Indian Strains Research Articles

Whole Genome Analysis of Selected Human Group A Rotavirus Strains Revealed Evolution of DS-1-Like Single- and Double-Gene Reassortant Rotavirus Strains in Pakistan During 2015-2016.

Acute gastroenteritis due to group A rotaviruses (RVAs) is the leading cause of infant and childhood morbidity and mortality particularly in developing countries including Pakistan. In this study we have characterized the whole genomes of five RVA strains (PAK56, PAK419, PAK585, PAK622, and PAK663) using the Illumina HiSeq platform. The strains PAK56 and PAK622 exhibited a typical Wa-like genotype constellation (G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, respectively), whereas PAK419, PAK585, and PAK663 exhibited distinct DS-1-like genotype constellations (G3P[4]-I2-R2-C2-M2-A2-N2-T1-E2-H2, G1P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2, and G3P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2, respectively). Despite their DS-1-like genotype constellation, strain PAK585 possessed the typical Wa-like G1P[8] genotypes, whereas both PAK419 and PAK663 possessed the G3 genotype. In addition, PAK419 also possessed the Wa-like NSP3 genotype T1, suggesting that multiple reassortments have occurred. On Phylogenetic analysis, all of the gene segments of the five strains examined in this study were genetically related to globally circulating human G1, G2, G3, G6, G8, G9, and G12 strains. Interestingly, the NSP2 gene of strain PAK419 showed closest relationship with Indian bovine strain (India/HR/B91), suggesting the occurrence of reassortment between human and bovine RVA strains. Furthermore, strains PAK419, PAK585, and PAK663 were closely related to one another in most of their gene segments, indicating that these strains might have been derived from a common ancestor. To our knowledge this is the first whole genome-based molecular characterization of human rotavirus strains in Pakistan. The results of our study will enhance our existing knowledge on the diversity and evolutionary dynamics of novel RVA strains including DS-1-like intergenogroup reassortant strains spreading in Asian countries including Pakistan, in the pre-vaccine era. Therefore, continuous surveillance is recommended to monitor the evolution, spread and genetic stability of novel reassortant rotavirus strains derived from such events.

Immunogenicity of recombinant outer membrane protein (OmpW) of Pasteurella multocida serogroup B:2 in mouse model

Haemorrhagic septicaemia (HS) caused by Pasteurella multocida serogroup B:2, in cattle and buffalo especially in tropical regions of Asian and African countries, is known to possess several outer membrane proteins (OMPs) as virulent factors which are being targeted to evaluate their immunogenicity and protective efficacy as candidate antigens for vaccine. In the present study, ompW gene encoding for OmpW protein of P. multocida serogroup B:2 strain P52, an Indian HS vaccine strain, has been cloned and over-expressed in recombinant Escherichia coli. The recombinant OmpW fusion protein (~37 kDa) including histidine tag was purified by affinity chromatography under denaturing condition and confirmed by Western blotting. Further, mice immunized with rOmpW (50μg/ dose) along with FCA/FIA resulted in antigen specific IgG antibodies as well as subtypes (IgG1 and IgG2a). The study indicated the potential possibilities to use the rOmpW antigen in developing subunit vaccine for HS as well as other diseases caused by members of Pasteurellaceae.

Phytochemical analysis of Rhazya stricta extract and its use in fabrication of silver nanoparticles effective against mosquito vectors and microbial pathogens

Worldwide, billions of people are at risk from viruses, parasites and bacteria transmitted by mosquitoes, ticks, fleas and other vectors. Over exploitation of chemical pesticides to overcome the mosquito borne diseases led to detrimental effects on environment and human health. The present research aims to explore bio-fabrication of metal silver nanomaterials using Rhazya stricta extract against deadly mosquito vectors and microbial pathogens. The phytochemical profile of the R. stricta extracts was studied by HPLC-MS and 1H NMR. Further, confirmation of the bio-fabricated silver nanoparticles (AgNPs) was carried out by UV–vis spectroscopy and characterization through FTIR, TEM, EDX, and XRD analyses. The R. stricta-fabricated AgNPs showed acute toxicity on key mosquito vectors from two different country (India and Kingdom of Saudi Arabia, KSA) strains, notably, with LC50 values of 10.57, 11.89 and 12.78 μg/ml on malarial, dengue and filarial key Indian strains of mosquito vectors, respectively, and 30.66 and 38.39 μg/ml on KSA strains of Aedes aegypti and Culex pipiens, respectively. In mosquito adulticidal activity, R. stricta extract alone exhibited LC50 values ranging from 304.34 to 382.45 μg/ml against Indian strains and from 738.733 to 886.886 against Saudi Arabian strains, while AgNPs LC50 boosted from 9.52 to 12.16 μg/ml and from 30.66 to 38.39 μg/ml, respectively. Moreover, it was noticed that at low concentration the tested AgNPs showed high growth retardation of important pathogenic bacteria such as Bacillus subtilis, Klebsiella pneumoniae and Salmonella typhi with inhibition zone diameters from 11.86 to 22.92 mm. In conclusion, the present study highlighted that R. stricta-fabricated AgNPs could be a lead material for the management of mosquito vector and microbial pathogens control.

