The genetic admixture and assimilation of Ahom: a historic migrant from Thailand to India.

The Northeastern region of India is considered a gateway for modern humans' dispersal throughout Asia. This region is a mixture of various ethnic and indigenous populations amalgamating multiple ancestries. One reason for such amalgamation is that, South Asia experienced multiple historic migrations from various parts of the world. A few examples explored genetically are Jews, Parsis and Siddis. Ahom is a dynasty that historically migrated to India during the 12th century. However, this putative migration has not been studied genetically at high resolution. Therefore, to validate this historical evidence, we genotyped autosomal data of the Modern Ahom population residing in seven sister states of India. Principal Component and Admixture analyses haave suggested a substantial admixture of the Ahom population with the local Tibeto-Burman populations. Moreover, the haplotype-based analysis has linked these Ahom individuals mainly with the Kusunda (a language isolated from Nepal) and Khasi (an Austroasiatic population of Meghalaya). Such unexpected presence of widespread population affinities suggests that Ahom mixed and assimilated a wide variety of Trans-Himalayan populations inhabiting this region after the migration. In summary, we observed a significant deviation of Ahom from their ancestral homeland (Thailand) and extensive admixture and assimilation with the local South Asian populations.

Genetic evidence for a single founding population of the Lakshadweep Islands.

Lakshadweep is an archipelago of 36 islands located in the Southeastern Arabian Sea. In the absence of a detailed archaeological record, the human settlement timing of this island is vague. Previous genetic studies on haploid DNA makers suggested sex-biased ancestry linked to North and South Indian populations. Maternal ancestry suggested a closer link with the Southern Indian, while paternal ancestry advocated the Northern Indian genetic affinity. Since the haploid markers are more sensitive to genetic drift, which is evident for the Island populations, we have used the biparental high-resolution single-nucleotide polymorphic markers to reconstruct the population history of Lakshadweep Islands.  Using the fine-scaled analyses, we specifically focused on (A) the ancestry components of Lakshadweep Islands populations; (B) their relation with East, West Eurasia and South Asia; (C) the number of founding lineages and (D) the putative migration from Northern India as the paternal ancestry was closer to the North Indian populations. Our analysis of ancestry components confirmed relatively higher North Indian ancestry among the Lakshadweep population. These populations are closely related to the South Asian populations. We identified mainly a single founding population for these Islands, geographically divided into two sub-clusters. By examining the population's genetic composition and analysing the gene flow from different source populations, this study contributes to our understanding of Lakshadweep Island's evolutionary history and population dynamics. These findings shed light on the complex interactions between ethnic groups and their genetic contributions in making the Lakshadweep population.

The matrilineal ancestry of Nepali populations.

The Tibetan plateau and high mountain ranges of Nepal are one of the challenging geographical regions inhabited by modern humans. While much of the ethnographic and population-based genetic studies were carried out to investigate the Tibetan and Sherpa highlanders, little is known about the demographic processes that enabled the colonization of the hilly areas of Nepal. Thus, the present study aimed to investigate the past demographic events that shaped the extant Nepalese genetic diversity using mitochondrial DNA (mtDNA) variations from ethnic Nepalese groups. We have analyzed mtDNA sequences of 999 Nepalese and compared data with 38,622 published mtDNA sequences from rest of the world. Our analysis revealed that the genomic landscapes of prehistoric Himalayan settlers of Nepal were similar to that of the low-altitude extant Nepalese (LAN), especially Newar and Magar population groups, but differ from contemporary high-altitude Sherpas. LAN might have derived their East Eurasian ancestry mainly from low-altitude Tibeto-Burmans, who likely have migrated from East Asia and assimilated across the Eastern Himalayas extended from the Eastern Nepal to the North-East of India, Bhutan, Tibet and Northern Myanmar. We also identified a clear genetic sub-structure across different ethnic groups of Nepal based on mtDNA haplogroups and ectodysplasin-A receptor (EDAR) gene polymorphism. Our comprehensive high-resolution mtDNA-based genetic study of Tibeto-Burman communities reconstructs the maternal origins of prehistoric Himalayan populations and sheds light on migration events that have brought most of the East Eurasian ancestry to the present-day Nepalese population.

