP2 is relatively conserved among three surface-exposed capsid proteins (VP1-VP3) of FMDV, but the level of conservation has not yet been reported. Here we analyzed the comparative evolutionary divergence of VP2 and VP1 to determine the level of conservation in VP2 at different hierarchical levels of three FMDV serotypes (O, A, and Asia1) currently circulating in Asia through an in-depth computational analysis of 14 compiled datasets and designed a consensus VP2 protein that can be used for the development of a serotype-independent FMDV detection tool. The phylogenetic analysis clearly represented a significant level of conservation in VP2 over VP1 at each subgroup level. The protein variability analysis and mutational study showed the presence of 67.4% invariant amino acids in VP2, with the N-terminal end being highly conserved. Nine inter-serotypically conserved fragments located on VP2 have been identified, among which four sites showed promising antigenicity value and surface exposure. The designed 130 amino acid long consensus VP2 protein possessed six surface-exposed B cell epitopes, which suggests the possible potentiality of the protein for the development of a serotype-independent FMDV detection tool in Asia. Conclusively, this is the first study to report the comparative evolutionary divergence between VP2 and VP1, along with proposing the possible potentiality of a designed protein candidate in serotype-independent FMDV detection.

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.

Identification and qualitative characterization of new therapeutic targets in Stenotrophomonas maltophilia through in silico proteome exploration.

Stenotrophomonas maltophilia is an emerging opportunistic pathogen, and immunocompromised patients are at a higher risk of getting infected with this nosocomial bacterium. The biggest concern is its inherent resistance to most of the commonly used antibiotics, leaving a few options for treatment. Moreover, recent studies have reported the emergence of its resistance to trimethoprim/sulfamethoxazole (TMP/SMX), the drugs of choice against this pathogen. In this study, we employed a subtractive proteome analysis approach to identify new drug targets against Stenotrophomonas maltophilia K279a. We identified 56 proteins to be essential for the survival of this pathogen, 33 of which are exclusively involved in its metabolism. We identified their subcellular locations and performed broad-spectrum analysis, interactome analysis, and functional analysis. Drug targeting properties and docking energy showed that 29 out of 33 proteins have the potential to serve as potential new therapeutic targets, and four proteins (dCTP deaminase, NAD(P)H:quinone oxidoreductase, dihydroneopterin aldolase, and α, α-trehalose-phosphate synthase) bind with high affinity to already approved or experimental drugs. Based on the broad-spectrum analysis and interactome analysis, we identified NAD(P)H:quinone oxidoreductase, dCTP deaminase, Phosphotransferase, and ATP-dependent Clp protease adapter (ClpS) as the most potential therapeutic targets. Notably, phosphotransferase and ClpS are new targets, i.e., they do not interact with any experimental or approved drugs. Overall, our study will guide the development of new and effective drugs for the treatment of Stenotrophomonas maltophilia infection.

Complete genome sequence of a potential foot-and-mouth disease virus serotype O vaccine strain from Bangladesh.

One of the six sublineages of the dominant O/ME-SA/Ind2001 lineage of foot-and-mouth disease virus (FMDV), Ind2001BD1 has already spread throughout 14 countries, including Bangladesh. Here, we report the complete genome sequence of the potential serotype O vaccine strain BAN/TA/Dh-301/2016, which has been shown to provide protection against all the circulating serotype O viruses in Bangladesh. The viral genome is 8,211 nucleotide (nt) long with an open reading frame (ORF) of 6999 nt. The ORF is flanked by a 1098-nt-long 5'-UTR and a 114-nt-long 3'-UTR. Compared to the Indian FMDV serotype O vaccine strain O/India/R2/75 (AF204276), ten mutations were identified in the major antigenic sites of BAN/TA/Dh-301/2016 (MK088170.1).

Development and serology based efficacy assessment of a trivalent foot-and-mouth disease vaccine.

Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals throughout the world. The endemicity of this disease in Bangladesh has been causing high economic loss and an impediment to the full potential surge of livestock industries. In Bangladesh, vaccination using imported or locally produced FMD vaccines is the existing practice of controlling the disease, although vaccine failure cases are very common. Hence, to address the problem, the present study was envisaged to develop an effective FMD vaccine tailored to the circulating indigenous foot-and-mouth disease virus (FMDV) strains. Three local circulating FMDVs O/BAN/TA/Dh-301/2016 (MK088170.1), A/BAN/CH/Sa-304/2016 (MK088171.1) and Asia1/BAN/DH/Sa-318/2018 (MH457186.1) isolates were selected as vaccine strains based on recent epidemiology, genetic and antigenic analyses. These serotype O, A and Asia1 vaccine strains showed strong antigenic relationship (r1 > 0.3) with 100% to 75% of the respective circulating viruses. The candidate viruses were successfully inactivated by 3.0 mM binary ethylenimine within 7-10 h after the onset of inactivation. Extrapolation of inactivation kinetics confirmed < 1 log10 TCID50 in a 10000-liter batch liquid preparation after 24 h inactivation cycle. The inactivated virus particles were significantly (p < 0.05) concentrated and the trivalent vaccine was formulated using 6 µg per dose per serotype antigen payload. The trivalent vaccine was administered in divided doses in different groups of cattle. All doses of the vaccine elicited significantly (p < 0.05) higher levels of antibodies as early as 14-day post-vaccination (dpv) and peak antibody titers were achieved in 28 dpv. The 'full dose' (6.0 µg per dose per serotype) vaccine elicited antibody titers expected to confer protection in 100% cattle of the respective group and maintained such level of antibodies beyond 180 dpv. Thus, the trivalent FMD vaccine prepared with 6.0 µg antigen per dose per serotype of the selected candidate viruses will confer protection against circulating FMDVs of Bangladesh and its neighboring countries.

Emergence of novel lineage of foot-and-mouth disease virus serotype Asia1 BD-18 (G-IX) in Bangladesh.

Foot-and-mouth disease virus (FMDV) is a highly evolutionary divergent pathogen causing great economic havoc in many countries. Among its seven existing serotypes, Asia1 is the least divergent with a single topotype both genetically and antigenically. It is reported sporadically in Indian subcontinent and was classified under lineage G-VIII. In 2018, serotype Asia1 re-emerged in Bangladesh after 2013, along with circulation of a novel serotype Asia1 BD-18 (G-IX) lineage. VP1 phylogeny and sequence variation clearly demonstrated the novel strains which was estimated to have at least >5% nucleotide divergence with distinct clade formation. Also, the Bayesian phylogeographic inferences traced back to the origin time of lineage G-IX in early 2017 and a possible origin in Bangladesh. Mutational analysis considering established eight lineages revealed that the virus strains belonged to lineage G-IX contained a unique mutation at 44 position in the B-C loop region of VP1. Inappropriate vaccination and inefficient outbreak surveillance possibly contributed to the current episode of emergence. Therefore, active surveillance and continued vigilance are essential to assess and timely detect the occurrence, extent and distribution of this novel Asia1 strains in Bangladesh and the neighbouring countries.

Near-Complete Genome Sequence of a Potential Foot-and-Mouth Disease Virus Serotype A Vaccine Strain Isolated from Bangladesh.

The near-complete genome sequence of foot-and-mouth disease virus (FMDV) serotype A potential vaccine strain BAN/CH/Sa-304/2016 is reported here. Its genome revealed antigenic heterogeneity with the current Indian vaccine strain IND40/00, with four amino acid substitutions in antigenically critical sites of the VP1 protein.