First Report on Identification of Volatiles from Egg and Larval Frass of Indian Strain of the American Bollworm Helicoverpa armigera (Hübner)

Globally Helicoverpa armigera, a polyphagous pest of many economic crops, has developed resistance to almost all groups of insecticides presently in used for its control. In cotton, its larvae cause severe damage and feeds on all plant parts including young leaves, square, flowers and bolls which in turn cause economic damage. Recent reports on development of its resistance to transgenic cotton which has Cry1Ac and Cry2Ab (Bt cotton) has given an indication of future threat to cotton growers. Therefore, use of semiochemicals as management strategy for these insects would be a great alternative as ethological pest management within insect pest management (IPM) to control this menace. These semiochemicals/volatile organic compounds can be present in insect (egg, larva, female) as well as in the host plant. In the present study, a total of seven volatiles have been identified from methanol extract of eggs and faecal pellets, out of which two volatiles; methyl ester of octadecanoic acid (methyl stearate) and methyl ester of hexadecanoic acid (methyl palmatate), were detected in egg samples. From faecal pellets five volatiles were identified namely octadecanoic acid (stearic acid) and its methyl ester, hexadecanoic acid (palmitic acid) and its methyl ester, tetradecanoic acid (myristic acid), caryophyllene and its oxide, phytol. Interestingly, methyl ester of octadecanoic acid and methyl ester of hexadecanoic acid were detected in both the samples. Volatiles observed in common may be used as effective semiochemicals in ethological pest management of Helicoverpa armigera. However, further study is needed to validate the competency of these fatty acids under field conditions.

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.

Whole-Genome Sequences of Four Indian Isolates of Azospirillum brasilense.

Azospirillum brasilense is used worldwide as a plant growth-promoting inoculant for agricultural crops. To understand how the genomes of Indian strains of A. brasilense compare with their South American counterparts, we determined the whole-genome sequences of four strains of A. brasilense isolated from the rhizosphere of grasses from India.

Predominance of Central Asian strain (ST 26) in Mycobacterium tuberculosis isolates from Balochistan by spoligotyping.

Tuberculosis is a chronic debilitating infectious disease causing a severe challenge to public health, especially in developing countries. The aim of this study was to examine genetic diversity in Mycobacterium tuberculosis strains circulating in the Balochistan region of Pakistan. One hundred isolates collected from patients visiting the Fatima Jinnah TB Hospital in Quetta were subjected to genotype analysis by spoligotyping. Three main genotypes were identified: Central Asian Strain 1 (CAS1) (n = 89), East African Indian (EAI) strain (n = 7) and Latin American Mediterranean (LAM) strain (n = 3). The CAS1 clade (ST 26) had high genetic diversity represented by seven different spoligopatterns, of which one had major predominace (n = 75). This is the first insight into the genotype of M. tuberculosis strains in the Balochistan region that might serve as a base line study for control of tuberculosis in the community.

Genetic diversity and evolutionary dynamics of dengue isolates from India.

Dengue virus (DENV) is the mosquito borne virus which causes Dengue Haemorrhagic Fever and Dengue Shock Syndrome. It consists of four distinct serotypes (DENV 1-4). DENV 1, 3 and 4 were classified into five genotypes (GI-GV), where as DENV-2 belongs to American and Cosmopolitan genotypes. Dengue virus is most prevalent in south and Southeast Asia including India. This study was initiated to study the genetic diversity and evolution among the Dengue isolates in India. Pairwise comparison of amino acid sequences among the serotypes has shown that DENV-3 is having less sequence diversity compared to other serotypes having differences in their amino acid numbers. We have analyzed the 50 Indian strains and 19 of those strains have been identified as recombinant strains by using RDP4 package, which are then excluded for future selection. Episodic positive selection of DENV was obtained using MEME with P value is ≤ 5. Positive selection on several codons was used to correlate the genetic diversity between serotypes. This study clearly established that diversity of amino acids and inter genotypic recombination of strains are the major cause for antigenicity variation and evolution of DENV within India.

