Distribution Pattern Of Genotypes Research Articles

Serotypic and genotypic profile of dengue virus outbreaks in India between 2011 and 2017.

The epidemiology of dengue has been demonstrating significant changes in recent years, with rising incidence of infection in countries with known endemicity and occurrence of fresh outbreaks in previously unaffected territories. India, which has been a traditional hotspot dengue virus (DENV) transmission in the endemic south-east Asian region, has also been affected by the sweeping changes in dengue epidemiology. Two remarkable developments characterize the alterations witnessed by India 2011-2017. Firstly, all parts of the country have witnessed abrupt replacement of existing DENV lineages with emerging novel strains. Secondly, co-circulation of multiple serotypes of DENV have been reported from all across the country 2011-2017; thereby hinting at the transition of the country towards hyper-endemicity. Considering the potential clinical implications of such epidemiological transformation in terms increasing involvement of pediatric patients and growing predisposition to serious complications, the present review provides an update on the serotypic and genotypic profile of dengue outbreaks that have been witnessed by different zones of India between 2011 and 2017. Dividing the country into northern, southern, eastern, western, central and north-eastern zones, we describe discrete zone-specific distribution patterns of DENV serotypes and genotypes and observe simultaneous circulation of different DENV strains in different parts of the country. Random shifts in the genetic characteristics of the circulating strains and the widespread co- circulation of all four serotypes underscore the need for undertaking continuous and representative molecular surveillance of the circulating DENV strains across the country for prompt identification of emerging strains and novel mutants; gain insights into the formulation of Dengue vaccines and develop a clearer understanding of the molecular basis of immune evasion, disease epidemiology and pathogenesis.

Kernel density as a population-screening tool for low phytic acid content in maize (Zea mays L.)

Aim: The present study was performed to find association of morphological traits with kernel phytic acid. Methodology: A set of 20 qualitative phenotypic observations were studied in 29 diverse germplasms and two F2 populations. Further correlated traits were quantitatively verified for their correlation and heritability. Results: Maize kernels characterized by low phytate content correlated with reduced seed density traits. Further insights from scanning electron microscopic studies revealed alterations in the distribution pattern of starch granules, among low and high phytate genotypes. Heritability studies indicated a strong heritable nature of the traits viz., kernel density, inorganic phosphorous and phytic acid, and were found to be inter correlated. Interpretation: Intercorrelation and heritable nature of the trait is viewed as a ‘risk index’ that directly influences the success of genetic selection for the phytic acid trait which is highly complex and involves more laboratory experimentation. The selected genotypes may be further screened using biochemical analysis for confirmation. Key words: Correlation, F2 population, Germplasm, Kernel density, Maize, Phytic acid

Prevalence of the virulence genes and their correlation with carbapenem resistance amongst the Pseudomonas aeruginosa strains isolated from a tertiary hospital in China.

Pseudomonas aeruginosa is one of the top-listed pathogens in nosocomial infection. It is notorious for its complicated virulence system and rapid adaptability to drugs or antimicrobials. In this study, we aimed to evaluate the prevalence of sixteen virulence genes in four groups including type III secretion system, biofilm formation, extracellular toxin biosynthesis and enzymes amongst 209 clinical Pseudomonas aeruginosa strains. We investigated the different distribution patterns of virulence genotypes based on carbapenem-resistant phenotype or the carriage of carbapenemase genes. The detection rate of each virulence gene varied greatly. phzM and plcN were detected in all collected strains, while pilB and exoU were only carried by a small portion of isolates (6.7% and 16.3%). Additionally, the number of genotypes observed in each group of examined virulence genes ranged from 4 to 8. Only the distribution of genotypes of type III secretion system showed statistical difference between carbapenem-mediated or carbapenem-resistant and carbapenem-sensitive strains. The virulence genotype of Pseudomonas aeruginosa was possibly interrelated to its resistance mechanism. Further research suggested that one particular TTSS genotype exhibited higher ratio in carbapenemase-producing strains and exoS was less frequently detected in CRPA strains carrying carbapenemase gene. Generally, the significant genetic diversity of virulence genes amongst Pseudomonas aeruginosa strains was highlighted in this study. Specific TTSS genotypes were associated with carbapenem-resistance. In particular, certain incompatibility might exist between exoS and carbapenemase genes, which provided valuable information for further understanding the relationship between carbapenem resistance and virulence.