Signatures of high altitude adaptation in Tibeto-Burman tribes of the Darjeeling Hill Region.

OBJECTIVES: The long-term isolation, endogamy practices, and environmental adaptations have shaped the enormous human diversity in India. The genetic and morphological variations in mainland Indians are well studied. However, the data on the Indian Himalayan populations are scattered. Thus, the present study attempts to understand variations in the selected parameter among four Tibeto-Burman speaking ethnic tribal populations from the Darjeeling Hill Region (DHR) in the Eastern Himalaya Biodiversity Hotspot region of India. METHODS: A total of 178 healthy male individuals (Lepcha 98, Sherpa 31, Bhutia 27, and Tibetans 22) living at an altitudinal range of 1467-2258 m above the sea level were studied for the 10 parameters namely, weight (kg), height (cm), body mass index (BMI) (kg/m2 ) systolic and diastolic pressure (mm of Hg), pulse rate (per minute), saturation of peripheral oxygen (SPO2 ) (%), hemoglobin (g/dl), hematocrit (HCT) (%), and blood glucose (mg/dl). The data was statistically analyzed using analysis of variance and multiple linear regression methods. RESULTS: Our analysis revealed comparatively lower hemoglobin and HCT levels, and higher systolic and diastolic blood pressure in the Sherpas followed by the Tibetans. This may be reflecting the persistence of high-altitude adaptation signatures even in lowlands. Interestingly, the Tibetans differed significantly from other populations in terms of their higher body weight, height, and BMI. CONCLUSION: Thus, our study showed the persistence of high altitude signatures in Tibetans and Sherpa inhabited the DHR. Additionally, we also observed significant differences in the anthropometric and physiological parameters among the Tibeto-Burman populations of the DHR.

Inferring Recombination Events in SARS-CoV-2 Variants In Silico.

Over the last 34 months, at least 10 severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) distinct variants have evolved. Among these, some were more infectious while others were not. These variants may serve as candidates for identification of the signature sequences linked to infectivity and viral transgressions. Based on our previous hijacking and transgression hypothesis, we aimed to investigate whether SARS-CoV-2 sequences associated with infectivity and trespassing of long noncoding RNAs (lncRNAs) provide a possible recombination mechanism to drive the formation of new variants. This work involved a sequence and structure-based approach to screen SARS-CoV-2 variants in silico, taking into account effects of glycosylation and links to known lncRNAs. Taken together, the findings suggest that transgressions involving lncRNAs may be linked with changes in SARS-CoV-2-host interactions driven by glycosylation events.

COVID-19: Impact on linguistic and genetic isolates of India.

The rapid expansion of coronavirus SARS-CoV-2 has impacted various ethnic groups all over the world. The burden of infectious diseases including COVID-19 are generally reported to be higher for the Indigenous people. The historical knowledge have also suggested that the indigenous populations suffer more than the general populations in the pandemic. Recently, it has been reported that the indigenous groups of Brazil have been massively affected by COVID-19. Series of studies have shown that many of the indigenous communities reached at the verge of extinction due to this pandemic. Importantly, South Asia also has several indigenous and smaller communities, that are living in isolation. Till date, despite the two consecutive waves in India, there is no report on the impact of COVID-19 for indigenous tribes. Since smaller populations experiencing drift may have greater risk of such pandemic, we have analysed Runs of Homozygosity (ROH) among South Asian populations and identified several populations with longer homozygous segments. The longer runs of homozygosity at certain genomic regions may increases the susceptibility for COVID-19. Thus, we suggest extreme careful management of this pandemic among isolated populations of South Asia.

Molecular characterization of 23 Y chromosomal STR markers in the Gurjar population of National Capital Region (NCR), India.