Identification of very virulent marek’s disease virus strains in India by sequence analysis of 132 bp repeats of BamH-HI region

The present study was aimed to screen the poultry samples for MDV (Marek’s disease virus) from Directorate of Poultry Research poultry farms (DPRF) and commercial poultry farms (CPF) in and around Hyderabad. The MDV was diagnosed with polymerase chain reaction using primers targeting for 132 bp repeats of BamHI-H region. The product of 302 bp and 434 bp were amplified in DPRF and CPF samples. Analysis of sequenced nucleotide data showed that the difference exist due to the presence of one or two repeats of 132 bp repeats in BamH-HI region. The homology was observed between all Indian and other published strains for 132 bp repeats of BamH-HI region. The percent of identity of DPR-2 (CPF) was 96.7 and 100% with DPR-3 (DPRF) and MDV-Anand4 isolate, respectively. The phylogenetic analysis of 132 bp repeats of BamH-HI Region of MDV revealed that the DPR-3(DPRF), DPR-2(CPF) and other Indian strains were clustered with very virulent plus pathogenic strain (584A), very virulent strains (595 and Md5)and virulent to moderate pathogenic strains, respectively. The present study seems the first report for the identification of single 132 bp repeats of MDV strains in India. This virulence may be due to the continuous adaptation of virus in poultry birds of different age groups and breeds maintained in DPR poultry farms. Therefore, there is a need to develop a new strategy and vaccines for birds against new highly virulent strains of the virus.

Genotypic Characterization of HIV-1 Subtype C in the Central Region of Nepal.

Human immunodeficiency virus type 1 (HIV-1) is a major causative agent of acquired immune deficiency syndrome. Subtype C (HIV-1C) is the most prevalent HIV-1 subtype worldwide. Although it is highly prevalent in Nepal, genotypic information on Nepalese HIV-1C is limited. We herein investigated the origin and dynamics of HIV-1C in Nepal. Nearly full-length sequencing of Nepalese HIV-1C strains and phylogenetic analyses were performed. The results obtained showed that Nepalese HIV-1C is closely related to the Indian and southern African strains and the introduction of HIV-1C into Nepal was estimated to be in the mid-1980s. These results suggest that multiple HIV-1C strains entered Nepal in the mid-1980s, and this was followed by a marked increase in the number of infection cases for the next decade. These results reflect the current transmission dynamics of HIV-1C strains in Nepal and provide valuable information for HIV monitoring and vaccine development.

Geographically Distinct North-East Indian Helicobacter pylori Strains are Highly Sensitive to Clarithromycin but are Levofloxacin Resistant

AbstractPurpose:Helicobacter pylori causes various gastro-intestinal diseases. Antibiotic resistance to commonly used antibiotics for the treatment of H. pylori infection is the major cause for treatment failure. The aim of this study is to determine the antimicrobial susceptibility pattern for clarithromycin and levofloxacin and find the evolutionary relationship of the partial sequence of 23S rRNA and gyraseA gene of H. pylori by phylogenetic analysis. Materials and Methods: A total of 46 H. pylori strains were tested for clarithromycin and levofloxacin susceptibility pattern and phylogenetic tree were reconstructed by PhyML software. Results: In this study, we observed that only 6.5% of North-East Indian H. pylori strains were resistant for clarithromycin showing mutation at A2143G and T2182C positions of 23S rRNA gene. Resistance for levofloxacin was observed in 89.1% of the H. pylori strains showing mutations at asparagine to lysine at 87 and aspartic acid to glycine/tyrosine/asparagine at 91 positions of gyraseA gene. The phylogenetic tree of the partial sequence of 23S rRNA and gyraseA gene depicts that the North-East Indian strains falls in different cluster when compared to other countries. Conclusions: Resistance for clarithromycin was less in North-East Indian strains but high for levofloxacin indicating that first-line therapy may be best and effective for eradication of H. pylori in this region. This study is the first report that showed antibiotic susceptibility pattern for clarithromycin and levofloxacin by mutation analysis. By partial sequencing of 23s rRNA and gyraseA gene, we found that North-East Indian strains are geographically distinct.