Trend of HPV Molecular Epidemiology in the Post-Vaccine Era: A 10-Year Study.

Cervical cancer, a major health concern among women worldwide, is closely linked to human papillomavirus (HPV) infection. This study explores the evolving landscape of HPV molecular epidemiology in Taiwan over a decade (2010-2020), where prophylactic HPV vaccination has been implemented since 2007. Analyzing data from 40,561 vaginal swab samples, with 42.0% testing positive for HPV, we reveal shifting trends in HPV genotype distribution and infection patterns. The 12 high-risk genotypes, in order of decreasing percentage, were HPV 52, 58, 16, 18, 51, 56, 39, 59, 33, 31, 45, and 35. The predominant genotypes were HPV 52, 58, and 16, accounting for over 70% of cases annually. The proportions of high-risk and non-high-risk HPV infections varied across age groups. High-risk infections predominated in sexually active individuals aged 30-50 and were mixed-type infections. The composition of high-risk HPV genotypes was generally stable over time; however, HPV31, 33, 39, and 51 significantly decreased over the decade. Of the strains, HPV31 and 33 are shielded by the nonavalent HPV vaccine. However, no reduction was noted for the other seven genotypes. This study offers valuable insights into the post-vaccine HPV epidemiology. Future investigations should delve into HPV vaccines' effects and their implications for cervical cancer prevention strategies. These findings underscore the need for continued surveillance and research to guide effective public health interventions targeting HPV-associated diseases.

Morphological and molecular diversity in mid-late and late maturity genotypes of cauliflower.

Genetic diversity is the prerequisite for the success of crop improvement programmes. Keeping in view, the current investigation was undertaken to assess the agro-morphological and molecular diversity involving 36 diverse mid-late and late cauliflower genotypes following α-RBD design during winter season 2021-22. Six morphological descriptors predicted as polymorphic using Shannon diversity index with maximum for leaf margin (0.94). The genotypes grouped into nine clusters based on D2 analysis with four as monogenotypic and gross plant weight (32.38%) revealed maximum contribution towards the genetic diversity. Molecular diversity analysis revealed 2-7 alleles among 36 polymorphic simple sequence repeats (SSR) with average of 4.22. Primer BoESSR492 (0.77) showed maximum polymorphic information content (PIC) with mean of 0.58. SSR analysis revealed two clusters each with two subclusters with a composite pattern of genotype distribution. STRUCTURE analysis showed homogenous mixture with least amount of gene pool introgression within the genotypes. Thus, based on morphological and molecular studies, the diverse genotypes namely, DPCaCMS-1, DPCaf-W4, DPCaf-US, DPCaf-W131W, DPCaf-S121, DPCaf-18, DPCaf-13, DPCaf-29 and DPCaf-CMS5 can be utilized in hybridization to isolate potential transgressive segregants to broaden the genetic base of cauliflower or involve them to exploit heterosis.

Molecular epidemiological study on rubella virus circulating in Yunnan Province during 2011-2021

Objective: To understand the genotype distribution and transmission pattern of rubella virus (RuV) circulating in Yunnan Province. Methods: Throat swab samples were collected from rubella outbreaks and sporadic cases in nine prefectures/cities of Yunnan Province from 2011 to 2021. Virus isolation, amplification of target genes and sequence determination were performed on the RuV-positive samples. The genotypes and lineages of Yunnan strains were determined by comparing them with the reference strains, and further phylogenetic analysis was performed with Yunnan strains and strains circulating in other provinces of China during the same period. Results: RuV circulating in Yunnan province during 2011-2021 showed significant genetic diversity, and three lineages, 1E-L1, 2B-L1 and 1E-L2, were detected. Two lineage-switches were also identified, including the conversion of 1E-L1 to 2B-L1 between 2012 and 2013, and the replacement of 2B-L1 to 1E-L2 after 2018. The time of the switches was basically consistent with the outbreak in Yunnan province in 2012 and the time of the rubella reemergence and epidemic between 2018 and 2019. The amino acid sequence of RuV virus strains in Yunnan province was highly conserved, and no important functional regions were changed. Conclusions: The transmission pattern of RuV in Yunnan province is generally consistent with the epidemic trend of RuV in other provinces of China.

TAS2R38 bitter taste perception in the Koṅkaṇī Sārasvata Brahmin population.