In the present study, DNA samples of 202 unrelated male individuals of Gurjar population were evaluated for the molecular diversity at 23 Y chromosomal Y-STR markers. Out of selected individuals, results showed 143 unique haplotypes. Highest degree of gene diversity (GD), polymorphic information content (PIC), and power of discrimination (PD) was observed as 0.7941, 0.7590, and 0.7902, respectively, for the locus DYS385a/b. Haplotype diversity (HD), gene diversity (GD), polymorphic information content (PIC), and power of discrimination (PD) was found to be 0.7079, 0.999999999989, 0.9999999996, and 0.999999999986, respectively, for the studied 23 Y-STR markers. Allele 11 of locus DYS392 was found to be the most frequent allele with the frequency of 0.762. In inter-population relationship, studied population showed genetic relatedness with the population of Jammu and Kashmir, India, and Ladakh, India. The haplotype data of the present study will not only enrich the existing Indian Y-STR data but will also be useful for forensic DNA application.

Forensic features and phylogenetic analyses of the population of Nayagarh (Odisha), India using 23 Y-STRs.

AIM: The present study was designed to explore the STR diversity and genomic history of the inhabitants of Nayagarh district of Odisha, India. We also tested the proficiency of the most recent, new generation PowerPlexR Y23 multiplex system for forensic characterisation and to decipher the phylogenetic affinities. SUBJECTS AND METHODS: The genetic diversity and polymorphism among 236 healthy unrelated male volunteers from Nayagarh district of Odisha, India was investigated. This investigation was carried out via 23 Y-chromosomal STRs using capillary electrophoresis. RESULT: A total 223 unique haplotypes were reported. Discrimination capacity (DC), gene diversity (GD) and power of discrimination (PD) were observed as 0.945, 0.999999999998333, and 0.99999999999794, respectively. Polymorphic information content (PIC) and matching probability (PM) were reported as 0.999999999925535 and 2.06 × 10-12, respectively. Simultaneously, the haplogroup analysis characterised with C2, E1b1a, E1b1b, G2a, H1, I2a, J2a, J2b, L, O, O1, O2, Q, R1a, R2, and T haplogroups, disclosing the possible geographical relatedness of the studied population to different areas of the world. CONCLUSION: Phylogenetic analysis with previously reported Indian and Asian populations showed the genetic closeness of the studied population to different Indian populations and the Bangladeshi population of Dhaka, whereas the Bhotra population of Odisha and Han population of China showed much less genetic affinity.

Haplogroup diversity in the Indian population using 23 Y-STRs.

BACKGROUND: A Y-STR polymorphism study is a convenient tool in molecular anthropology and forensic DNA analysis. AIM: Through standard ethical procedures, the proposed study explored the genetic scenario in male lineage in Madhya Pradesh, a central Indian state, by Y-STR genotyping and haplogroup studies. SUBJECTS AND METHODS: Five hundred and eleven unrelated male blood samples were directly amplified, and fragment separation was done using capillary electrophoresis to generate a Y-STR profile for 23 forensic relevant markers through PowerPlex® Y 23 multiplex system. The different statistical methods were applied for studying the forensic and genetics parameters. Subsequently, population comparison was performed by AMOVA, PCoA, and MDS plot, and Haplogroups were predicted with Whit Athey's haplogroup predictor tool. CONCLUSION: These data represented the potential value of the PowerPlex® Y-23 multiplex system for the forensic and human genetics application in the population of Madhya Pradesh, India. Simultaneously the Haplogroup analysis revealed information about the multi-geographic origin as well as multi-ethnic genetic affinities of the Madhya Pradesh population.

An evaluation of inter and intra population structure of Uttar Pradesh, inferred from 24 autosomal STRs.

