ABSTRACT
Background SARS CoV-2, the causative agent for the ongoing COVID-19 pandemic, enters the host cell by activating the ACE2 receptor with the help of two proteases, i.e., Furin and TMPRSS2. Therefore, variations in these genes may account for differential susceptibility and severity between populations. Our previous studies have shown that ACE2 and TMPRSS2 gene variants are essential in understanding COVID-19 susceptibility among Indian populations. However, there is a knowledge gap regarding Furin gene variants and their phylogenetic structure among diverse Indian and South Asian ethnic groups and their impact on disease vulnerability, which needs to be investigated.Material and methods Considering the role of the Furin gene in the pathogenesis of SARS-CoV-2. We have used 450 samples from diverse Indian states and performed linear regression to analyse the Furin gene variant's allele frequency with COVID-19 CFR that could be epidemiologically associated with disease severity outcomes among populations. Associated genetic variants were further evaluated for their expression and regulatory potential through various Insilco analyses. Additionally, we examined the Furin gene architecture using next-generation sequencing (NGS) data from 393 diverse global samples, with a particular emphasis on South Asia, to investigate its phylogenetic makeup and the distribution of haplotypes among distinct global populations.Results We found a significant positive association for the rs1981458 with COVID-19 CFR among diverse Indian populations. Further QTL and other regulatory analyses showed various significant associations and positive regulatory roles of this SNP and Furin gene, mainly in Immune cells and virus infection process, highlighting their role in host immunity and viral assembly and processing. The Furin protein-protein interaction suggested that COVID-19 may contribute to Pulmonary arterial hypertension via a typical inflammation mechanism. The phylogenetic architecture of the Furin gene demonstrated a closer genetic affinity between West Eurasian and South Asians. Therefore, it is worth proposing that in the context of the Furin gene, the COVID-19 susceptibility of South Asians will be more similar to the West Eurasian population. Our previous studies on the ACE2 and TMPRSS2 genes showed a contrasting genetic affinity of South Asian with East Eurasians and West Eurasians, respectively. Therefore, we modelled COVID-19 susceptibility for susceptibility of South Asia in between these two major ancestries with an inclination towards West Eurasians.Conclusion In conclusion, this study, for the first time, concluded the role of rs1981458 in COVID-19 severity among the Indian population and outlined its regulatory potential in COVID-19 and genetic structure and susceptibility for COVID-19 susceptibility of South Asia is inclined to West Eurasian population. We believe this insight may well be utilised as a genetic biomarker to identify vulnerable populations, which might be directly relevant for developing policies and allocating resources more effectively during an epidemic.
Subject(s)
Hypertension, Pulmonary , Tumor Virus Infections , Inflammation , COVID-19ABSTRACT
After the spill to humans, in the timeline of SARS-CoV-2, several positively selected variants have emerged. A phylogeographic study on these variants can reveal their spatial and temporal distribution. In December 2020, the alpha variant of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which has been designated as a variant of concern (VOC) by WHO, was discovered in the southeastern United Kingdom (UK). Slowly, it expanded across India, with a considerable number of cases, particularly in North India. The study focuses on determining the prevalence and expansion of the alpha variants in various parts of India. The genetic diversity estimation helped us understand various evolutionary forces that have shaped the spatial distribution of this variant during the peak. Overall, our study paves the way to understand the evolution and expansion of a virus variant.
Subject(s)
Severe Acute Respiratory SyndromeABSTRACT
With the roll-out of worlds largest vaccine drive for Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) by Government of India on January 16 2021, India has targeted to vaccinate its entire population by the end of year 2021. Struggling with vaccine procurement and production earlier, India came up with these hurdles but the Indian population still did not seem to be mobilizing swiftly towards vaccination centers. With the initial hesitancy, as soon as the vaccination started to speedup, India was hit severely by the second wave. The severe second wave has slowed down the vaccination pace and also it was one of the major contributing factor of vaccine hesitancy. To understand the nature of vaccine hesitancy and factors underlying it, we conducted an extensive online and offline surveys in Varanasi and adjoining regions using structured questions. Majority of respondents though were students (0.633), respondents from other occupations such as government officials (0.10) were also included in the study. We observed several intriguing opinions on our eleven questions. It is interesting to note that the majority of the people (0.75) relied on fake news and did not take COVID-19 seriously. Most importantly, we noticed that a substantial proportion of respondents (relative frequency 0.151; mean age 24.8 years) reported that they are still not interested in vaccination. People who have neither been vaccinated nor have ever been infected may become the medium for spreading the virus and creating new variants. This could also lead to a resistant variant of the vaccine in the future. We expect that this extensive survey may help the government to upgrade their vaccination policies for COVID-19 in North India.