The TAS2R38 gene carries markers for phenylthiocarbamide (PTC) sensitivity. Various studies have investigated the genotype-phenotype association pattern for bitter tasting ability and other factors in different populations. However, a paucity of such information for endogamous Indian populations is the reason behind this study. To study the association of phenylthiocarbamide (PTC) sensitivity with TAS2R38 gene variations in Koṅkaṇī Sārasvata Brahmin population. We studied the association of the alleles rs714598, rs1726866, rs10246939 with PTC sensitivity and other factors in the Koṅkaṇī Sārasvata Brahmin population. DNA was extracted from 114 individuals belonging to the Koṅkaṇī Sārasvata Brahmin community. The TAS2R38 gene was sequenced to find the genotype distribution pattern. The association between genotype and phenotype was checked using the Chi-Square test and multifactorial logistical regression. We observed a 58.8% frequency of the AVI haplotype, which is the most prevalent in European populations. A higher number of non-taster haplotypes and diplotypes were observed in Koṅkaṇī Sārasvata Brahmins, with the allele rs10246939 showing a significant association with PTC bitter taste sensitivity in both allelic (p = 8.6 × 10-4; Allele-G, OR = 3.57 [95% CI = 1.66-7.69]) and genotype-based (p = 6.9 × 10-4; genotype-AG, OR = 3.11 [95% CI = 0.73-13.20]; genotype-GG, OR = 40 [95% CI = 3.58-447.03]) tests. Our results are in line with earlier studies, which report an association between PTC sensitivity and the TAS2R38 gene in different populations. In the global context, Koṅkaṇī Sārasvata Brahmins, who are mostly distributed along the southwestern coast of India, show a PTC sensitivity pattern slightly similar to that of West Eurasian populations. Our findings suggest ancestry specific selection in TAS2R38 gene variations for taste sensitivity at global level.

Genetic divergence studies for yield and its component traits in Mung bean (Vigna radiata L. Wilczek)

The present investigation was carried out at Genetics and Plant Breeding (GPB) farm, College of Agriculture, Central Agricultural University, Imphal, Manipur during kharif 2021 using 60 genotypes of Mung bean. Mahalanobis D2 statistics was used to evaluate the diversity. A total of fourteen clusters were formed with maximum number of genotypes in cluster I i.e., 29 genotypes followed by cluster II with 17 genotypes, cluster XII with 3 genotypes, all the remaining clusters were mono genotypic. It was found that the pattern of genotype distribution into different clusters was random and unrelated to geographic diversity. Results on genotype diversity between clusters IV and IX revealed the greatest inter-cluster distances, whereas cluster XII had the greatest intra-cluster distances. The largest cluster mean for seed yield per plant was found in cluster IX. Further, maximum contribution towards divergence was by number of seeds per plant (52.49%) followed by seed yield (17.8%) and days to 50% flowering (7.34%), while minimum by pod length which had shown 0% contribution.

Mapping hepatitis B virus genotypes on the African continent from 1997 to 2021: a systematic review with meta-analysis

Hepatitis B virus (HBV) has ten genotypes (A–J) and over 40 sub-genotypes based on the divergence of ≥ 8% and 4 to < 8% in the complete genome respectively. These genotypes and sub-genotypes influence the disease prognosis, response to therapy and route of viral transmission. Besides, infection with mixed genotypes and recombinant genotypes has also been reported. This study aimed at mapping the de novo genotypes and correlate them with the immigration trends in order to inform future research on the underlying reasons for the relative distribution of HBV genotypes from a large sample size pooled from many primary studies. Data was extracted from 59 full research articles obtained from Scopus, PubMed, EMBASE, Willy library, African Journal Online (AJOL) and Google Scholar. Studies that investigated the genotypes, sub-genotypes, mixed genotypes and recombinant were included. The Z-test and regression were used for the analysis. The study protocol is registered with PROSPERO under the registration number CRD42022300220. Overall, genotype E had the highest pooled prevalence significantly higher than all the other genotypes (P < 0.001). By region, genotype A posted the highest pooled prevalence in eastern and southern Africa, E in west Africa and D in north Africa (P < 0.0001). Regarding the emerging genotypes B and C on the African continent, genotype B was significantly higher in south Africa than C (P < 0.001). In contrast, genotype C was significantly higher in east Africa than west Africa (P < 0.0001). The A1 and D/E were the most diverse sub-genotypes and genotype mixtures respectively. Finally, we observed a general progressive decrease in the prevalence of predominant genotypes but a progressive increase in the less dominant by region. Historical and recent continental and intercontinental migrations can provide a plausible explanation for the HBV genotype distribution pattern on the African continent.