Molecular and phylogenetic analysis of Chikungunya virus in Central India during 2016 and 2017 outbreaks reveal high similarity with recent New Delhi and Bangladesh strains

Central India witnessed Chikungunya virus (CHIKV) outbreaks in 2016 and 2017. The present report is a hospital based cross-sectional study on the serological and molecular epidemiology of the outbreak. Mutational and phylogenetic analysis was conducted to ascertain the genetic relatedness of the central Indian strains with other Indian and global strains. Chikungunya infection was confirmed in the clinically suspected patients by the detection of anti-CHIKV IgM antibody by ELISA and viral RNA by RT-PCR. A representative set of the RT-PCR positive samples were sequenced for E1 gene and analyzed to identify the emerging mutations and establish their phylogenetic relationship, particularly with other contemporary strains. Phylogenetic analysis revealed the present strains to be of East Central South African (ECSA) genotype. Emergence of a variant strain was observed in the year 2016, which became the predominant strain in this region in 2017. The strains showed significant identity with recent New Delhi strains of 2015 and 2016 and Bangladesh strains of 2017. The epidemic mutation A226V which emerged in 2006 outbreaks of India and Indian Ocean Islands was found to be absent in the current strains. Among the important mutations viz. K211E, M269 V, D284E, I317V & V322A observed in the recent strains. I317V is a novel mutation which has emerged very recently as it was found only in central Indian (2016, 2017), New Delhi strains (2015, 2016) and Bangladesh strains (2017). This study has identified a unique mutation E1:I317V in the Central Indian strains, which is present only in recent New Delhi and Bangladesh strains till date. This study highlights the need for continuous molecular surveillance of circulating CHIKV strains in order to facilitate the prompt identification of novel strains of this virus and enable the elucidation of their clinical correlates.

Prevalence of Fowl Adenovirus Serotype 4 and Co-Infection by Immunosuppressive Viruses in Fowl with Hydropericardium Hepatitis Syndrome in Shandong Province, China.

Fowl adenovirus serotype 4 (FAdV-4) is the pathogenic agent of hydropericardium hepatitis syndrome (HHS) in chickens and ducks, which has caused huge economic losses for the Chinese poultry industry since 2015. In order to objectively determine the prevalence and co-infection status of the virus in Shandong province in China, we analyzed a total of 679 clinical cases of chickens and ducks from 36 farms in the province. The results showed that the FAdV-4 infection rate was 65.2% (443/679), and the rate in breeder ducks was almost two-fold higher than that in breeder chickens (68.57% vs. 34.30%). Notably, co-infection by H9N2 avian influenza virus, infectious bursal disease virus, and/or chicken infectious anemia virus was very common in the 443 FAdV-4-positive cases. Furthermore, phylogenetic analysis of the hexon genes of four Shandong FAdV-4 isolates revealed that these strains clustered into Indian reference strains, indicating that the Shandong FAdV-4 strains might have originated in India. These findings provide the first data on the prevalence and co-infection status of FAdV-4 in Shandong province, which may serve as a foundation for the prevention of FAdV-4 in the field.

Whole-genome-based characterization of three human Rotavirus C strains isolated from gastroenteritis outbreaks in Western India and a provisional intra-genotypic lineage classification system.

The number of whole-genome sequences of human rotavirus C (RVC) strains available in public databases is recently increasing. Thus far from India only a single whole genome of human RVC of a sporadic case was available. In this study, nearly full-length genome sequencing and phylogenetic analyses of three RVC strains isolated from three different gastroenteritis outbreaks during 2010-2014 in Western India was carried out. Further, an intra-genotypic lineage classification system for human RVCs based on the nucleotide divergence cut-off values was proposed by using the algorithm of the Rotavirus Classification Working Group. Two lineages could be defined for all the genes except the VP7 gene and the M3 VP3 genotype. Provisional classification of the lineages indicated the absence of reassortment events in the genomic constellation of Indian strains, contrary to earlier reports. The comparatively higher variability of the NSP1, NSP3, NSP5 and M2 VP3 genotype, emphasizes their utility in lineage classification.

Genome analysis provides insight about pathogenesis of Indian strains of Rhizoctonia solani in rice.

The Rhizoctonia solani species complex is comprised of strains belonging to different anastomosis groups and causes diseases in several economically important crops, including rice. However, individuals within same anastomosis group exhibit distinct morphological and pathological differences on the same host. In this study, we have sequenced the genome of two aggressive Indian strains (BRS11 and BRS13) belonging to AG1-IA anastomosis group and compared them with the available genome of R. solani AG1-IA. We identified several SNPs and Indels in both of these genomes, in comparison to the AG1-IA genome. Furthermore, we observed expansion and emergence of orthogroups in these Indian strains and identified those potentially associated with pathogenesis. Amongst them, transposable elements, cell wall degrading enzymes, transcription factors, and oxalate decarboxylase were noteworthy. The current study unravels genetic variations and identifies genes that might account for pathogenicity variations amongst R. solani strains.

