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Background: Dystrophic epidermolysis bullosa (DEB) is due to variation in the COL7A1 gene. The clinical phenotype and severity depends on the type of variation and domain of the affected protein. Objectives: To characterize the spectrum of COL7A1 variations in a cohort of DEB patients from India, to correlate these findings with clinical phenotypes and to establish a genotype-phenotype correlation. Methods: This was a retrospective, observational study involving patients with DEB diagnosed on the basis of clinical manifestations, Immuno-fluorescence antigen mapping (IFM) and genetic analysis. A genotype-phenotype correlation was attempted and observations were further explained using IFM on skin biopsies and molecular dynamic simulations. Descriptive statistics were performed using SPSS version 20.0 with P values of <0.05 considered significant. Results: We report 68 unrelated Indian DEB patients classified as RDEB-Intermediate (RDEB-I), RDEB-Severe (RDEB-S) or DDEB based on the EB diagnostic matrix, immunofluorescence antigen mapping and genetic data. Of 68 DEB patients, 59 (86.76%) were inherited in a recessive pattern (RDEB) and 9 (13.24%) in a dominant pattern (DDEB). Limbal stem cell deficiency was seen in four cases of RDEB-S very early in the course of the disease. A total of 88 variants were detected of which 66 were novel. There were no hotspots and recurrent variations were seen in a very small group of patients. We found a high frequency of compound heterozygotes (CH) in RDEB patients born out of non-consanguineous marriage. RDEB patients older than two years who had oral mucosal involvement, and/or deformities, were more likely to have esophageal involvement. Genotype phenotype correlation showed a higher frequency of extracutaneous manifestations and deformities in patients with Premature Termination Codons (PTCs) than in patients with other variations. Molecular simulation studies in patients with missense mutations showed severe phenotype when they were localized in interrupted regions of GLY-X-Y repeats. Conclusion: This large study of DEB patients in South Asia adds to the continually expanding genetic database of this condition. This study has direct implications on management as this group of patients can be screened early and managed appropriately. [ABSTRACT FROM AUTHOR]

Objectives: Indian caste system is unique as it has an inimitable type of class system where the social ordering is done based on birth. Within the caste system, there is a distinct endogamous population known as the Kayastha, who have had inconclusive stratification records due to unidentified historical records. Methods: To gain a more inclusive view on the history and genetic affinities of Kayastha people, complete mitochondrial genomes from 15 individuals of a Kayastha population from North‐western India have been sequenced. Results: Interestingly, three novel sub‐clades (U2b2a, M3d2, and M33a3b) have been identified that represent unique Kayastha motifs. Conclusion: The haplotype‐based analysis suggests that the Kayastha population shares genetic affinities with the Indo‐European and Sino‐Tibetan populations found in the trans‐Himalayan region. The FST based population comparison and the MDS plot indicates that Kayastha people have close maternal genetic affinity with the available genetic database of Brahmins, Kashmiris, and Tharus. The maternal genetic lineages among Kayastha population shows deep in situ origin that emerged much before settled life developed on this sub‐continent. Both mtDNA and Y‐chromosome markers, trace the genetic lineages of Kayastha population with Tharus, who regard themselves Kshatriya, corroborated by the oral history of the Kayasthas for their Kshatriya affiliation. It also validates genetic heritage of earliest settlers of India in both indigenous tribal and caste populations. [ABSTRACT FROM AUTHOR]

The Psyra Walker, 1860, is a typical Sino-Himalayan genus of the subfamily Ennominae, currently known by 18 species/4 subspecies globally and 9 species from India. This study aims to revise the taxonomy and ecology of Indian Psyra by providing a morphology-based diagnostic key, highlighting their altitudinal, habitat and seasonal preferences, and modelling their distribution based on current and future climatic scenarios. Here, we describe a new species, P. variabilissp. nov. and document 4 species and 1 subspecies as new to India, viz. P. gracilis, P. szetschwana, P. dsagara, P. falcipennis and P. debilis debilis, thus updating the global species count to 19 with 14 species/1 subspecies from India. We also submitted partial mitochondrial COI sequences of P. crypta, P. similaria, P. spurcataria and P. gracilis as novel to the global genetic database and calculated the overall genetic divergence was 5.17% within the genus, suggesting strong monophyly. Being a typical montane genus, most of the species of Psyra were active within 2000–2280 m altitude, 10.55–15.7°C annual mean temperature, 1200–2300 mm annual precipitation and 168–179 NDVI. Psyra species were predominant in wet temperate, mixed coniferous and moist temperate deciduous forests, their abundance and richness being at peak during post-monsoon months of October–November. The major bioclimatic variables influencing the overall distribution of the genus were mean temperature of warmest quarter, temperature seasonality and precipitation of coldest/driest quarter. While two of the modelled species were predicted to lose area occupancy under future climatic scenarios, the narrow-specialist, Trans-Himalayan species P. debilis debilis was projected to gain up to 75% additional area in the years 2041–60. The results of this study will be helpful to identify sites with maximum area loss projection in ecologically fragile Indian Himalaya and initiating conservation management for such climatically vulnerable insect species groups. [ABSTRACT FROM AUTHOR]