Association of traits promoting resistance to the adzuki bean beetle, Callosobruchus chinensis (L.) (Coleoptera: Bruchidae) in pea genotypes grown at various soil fertility levels

Adzuki bean beetle, Callosobruchus chinensis (L.) (Coleoptera: Bruchidae), is one of the most important pests of pea (Pisum sativum L.) crops in Ethiopia. The study focused on the association of resistance potential in the no-choice test of pea genotypes managed at different fertility levels and trait contributions. Based on the significance of fertility levels, genotypes were grouped into four, six, and five clusters, viz. Under neither rhizobium and phosphorus, rhizobium alone and rhizobium and phosphorus, respectively. Regardless of fertility levels, the inter-cluster distance (D2) values of the two potential clusters were highly significant (P < 0.01). At all fertility levels, the average performance of genotypes in each cluster for individual traits to infestation varied significantly. Genotype distribution patterns tended to group together into a small number of clusters. Eighty genotypes of the pea (Pisum sativum L. subsp. sativum and Pisum sativum L. subsp. abyssinicum A. Braun) were systematically managed under three fertility levels, and the first four principal components accounted for 94%, 92.3%, and 94.2% of the total variation. The primary trait that determines the resistance potential of pea genotypes is the trait susceptibility index (SI), which exhibits highly significant and adverse associations with critical traits such as the date of adult emergency and the percentage of seed coat, while exhibiting highly significant and favorable associations with the remaining traits at all fertility levels. The remaining characteristics showed highly significant positive or negative correlations within and particularly with the characteristics that determine resistance. Therefore, the cultivar "Adi" from "Pisum sativum L. subsp. sativum" had higher susceptibility compared to other genotypes, while the small-seeded pea genotypes "Pisum sativum L. subsp. abyssinicum A. Braun"; fpcoll-1/07, fpcoll-2/07, fpcoll-21/07, and fpcoll-43/07 were moderately resistant.

Genotype Distribution and Antibiotic Susceptibility Pattern of Clinical Isolates of Group B Streptococcus in a Tertiary Care Hospital in Puducherry, South India.

Streptococcus agalactiae apart from being a colonizer in the genital region is also associated with several other invasive infections in all age groups. With the varied distribution of serotypes across different regions of the world, universal vaccination is also unattainable. However, in India, the knowledge of group B Streptococcus (GBS) genotype distribution is deficient. Thus, this study was initiated to add data on this aspect. Methodology. A cross-sectional study was conducted using isolates of group B Streptococcus from all clinical specimens. Along with that, the clinical specimen type and the antibiotic resistance profile of the isolates were correlated with the genotypes recognized through a multiplex PCR assay. Among the 86 isolates subjected to multiplex PCR for genotype identification, five genotypes were identified with genotype Ib as the predominant one (34.9%), followed by III (20.9%), II (16.3%), Ia (12.7%), and V (11.6%). The results demonstrated a correlation of types Ib and III with vaginal colonization and type II with urine specimens in the current study. This preliminary study exhibited the distribution of common genotypes and their antibiotic resistance profiles in various GBS isolates. However, multiple studies across the country with larger sample sizes are needed to validate these findings.

Distribution of Genotypes of Hepatitis C Virus Studied in a Tertiary Care Hospital in Uttarakhand, India: A Retrospective Study