Genomic analysis of Indian strains of Salmonella enterica subsp. enterica serovar Typhi indicates novel genetic repertoire for pathogenicity and adaptations.

In the era of emerging antibiotic resistance, Salmonella enterica subsp. enterica serovar Typhi the causative agent of typhoid, is a threat for healthcare systems in developing countries especially India, where the disease is highly endemic. Genetic diversity among different strains may be the cause of variable severity of disease in different regions of the world. To explore this genetic diversity, genome annotation by rapid annotation using subsystem technology (RAST) was carried out for genomes of four Salmonella Typhi strains from two distinct areas available in thepublic domain. Two clinical strains were from India (P-stx-12 and E02-1180) and the other two strains considered as reference strains were from the endemic regions of Papua New Guinea (UJ308A and UJ816A). We report that Indian clinical strains possess several similar genes responsible for virulence and pathogenicity as those present in the reference strains. Interestingly, Indian clinical strains also possess 34 additional potential virulence genes that are absent in thereference strains, suggesting the more dreadful nature of Indian clinical strains as compared to those causing endemic typhoid. Indian strains contained genes coding for; Colicin V and bacteriocin production; multidrug resistance efflux pumps; ABC transporters; Type III and Type VI secretion systems, siderophore aerobactin, pathogenicity islands and Vi polysaccharide biosynthesis and transport. These unique genes are also reported in the genomes of other six clinical strains of India analyzed through RAST and IslandViewer 4 for validation purpose. This study highlights the presence of potential genes as molecular targets to overcome the future endemic outbreaks in India.

Study of Steinernema hermaphroditum (Nematoda, Rhabditida), from the West Uttar Pradesh, India.

The entomopathogenic nematodes have been reported from all continents (except Antarctica) and almost all regions of the world. Surveys of EPNs in India has resulted in the recovery of several isolates of Steinernema. Among one of them, isolate CS34 was identified as S. hermaphroditum Stock, Griffin & Chaerani, 2004. We investigated the identification and the pathogenicity of S. hermaphroditum in District Meerut of Western Uttar Pradesh, India. The Steinernema was examined for its pathogenicity and accurate identification by the mean of morphological and molecular technique and its geographical distribution was mapped based on meta-analysis of the ITS GenBank records. The surveys of agricultural soils of district Meerut, India, resulted in the isolation of one strain from entomopathogenic nematode labelled CS34 through Galleria baiting technique. Morphological characters and morphometrical analysis indicated that the strain CS34 was closely related to the "glaseri" group of Steinernema spp. The Nblast results indicated that ITS rDNA sequence had no nucleotide differences in comparison with the S. hermaphroditum (JQ687355). However, one variation in the D2-D3 segment of 28S rDNA was observed in comparison with the AY598358. The phylogenetic analysis using ITS and 28S rDNA indicated that the Indian S. hermaphroditum could be placed together with other S. hermaphroditum, with strong posterior probability. Besides, the PCA analysis demonstrated some variability within the test populations. The distribution of S. hermaphroditum based on meta-analysis of the GenBank records showed its presence in the three Asian countries-India, Thailand and Indonesia. The Indian strain of S. hermaphroditum also tested positively for its virulence against three major pests, namely, Galleria mellonella, Helicoverpa armigera, and Spodoptera litura, with resultant which showed good efficacy on the mortalities. In conclusion, the economy of India is agriculture-based, but there are huge losses due to different insect pests infesting different crops. Steinernema hermaphroditum CS34 is an indigenous species to Indian subcontinent and efforts should be made to evaluate its virulence and pathogenicity against the other agricultural pests hampering productivity throughout the country. This may lead to incorporate S. hermaphroditum strain CS34 as a regular biological control agent against important lepidopteran pest in integrated pest management programs in the future.