AIM: The present study was designed to explore the STR diversity and genomic history of the inhabitants of the most populous subdivision of the country. A set of 24 hypervariable autosomal STRs was used to estimate the genetic diversity within the studied population. A panel of 15 autosomal STRs, which is most common in the previously reported data sets, was used to estimate the genetic diversity between the studied population, and obtained unique relations were reported here. METHOD: The genetic diversity and polymorphism among 636 individuals of different ethnic groups, residing in Bareilly, Pilibhit, Shahjahanpur, Gorakhpur, Jhansi, and Varanasi regions of Uttar Pradesh, India, was investigated. This investigation was carried out via 24 autosomal STRs. RESULT: The 24 loci studied showed the highest value of combined power of discrimination (CPD = 1), combined power of exclusion (CPE = 0.99999999985), combined paternity index (CPI = 6.10 × 109) and lowest combined matching probability (CPM = 7.90 × 10-31). CONCLUSION: The studied population showed genetic closeness with the population of Uttarakhand, the Jats of Delhi,the Jat Sikh (Punjab), and the population of Rajasthan. Among the tested loci, SE33 and Penta E were found to be most useful in terms of the highest discrimination power, lowest matching probability, the highest power of exclusion, and highest polymorphism information content for the Uttar Pradesh population .

SARS-CoV-2 transgressing LncRNAs uncovers the known unknowns.

SARS-CoV-2 harbors many known unknown regions in the form of hypothetical open reading frames (ORFs). Although the mechanisms underlying the disease pathogenesis are not clearly understood, molecules such as long noncoding RNAs (lncRNAs) play a key regulatory role in the viral pathogenesis from endocytosis. We asked whether or not the lncRNAs in the host are associated with the viral proteins and argue that lncRNA-mRNAs molecules related to viral infection may regulate SARS-CoV-2 pathogenesis. Toward the end of the perspective, we provide challenges and insights into investigating these transgression pathways.

The Genetic Ancestry of Modern Indus Valley Populations from Northwest India.

The Indus Valley has been the backdrop for several historic and prehistoric population movements between South Asia and West Eurasia. However, the genetic structure of present-day populations from Northwest India is poorly characterized. Here we report new genome-wide genotype data for 45 modern individuals from four Northwest Indian populations, including the Ror, whose long-term occupation of the region can be traced back to the early Vedic scriptures. Our results suggest that although the genetic architecture of most Northwest Indian populations fits well on the broader North-South Indian genetic cline, culturally distinct groups such as the Ror stand out by being genetically more akin to populations living west of India; such populations include prehistorical and early historical ancient individuals from the Swat Valley near the Indus Valley. We argue that this affinity is more likely a result of genetic continuity since the Bronze Age migrations from the Steppe Belt than a result of recent admixture. The observed patterns of genetic relationships both with modern and ancient West Eurasians suggest that the Ror can be used as a proxy for a population descended from the Ancestral North Indian (ANI) population. Collectively, our results show that the Indus Valley populations are characterized by considerable genetic heterogeneity that has persisted over thousands of years.

A case of "false tri-allelic pattern" on D7S820, caused by invasion of a short SE33 allele into the bins of D7S820.

Autosomal short tandem repeats (asSTR) serve as genetic markers for discriminating individuals and have been extensively used for criminal investigations as well as the establishment of genetic relationships. Tri-allelic pattern usually occurs due to chromosomal duplication, trisomy, and chimerism during mitotic division, but a false tri-allelic pattern at the D7S820 locus was encountered in our laboratory during the analysis of a case exhibit. DNA isolation from exhibit for profiling was done as per manufacturer's protocol. This is the first report which observed false tri-allelic pattern (10, 11, 14.1 allele) on D7S820 locus by analysis with GlobalFiler™ PCR Amplification Kit in Indian population. Findings were re-confirmed using other available asSTR kits in the laboratory, viz., AmpFLSTR™ Identifiler™ Plus PCR Amplification Kit and PowerPlex® Fusion 6C System. Two alleles (10, 11) found at D7S820, apart from SE33 marker, showed homozygous condition, but one Off Marker (OMR) peak was observed before start of SE33 marker region with the analysis using PowerPlex® Fusion 6C System. As it has been confirmed that the OMR allele belongs to the SE33 locus, this could be possible because of the adjacent locations of the D7S820 and the SE33 in the GlobalFiler® PCR amplification kit. 14.1 allele appeared within the allelic window of D7S820. The false tri-allelic pattern was due to the overlapping of SE33 marker allele (1.2 repeat) with bin window of D7S820 Marker. This finding might create confusion for the establishment of genetic relationships. We, therefore, conclude that such uncommon observations with rare events should be carefully investigated and interpreted.