Background: Malaria continues to be a major public health problem in the Northeastern part of India despite the implementation of vector control measures and changes in drug policies. To develop successful vaccines against malaria, it is important to assess the diversity of vaccine candidate antigens in field isolates. This study was done to assess the diversity of Plasmodium falciparum AMA-1 vaccine candidate antigen in a malaria-endemic region of Tripura in Northeast India and compare it with previously reported global isolates with a view to assess the feasibility of developing a universal vaccine based on this antigen. Methods: Patients with fever and malaria-like illness were screened for malaria and P. falciparum positive cases were recruited for the current study. The diversity of PfAMA-1 vaccine candidate antigen was evaluated by nested PCR and RFLP. A selected number of samples were sequenced using the Sanger technique. Results: Among 56 P. falciparum positive isolates, Pfama-1 was successfully amplified in 75% (n = 42) isolates. Allele frequencies of PfAMA-1 antigen were 16.6% (n = 7) for 3D7 allele and 33.3% (n = 14) in both K1 and HB3 alleles. DNA sequencing revealed 13 haplotypes in the Pfama-1 gene including three unique haplotypes not reported earlier. No unique amino-acid substitutions were found. Global analysis with 2761 sequences revealed 435 haplotypes with a very complex network composition and few clusters. Nucleotide diversity for Tripura (0.02582 ± 0.00160) showed concordance with South-East Asian isolates while recombination parameter (Rm = 8) was lower than previous reports from India. Population genetic structure showed moderate differentiation. Conclusions: Besides documenting all previously reported allelic forms of the vaccine candidate PfAMA-1 antigen of P. falciparum, new haplotypes not reported earlier, were found in Tripura. Neutrality tests indicate that the Pfama-1 population in Tripura is under balancing selection. This is consistent with global patterns. However, the high haplotype diversity observed in the global Pfama-1 network analysis indicates that designing a universal vaccine based on this antigen may be difficult. This information adds to the existing database of genetic diversity of field isolates of P. falciparum and may be helpful in the development of more effective vaccines against the parasite. [ABSTRACT FROM AUTHOR]

Dengue (DEN) is the most common cause of mosquito‐borne endemic viral diseases in the tropical and subtropical countries. DEN outbreaks associated with multiple dengue virus (DV) serotypes have been regularly reported in different parts of India. This study was done during DEN outbreaks in 2015 to 2016 in UP and Bihar where DEN‐2 was found as the only prevalent serotype. DV‐2 was the only serotype amplified in serotype‐specific reverse‐transcription polymerase chain reaction from sera of 210 (65.21%) out of 322 DV NS1 antigen‐positive patients. Further genetic analysis based on full‐length envelope (E) protein sequence derived from patient's sera as well as DV isolate showed the circulation of lineages I and III of DV‐2 cosmopolitan genotype during 2015 and lineage II during 2016. Finally, the phylogenetic analysis using the E gene sequence revealed that these DV‐2 strains have a close genetic relationship with the recently reported DV‐2 genotypes from DEN outbreaks reported from different parts of north India. These results showed the circulation of cosmopolitan genotype of DV‐2 in eastern Uttar Pradesh and western Bihar, India. The genetic database generated on circulating DV strains in this study will be useful as reference for disease surveillance and strengthening laboratory diagnosis protocols. Highlights: In the study, we observed that DV‐2 Cosmopolitan is the major genotype associated with the dengue outbreak during 2015 and 2016 in eastern Uttar Pradesh and Western Bihar of India. Further, we also observed that shift in lineage of DV‐2 Cosmopolitan genotype from I and III during 2015 to lineage II during 2016. [ABSTRACT FROM AUTHOR]

• First forensic DNA profiling system for Indian Greater one-horned rhinoceros. • The 14 marker panel was standardised following ISFG guidelines. • Markers were tested for peak characteristics, allele calling inconsistencies, and polymorphism. • Panel was used to provide scientific evidence for 15 alleged rhino poaching cases in India. The Greater one-horned (GoH) rhinoceros is one of the most charismatic endemic megaherbivores of the Indian subcontinent. Threatened by poaching, habitat loss and disease, the species is found only in small areas of its historical distribution. Increasing demands for rhino horns in chinese traditional medicine has put the existing population under continuing threat, and large profits and low conviction rates make poaching difficult to contain. DNA forensics such as the RhoDIS-Africa program has helped in combating illegal rhino horn trade, but the approach is yet to be optimised for Indian GoH rhinoceros. Here we followed the International Society for Forensic Genetics (ISFG) guidelines to establish a 14 dinucleotide microsatellite panel for Indian GoH rhinoceros DNA profiling. Selected from a large initial pool (n = 34), the microsatellite markers showed high polymorphism, stable peak characteristics, consistent allele calls and produced precise, reproducible genotypes from different types of rhino samples. The panel also showed low genotyping error and produced high statistical power during individual identification (P IDsibs value of 1.2*10−4). As part of the official RhoDIS-India program, we used this panel to match poached rhino carcass with seized contraband as scientific evidence in court procedure. This program now moves to generate detailed allele-frequency maps of all GoH rhinoceros populations in India and Nepal for development of a genetic database and identification of poaching hotspots and trade routes across the subcontinent and beyond. [ABSTRACT FROM AUTHOR]

The article discusses a study on the use of insilico approach for molecular determinants analysis and co receptor tropism prediction of V3 loop of HIV-1 C clade sequences. The study retrieves HIV-1 C type env sequences of Indian isolates from HIV sequence database. It reveals a lower numbers of positive charges of v3 loop thus reveals the prevalence of R5 tropism.