Antimicrobial resistance and its relationship with biofilm production and virulence-related factors in Yersinia enterocolitica biotype 1A

The aim of the present study was to determine antimicrobial susceptibilities, biofilm production and, to discern a relationship between antimicrobial resistance, biofilm potential and virulence-related genes in strains of Yersinia entercocolitica biotype 1A. Thirty strains of Y. enterocolitica biotype 1A including clinical and non-clinical strains were investigated. Antimicrobial susceptibility for 15 antibiotics (representing different classes) was determined by disk-diffusion assay. Biofilm potential was determined on two different culture media using crystal violet assay. Also, a co-relation was studied between antimicrobial susceptibilities, biofilm production and virulence-related genes. All strains of biotype 1A produced biofilms and exhibited varied level of susceptibilities for different antibiotics. More than 60% of the strains were strong to moderate biofilm producers and, were exclusively associated with REP/ERIC clonal group B. Moderate and strong biofilm producers exhibited both sensitive and resistant phenotypes towards different antibiotics. Interestingly, weak biofilm producers were resistant to amoxicillin, amoxicillin-clavulanate and cefazolin. Analysis of antimicrobial susceptibilities, biofilm potential and virulence-related genes did not reveal any unequivocal relationships. The differential biofilm potential of Indian strains of Y. enterocolitica biotype 1A, suggests that biotype 1A strains are heterogeneous in nature.

Xanthomonas citri pv. viticola Affecting Grapevine in Brazil: Emergence of a Successful Monomorphic Pathogen.

The pathovar viticola of Xanthomonas citri causes bacterial canker of grapevine. This disease was first recorded in India in 1972, and later in Brazil in 1998, where its distribution is currently restricted to the northeastern region. A multilocus sequence analysis (MLSA) based on seven housekeeping genes and a multilocus variable number of tandem repeat analysis (MLVA) with eight loci were performed in order to assess the genetic relatedness among strains from India and Brazil. Strains isolated in India from three related pathovars affecting Vitaceae species and pathogenic strains isolated from Amaranthus sp. found in bacterial canker-infected vineyards in Brazil were also included. MLSA revealed lack of diversity in all seven genes and grouped grapevine and Amaranthus strains in a monophyletic group in X. citri. The VNTR (variable number of tandem repeat) typing scheme conducted on 107 strains detected 101 haplotypes. The total number of alleles per locus ranged from 5 to 12. A minimum spanning tree (MST) showed that Brazilian strains were clearly separated from Indian strains, which showed unique alleles at three loci. The two strains isolated from symptomatic Amaranthus sp. presented unique alleles at two loci. STRUCTURE analyses revealed three groups congruent with MST and a fourth group with strains from India and Brazil. Admixture among populations were observed in all groups. MST, STRUCTURE and e-BURST analyses showed that the strains collected in 1998 belong to two distinct groups, with predicted founder genotypes from two different vineyards in the same region. This suggest that one introduction of grape planting materials contaminated with genetically distinct strains took place, which was followed by pathogen adaptation. Genome sequencing of one Brazilian strain confirmed typical attributes of pathogenic xanthomonads and allowed the design of a complementary VNTR typing scheme dedicated to X. citri pv. viticola that will allow further epidemiological survey of this genetically monomorphic pathovar.

Phylogenetic analysis of partial pre-membrane and envelope sequences of dengue viruses circulating in India

ObjectivePhylogenetic characteristics of circulating Indian dengue viruses (DENV) were analysed using partial pre-membrane (PrM) and envelope (E) sequences. An immunodominant region was analysed for mutations, and alignment with common DENV PCR primers and probes was determined. MethodsPublished Indian PrM and E DENV sequences were analysed with hitherto unpublished PrM sequences from this study site. Alignments of DENV were checked for mutations in an immunodominant region and against the commonly used PCR primers and probes. ResultsAll four serotypes of DENV circulate in India. Genotype (G) GIII and GI of DENV-1 co-circulated in the south with significant PrM mutations before and after 2012. DENV-2 American genotype was first reported after which the Cosmopolitan genotype co-circulated with it in the southwest. The Cosmopolitan strain has been the only DENV-2 genotype circulating, although an Asian American genotype was recently reported. Significant mutations were found in the E region of DENV-2 strains. DENV-3 strains were GIII across the country. DENV-4 GI from the south and west has now spread across India. No significant mutations were found for DENV-3 or DENV-4. Indian strains showed mutations in an immunodominant region of the E gene and in the regions targeted by commonly used PCR primers and probes. ConclusionsThe genetic variability of Indian DENV with co-circulation of multiple genotypes suggests that genotype surveillance is crucial to determining the composition of dengue vaccines and understanding their contribution to epidemiology, virus fitness and pathogenesis. Some mutations seen in an immunodominant region of the E gene may allow these viruses to evade host immune cells. The mutations in the regions targeted by commonly used primers and probes necessitate higher degeneracy.