Forensic characterization and genetic evaluation in the Central Indian population using 27 Y-STRs.

INTRODUCTION: Forensic characterization and genetic evaluation study in the 539 randomly selected unrelated adult healthy individuals belonging to the Central Indian population was undertaken. METHODS: The study was performed using a multiplex of 27 Y-STRs incoporated in Yfiler™ Plus multiplex kit. RESULTS: Out of 539 samples, 6 samples were observed for large deletion and tri-allelic patterns, which were removed from the analysis, and out of 533 samples, a total of 507 haplotypes were found, and out of these haplotypes, 482 unique haplotypes were found in this piece of work. The forensically important parameters, i.e., gene diversity (GD) and discrimination capacity (DC), were found to be 0.669 and 0.951, respectively, for the tested Y STR loci. The genetic data of this study will enrich the Y STR data bank and being used as a potential tool for forensic DNA and various genetic studies.

Genetic diversity and forensic characterization of 15 autosomal microsatellite markers in the North-east Indian Tripuri population.

This study was conducted to explore the genomic diversity and forensic characterization of 15 autosomal microsatellite markers in the East Indian Tripuri population. In the studied population, we observed 158 different alleles with the average 10.53 alleles per locus. The locus D2S1338 (PIC= 0.862) was found to be the most polymorphic wheres locus TPOX (PIC= 0.647) as the least polymorphic, among all the studied loci. The locus FGA was found with the highest number of effective alleles (Nall=19) whereas locus TH01 showed least number of effective alleles (Nall=6). The cumulative values for matching probability (CPm), power of discrimination (CPD), power of exclusion CPE), and paternity index (CPI) were found as 1.94×10-18, 1, 0.999998, and 4.8×105 respectively. The studied population showed genetic closeness with the Gorkha population. In neighbor-joining tree, Tripura population pooled with the population of Nepal and Tibet. The genetic data obtained from the present study will not only enrich the existing autosomal STR database but will also be useful for forensic DNA application and genealogical studies.

Genomic insight into Y-STR diversity in the population of Odisha, India.

This study evaluated the haplotype diversity of 17 Y chromosomal genetic markers among 202 unrelated males who were randomly selected in the population of Odisha, India. Out of total 196 haplotypes observed in this study, 190 were unique haplotypes. Forensic relevant parameters, viz., gene diversity (GD) and discrimination capacity (DC), were calculated as 0.999999998 and 0.970 respectively, for the studied population. The highest genetic diversity was observed at the locus DYS385a/b (0.9541) and lowest at the locus DYS437 (0.3326) among all the studied Y chromosomal loci. The polymorphic information content (PIC), power of discrimination (PD), and matching probability (PM) was found to be 0.999999965, 0.999999998, and 1.6×10-9 for the tested Y STR loci. The genetic data observed in this study would enrich the existing Y STR data of the Indian population and would also be useful for forensic application.

The association of ABO blood group with the asymptomatic COVID-19 cases in India.

The COVID-19 pandemic resulted in multiple waves of infection worldwide. The large variations in case fatality rate among different geographical regions suggest that the human susceptibility against this virus varies substantially. Several studies from different parts of the world showed a significant association of ABO blood group and COVID-19 susceptibility. It was demonstrated that individuals with blood group O are at the lower risk of coronavirus infection. To establish the association of ABO blood group in SARS-CoV-2 susceptibility, we for the first time analysed SARS-CoV-2 neutralising antibodies among 509 individuals, collected from three major districts of Eastern Uttar Pradesh region of India. Interestingly, we found neutralising antibodies in a significantly higher percentage of people with blood group AB (0.36) followed by B (0.31), A (0.22) and lowest in people with blood group O (0.11). We further estimated that people with blood group AB are at comparatively higher risk of infection than other blood groups. Thus, among the asymptomatic SARS-CoV-2 recovered people blood group AB has highest, whilst individuals with blood group O has lowest risk of infection.

Genomic polymorphism in tribal population of Tripura: Signifying their closer affinity with the Nepalese and Tibetan populations.