Introduction: With more than one million cases of Hepatitis C viral infection reported annually, it has become a major global problem. Hepatitis C Virus (HCV) is classified into 7 genotypes and 67 subtypes. Various genotypes show a wide geographical distribution worldwide. Genotypes 1 and 3 are the most common genotypes reported from India. There is minimal data available on the distribution and frequency of HCV genotypes in Uttarakhand. Aim: This three years retrospective study was undertaken to find out the distribution pattern of HCV genotypes among HCV- infected patients attending a tertiary care hospital in this Sub- Himalayan state of Uttarakhand. Materials and Methods: A total of 306 samples were tested for HCV genotyping in 3 years duration i.e., January 2018 to December 2020 at the Molecular Laboratory of Shri Guru Ram Rai Institute of Medical and Health sciences and associated Shri Mahant Indiresh Hospital, Dehradun. Genotyping was performed using HCV genotype specific Real-Time Polymerase Chain Reaction (RT-PCR) assay on Rotor-Gene Q using TRUPCR HCV Genotyping Kit (3B BlackBio Biotech India Ltd.,) as per manufacturer’s instructions. This test kit detects HCV genotypes 1, 1a, 2 (2a/ 2b), 3, 4, 5a, and 6. Results: Genotype 3 (72.7%) was the commonest genotype detected, followed by genotype 1 (13%), genotype 1a (6.25%) and genotype 4 (2.8%). Genotype 3 was the most dominant genotype in all the 3 years of the study. Two cases of genotype 5a (1.13%) and three cases of genotype 6 (1.7%) were also detected in our study. We also detected a case of mixed infection by genotype 1 and genotype 6. Conclusion: The most common genotype detected was three during the study period. Detection of genotype 5a and 6 ascertained the impact of interstate migration of people.

Fine-scale genetic diversity and genet dynamics of the fairy ring fungus Floccularia luteovirens on the Qinghai–Tibet plateau

The fungus Floccularia luteovirens is mainly distributed in the alpine meadows of the Qinghai–Tibet plateau. Its fruit bodies tend to form fairy rings with a visible stimulating zone. Our previous studies have investigated the large-scale genetic structure among wild populations of F. luteovirens, but the mechanisms underlying the current genotype distribution pattern remain unknown. The balance between sexual and asexual reproduction affects the establishment and structure of populations. Measuring genet size and density is an effective approach to investigating the reproduction strategies of this species. In the current study, 234 fruit bodies and 79 soil samples were collected from three sampling sites over 3y, revealing that F. luteovirens exhibits relatively large genets. Very few new genets were detected over the 3y, illustrating that this species relies more on vegetative growth and can persist for long periods underground as mycelia. Moreover, the underground genet data showed a close relationship with the above-ground genet data. Our study found limited fine-scale gene flow, contrary to our previous large-scale genetic study of F. luteovirens, the present study found limited fine-scale gene flow of this species. The commercial trade of F. luteovirens fruit bodies by humans probably enhances the gene flow over QTP.

The Study of Genetic Divergence in Rice (Oryza Sativa L.) Genotypes with Grain Yield and Different Morpho-Physiological Traits using Mahalanobis’ D2 Analysis

The current study attempted to study genetic divergence in rice (Oryza sativa L.) genotypes with grain yield and different morpho-physiological traits among 18 rice varieties using Mahalanobis' D2 analysis. Keeping this in mind, the performance of the studied genotypes, as well as the association between various morpho-physiological and yield contributing traits among the genotypes, were evaluated in the field. The experiments were conducted from July to December 2018 at the Agronomy Field, Department of Agronomy and Agricultural Extension, Faculty of Agriculture, Rajshahi University. In terms of grain yield and other morpho-physiological traits, the genotypes differed significantly. The genotypes were classified into five clusters using Mahalonobis' D2 statistics and Tocher's method (Table 3). Cluster IV was the smallest of the clusters. Cluster l is the largest, with six genotypes. Clusters II and lV each contained three and two genotypes. The pattern of genotype distribution among various clusters reflected the significant genetic variability present in the genotypes, which may be due to adaptation of these genotypes to specific environmental conditions. Genotypes from different clusters are expected (inter-cluster). The intra (bold) and inter-cluster distances from D2 analysis (Table 4). Cluster I has the greatest intra cluster distance (0.956), while Cluster IV has the smallest (0.3583). The greatest inter-cluster distance is observed between cluster IV and (8.190), while the smallest inter-cluster distance is observed between cluster II and IV (2.924). In both vectors, the average inter-cluster distances were greater than the average intra-cluster distances, indicating the presence of greater genetic diversity among genotypes from different clusters than those from the same cluster. These findings indicated that these five traits contributed the most to the divergence among the eighteen rice genotypes. The results revealed that the clusters were remarkably distinct for the majority of the traits, indicating proper clustering. The most effective tiller, grain panicle, effective grain panicle, and days to maturity were found in Cluster V. The intra-cluster mean for grain yield was the lowest in this cluster. Cluster III had the lowest grain yield per acre. This was the cluster with the lowest initial grain yield. The intra-cluster mean for effective tiller and days to maturity was highest in this cluster. Cluster II had the smallest grain yield and the second smallest thousand grain weight. Cluster V had the shortest panicle length intra-cluster.