Subject(s)
Coronavirus Infections , Severe Acute Respiratory Syndrome , COVID-19ABSTRACT
SARS-CoV2, the causative agent for COVID-19, an ongoing pandemic, engages the ACE2 receptor to enter the host cell through S protein priming by a serine protease, TMPRSS2. Variation in the TMPRSS2 gene may account for the difference in population disease susceptibility. The haplotype-based genetic sharing and structure of TMPRSS2 among global populations have not been studied so far. Therefore, in the present work, we used this approach with a focus on South Asia to study the haplotypes and their sharing among various populations worldwide. We have used next-generation sequencing data of 393 individuals and analysed the TMPRSS2 gene. Our analysis of genetic relatedness for this gene showed a closer affinity of South Asians with the West Eurasian populations therefore, host disease susceptibility and severity particularly in the context of TMPRSS2 will be more akin to West Eurasian instead of East Eurasian. This is in contrast to our prior study on ACE2 gene which shows South Asian haplotypes have a strong affinity towards West Eurasians. Thus ACE2 and TMPRSS2 have an antagonistic genetic relatedness among South Asians. We have also tested the SNPs frequencies of this gene among various Indian state populations with respect to the case fatality rate. Interestingly, we found a significant positive association between the rs2070788 SNP (G Allele) and the case fatality rate in India. It has been shown that the GG genotype of rs2070788 allele tends to have a higher expression of TMPRSS2 in the lung compared to the AG and AA genotypes, thus it might play a vital part in determining differential disease vulnerability. We trust that this information will be useful in underscoring the role of the TMPRSS2 variant in COVID-19 susceptibility and using it as a biomarker may help to predict populations at risk.
Subject(s)
Graft vs Host Disease , COVID-19ABSTRACT
Studies worldwide have shown that the available vaccines are highly effective against SARS-CoV-2. However, there are growing laboratory reports that the newer variants of concerns (VOCs e.g. Alpha, Beta, Delta etc) may evade vaccine induced defense. In addition to that, there are few ground reports on health workers having breakthrough infections. In order to understand VOC driven breakthrough infection we investigated 14 individuals who tested positive for SARS-CoV-2 after being administered a single or double dose of Covishield (ChAdOx1, Serum Institute of India) from the city of Varanasi, which is located in the Indian state of Uttar Pradesh. Genomic analysis revealed that 78.6% (11/14) of the patients were infected with the B.1.617.2 (Delta) variant. Notably, the frequency (37%) of this variant in the region was significantly lower (p<0.01), suggesting that the vaccinated people were asymmetrically infected with the Delta variant. Most of the patients tested displayed mild symptoms, indicating that even a single dose of the vaccine can help in reducing the severity of the disease. However, more comprehensive epidemiological studies are required to understand the effectiveness of vaccines against the newer VOCs.
Subject(s)
Breakthrough PainABSTRACT
The ongoing COVID-19 pandemic has been a scientific, medical and social challenge. Since clinical course of this disease is largely unpredictable and can develop rapidly causing severe complications, it is important to identify laboratory biomarkers which may help to classify patient’s severity during initial stage. Previous studies have suggested C - reactive protein (inflammatory) and D-dimer (biochemical) as an effective biomarker. The differential severity in patients across the world and our limited understanding in the progression of the disease calls for a multi-country analysis for biomarkers. Therefore, we have analyzed these biomarkers among 228 Bangladeshi COVID-19 patients. We show significant association of COVID-19 severity with these two biomarkers. Thus, we suggest using these biomarkers for Bangladeshi COVID-19 patients for disease monitoring. Such validated preventive measures may decrease the case fatality ratio substantially.