BACKGROUND: India is the second most populous country in the world, which is aligned into various community segments. AIM: To evaluate the genetic diversity of the tribal population of Tripura, we carried out this study. SUBJECTS AND METHODS: 15 autosomal STR markers were used for investigation of genomic diversity, inter- and intra- population relationships among the studied population, and other reported neighbouring tribal and caste populations. RESULTS: Results indicated that the tribals of Tripura share their closer genetic affinity with the Trans-Himalayan (Nepalese, Bhutanese and Tibetan) populations. Locus D18S51 was found as the most discriminatory among all the studied loci with uppermost discrimination power (PD = 0.964) and lowest matching probability (Pm = 0.036) in the study. All the evaluated loci herein are useful, having the maximum value of combined power of discrimination (CPD = 1), combined power of exclusion (CPE = 0.99999746), combined paternity index (CPI = 3 × 105) and combined matching probability (CPm = 2.12 × 1 0 -7). CONCLUSION: Population genetic analysis showed that the studied population has genetic relatedness with the compared Nepalese and Tibetan populations i.e., Kathmandu, Tibet, Newar, and Gorkhas, followed by eastern and central Indian populations.

Population genetic data of 22 autosomal STR loci for the Scheduled Caste population of Rajasthan India.

AIM: To study the genetic structure of the Scheduled Caste population of Rajasthan and its relationship with Indian and global populations using expanded 20 CODIS STR loci (autosomal) markers. SUBJECTS AND METHODS: Blood samples of 226 healthy, unrelated adult individuals of the Scheduled Caste population of the Indian state of Rajasthan were taken from the routine casework of authors after obtaining written informed consent. Autosomal STR markers included in PowerPlex® Fusion 5 C and GlobalFiler™ PCR amplification kits were used to explore the genetic diversity of the studied population. Amplicons were separated using Genetic Analyser 3500XL as per the recommended protocol. RESULTS: Observed heterozygosity for the studied population ranged from 0.681(CSF1PO) to 0.881 (D1S1656).Combined Discrimination Power and Combined Exclusion Power were observed as 1 and 0.9999999852, respectively. The highest Discrimination Power was observed for the locus D1S1656. In the population comparison test, Nei's Da distance-based Neighbor-Joining (NJ) dendrogram revealed two significant clusters of geographically close Indian and East Asian populations along with a few small groups of outlier populations. CONCLUSION: The matching probability for 20 STR markers was observed as 7.02 × 10-24 and paternity index as 5.55 × 107. These values play a key role in forensic applications.The studied population showed a higher genetic affinity with geographically closer populations than the distant ones. This caste-based population data is expected to play an important role in forensic DNA applications and genetic studies.

Decoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis.

Because of the ongoing pandemic around the world, the mechanisms underlying the SARS-CoV-2-induced COVID-19 are subject to intense investigation. Based on available data for the SARS-CoV-1 virus, we suggest how CoV-2 localization of RNA transcripts in mitochondria hijacks the host cell's mitochondrial function to viral advantage. Besides viral RNA transcripts, RNA also localizes to mitochondria. SARS-CoV-2 may manipulate mitochondrial function indirectly, first by ACE2 regulation of mitochondrial function, and once it enters the host cell, open-reading frames (ORFs) such as ORF-9b can directly manipulate mitochondrial function to evade host cell immunity and facilitate virus replication and COVID-19 disease. Manipulations of host mitochondria by viral ORFs can release mitochondrial DNA (mtDNA) in the cytoplasm and activate mtDNA-induced inflammasome and suppress innate and adaptive immunity. We argue that a decline in ACE2 function in aged individuals, coupled with the age-associated decline in mitochondrial functions resulting in chronic metabolic disorders like diabetes or cancer, may make the host more vulnerable to infection and health complications to mortality. These observations suggest that distinct localization of viral RNA and proteins in mitochondria must play essential roles in SARS-CoV-2 pathogenesis. Understanding the mechanisms underlying virus communication with host mitochondria may provide critical insights into COVID-19 pathologies. An investigation into the SARS-CoV-2 hijacking of mitochondria should lead to novel approaches to prevent and treat COVID-19.