Burden and Associated Genotype Patterns of High-Risk Human Papilloma Virus Infection and Cervical Cytology Abnormalities among Women in Central India.

Background The epidemiology of human papilloma virus (HPV) infection and the pattern of HPV genotype distribution are much-needed parameters to assess the risk of cervical cancer among females. However, due to less availability of data on HPV burden and its genotypes from various geographical regions in India makes cervical cancer screening modalities and vaccination strategies difficult to implement. Objective The present study was conducted to identify the various genotypes particularly high-risk HPV types in premalignant or malignant cervical lesions. Methods The study was a hospital-based cross-sectional study wherein 295 symptomatic women were screened by Pap smear and multiplex real-time PCR was performed for HPV genotypes identification in women with abnormal cervical cytology. Results Out of 295 women, 237 (80.3%), 45 (15.3%), and 13 (4.4%) women had normal Pap smear, squamous cell carcinoma and precancerous cytology, respectively. Among these 58 women having abnormal cervical cytology, HPV was detected in 48 (81.0%) participants. Most common HPV genotypes in our study were HPV 16 (n = 29; 60.4%) followed by mixed infections; i.e., more than one type of HPV was detected (n = 10, 20.8%). HPV 18 was detected only in 6.25%, whereas other high-risk HPV genotypes were found to be 12.5%. Conclusion HPV positivity was >80% in women having abnormal Pap smear. The prevalence of HPV 18 was found to be much less in Central India, compared to other parts of country. HPV 16 was the most common genotype followed by mixed HPV genotype infections. It is evident from our study that symptomatic women even if having normal Pap smear should be screened for HPV and followed up with periodic Pap smears for detecting any change in cervical cytology, thus preventing cervical cancer in women.

Distribution of HCV genotypes and HCV RNA viral load in hepatitis infected patients of Kolar region, Karnataka, India.

Decisions and disease progression prediction, understanding the distribution of the hepatitis C virus (HCV) genotype and its association with viral load is significant for treatment. Therefore, it is of interest to document the distribution pattern of HCV genotypes and their association with viral load among HCV infected patients in Kolar, Karnataka. Seventy-four HCV-positive patients and not on antiviral therapy were enrolled from R.L. Jalappa hospital in Kolar, Karnataka. Blood samples were taken and demographics were recorded. HCV RNA was isolated after plasma was separated. qPCR was performed to measure the viral load, and RT-PCR was performed to determine the genotype. Genotype 3 was the prevalent (n=11, 40.7%) followed by genotype 4 (n=8, 29.6%), 2 (n=6, 22.2%), 1 (n= 13.7%), and mix (n=1, 13.7%). The median viral load of genotype 3 was a 2,87,835 IU/mL (IQR 10, 780-3, 71, 66) , genotype 2 was 81,030 IU/mL (IQR 66,495-95,565), genotype 4 was 43, 410 IU/mL (IQR 38, 355-48, 465) belongs to viral load less than 8,00,000 IU/mL. The median viral load genotype 3 was a 1, 05, 19, 500 IU/mL (IQR 49, 37, 250-2, 36, 71, 500), genotype 2 was 2,55,99,000 IU/mL (IQR 2,00,10,000-32,725,500), genotype 4 was 1,67,40,000 IU/mL (IQR 1,45,50,000-17,493,000) belonging to viral load more than 8,00,000 IU/mL category. A correlation between genotype and viral load was observed (p =1.5x10-12), of which genotype 3 showed a high viral load. Thus, HCV genotypes 1 2, 3, 4, and mixed genotype was observed in the patients studied. HCV genotype was associated with viral load in patient plasma. This data finds use in the treatment and prevention of hepatitis C in Kolar, Karnataka.