Subject(s)
COVID-19ABSTRACT
The ongoing COVID-19 pandemic has been a scientific, medical and social challenge. Since clinical course of this disease is largely unpredictable and can develop rapidly causing severe complications, it is important to identify laboratory biomarkers which may help to classify patient’s severity during initial stage. Previous studies have suggested C - reactive protein (inflammatory) and D-dimer (biochemical) as an effective biomarker. The differential severity in patients across the world and our limited understanding in the progression of the disease calls for a multi-country analysis for biomarkers. Therefore, we have analyzed these biomarkers among 228 Bangladeshi COVID-19 patients. We show significant association of COVID-19 severity with these two biomarkers. Thus, we suggest using these biomarkers for Bangladeshi COVID-19 patients for disease monitoring. Such validated preventive measures may decrease the case fatality ratio substantially.
Subject(s)
COVID-19ABSTRACT
The COVID-19 pandemic has resulted several waves of infection in many countries worldwide. The large variations in case fatality ratio among different geographical regions suggests 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 shown 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 as well as blood groups among 509 random individuals from three major districts of Eastern Uttar Pradesh region of India.. Interestingly, we found neutralising antibodies in 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). This indicates that people with blood group AB are at comparatively higher risk of infection than other blood groups. Further, in line to previous reports we too observed that people with blood group O have significantly decreased risk of SARS-CoV-2 infection. Thus, among the asymptomatic SARS-CoV-2 infected individuals with blood group AB has highest, whilst blood group O has lowest risk of infection.
Subject(s)
COVID-19 , Coronavirus InfectionsABSTRACT
Infection born by Coronavirus SARS-CoV-2 has swept the world within a time of a few months. It has created a devastating effect on humanity with social and economic depressions. Europe and America were the hardest hit continents. India has also lost several lives, making the country fourth most deadly worldwide. However, the infection and death rate per million and the case fatality ratio in India were substantially lower than many of the developed nations. Several factors have been proposed including the genetics. One of the important facts is that a large chunk of Indian population is asymptomatic to the SARS-CoV-2 infection. Thus, the real infection in India is much higher than the reported number of cases. Therefore, the majority of people are already immune in the country. To understand the dynamics of real infection as well as level of immunity against SARS-CoV-2, we have performed antibody testing (serosurveillance) in the urban region of fourteen Indian districts encompassing six states. In our survey, the seroprevalence frequency varied between 0.01-0.48, suggesting high variability of viral transmission among states. We also found out that the cases reported by the Government were several fold lower than the real infection. This discrepancy is majorly driven by a higher number of asymptomatic cases. Overall, we suggest that with the high level of immunity developed against SARS-CoV-2 in the majority of the districts, it is less likely to have a second wave in India.
Subject(s)
COVID-19 , Depressive DisorderABSTRACT
With the growing evidence on the variable human susceptibility against COVID-19, it is clear that there are some genetic loci modulating the severity. Recent studies have identified several loci associated with the higher severity. More recently, a study has identified 50kb segment introgressed from Neanderthal adding risk for COVID-19, and is present among 16% and 50% people of European and South Asian origin respectively. Contrary to that, our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations respectively, was probably responsible for the low case fatality ratio among South Asian populations. This result was also consistent with the realtime infection rate and case fatality ratio among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the realtime infection rates and case fatality ratio in India. We found out that that the polymorphism present in 50kb introgressed segment (rs10490770) did not show any significant correlation with the realtime infection and case fatality ratio in India.With the growing evidence on the variable human susceptibility against COVID-19, it is clear that there are some genetic loci modulating the severity. Recent studies have identified several loci associated with the higher severity. More recently, a study has identified 50kb segment introgressed from Neanderthal adding risk for COVID-19, and is present among 16% and 50% people of European and South Asian origin respectively. Contrary to that, our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations respectively, was probably responsible for the low case fatality ratio among South Asian populations. This result was also consistent with the realtime infection rate and case fatality ratio among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the realtime infection rates and case fatality ratio in India. We found out that that the polymorphism present in 50kb introgressed segment (rs10490770) did not show any significant correlation with the realtime infection and case fatality ratio in India.