Genomic divergence of Hepatitis C virus towards common prescribed interferon regimens on sustained virologic response (SVR) ‎

Hepatitis C is one of the dangerous diseases which if left untreated can cause the loss of life. The study&#39;s main to detect HCV RNA in Hepatitis C patients using a real-time polymerase chain reaction to determine the genotype distribution pattern, and role of its genomic divergence toward commonly prescribed interferon regimens. A cross-sectional study with 980 patients was conducted in a tertiary care hospital were chosen and their blood samples were collected which was screened. Real-time

Association of SOD1 Gene Promotor 50 bp Indel Polymorphism with Susceptibility of Type 2 Diabetes Mellitus

Introduction: Oxidative stress plays an essential role in the pathogenesis of type 2 diabetes mellitus (T2DM). An antioxidant enzyme superoxide dismutase 1 (SOD1) dissociates free superoxide radicals and provides protection against oxidative damage. The aim of this study was to investigate the role of promotor region 50 bp Indel SOD1 polymorphism with the pathogenesis of type 2 diabetic mellitus among Pakistani population. Materials and Methods: This was a case-control study comprised of n=359 subjects, divided into n=178 type 2 diabetic patients and n=181 controls. Screening of SOD1 promotor 50 bp Indel polymorphism was carried out by conventional polymerase chain reaction (PCR). Statistical interpretations were done by software SPSS® version 20.0 and SNPStats©. Results: Genotype distribution pattern of SOD1 polymorphism indicated that homozygous mutant D/D genotype frequency was two folds reduced in T2DM (0.01) in comparison to controls population (0.02). Heterozygous I/D genotype frequency was higher in T2DM subjects (0.22) as compared to controls (0.17). An insignificant association of SOD1 polymorphism was detected with predisposition of T2DM (OR=1.14, Fisher’s exact=2.0, p=0.325). Genetic analysis further revealed that dominant model showed significant association against the pathogenicity of disease (OR=0.45, p&lt;0.05). Conclusion: SOD1 50 bp Indel polymorphism inferred no significant association with susceptibility of type 2 diabetes mellitus in Pakistan. However, a significant contribution of dominant SOD1 genotype was evident in a defensive response against the risk for type 2 diabetes mellitus

Agro-morphological and molecular diversity in different maturity groups of Indian cauliflower (Brassica oleraceavar. botrytis L.).

The present study analysed the molecular and agro-morphological diversity in a set of 92 diverse cauliflower genotypes and two each of cabbage and broccoli. Field evaluation of the genotypes was done in randomized block design (RBD) at two locations (i.e. IARI, New Delhi and ICAR-RC-NEH Region, Barapani) during Rabi2019-20. Genotypes showed variation for all the eight observed traits at both locations and, the differences in early and snowball groups were distinct. Pusa Meghna, DC-33-8, Pusa Kartiki and CC-14 were earliest for curd initiation. Genotypes showed higher values for curd traits at Delhi. Molecular diversity was detected with 90 polymorphic simple sequence repeats (SSR). Number of alleles ranged from 1 to 9 with mean value of 2.16 and the highest polymorphic information content (PIC) value was observed for primer BoGMS0742 (0.68) with a mean value of 0.18. Cluster analysis using agro-morphological traits substantiated classification of the genotypes for maturity groups. However, SSR analysis revealed four clusters and with a composite pattern of genotype distribution. STRUCTURE analysis also supported the admixture and four subpopulations. The studyindicates for introgression of genetic fragments across the maturity groups, thereby, potential for use in further genetic improvement and heterosis breeding.

Allele and genotype frequencies of CYP3A4, CYP3A5, CYP3A7, and GSTP1 gene polymorphisms among mainland Tibetan, Mongolian, Uyghur, and Han Chinese populations.

Over 50% prescribed drugs are metabolised by cytochrome P450 3A (CYP3A) and glutathione S-transferase pi (GSTP1) adds a glutathione to the oxidative products by CYP3A, which increases the hydrophilic property of metabolites and facilitates the excretion. Single nucleotide polymorphisms (SNPs) of CYP3A and GSTP1show a diverse allele and genotype frequencies distribution among the world populations. The present study aimed to investigate the genotype and allele frequency distribution patterns of CYP3A4, CYP3A5, CYP3A7 and GSTP1 polymorphisms among healthy participants in mainland Tibetan, Mongolian, Uyghur, and Han Chinese populations. Blood samples were collected from 842 unrelated healthy subjects (323Tibetan, 134Mongolian, 162 Uyghur, and 223 Han) for genotyping analysis. Variant allele frequencies of CYP3A4 rs2242480, CYP3A5 rs776746, CYP3A7 rs2257401, and GSTP1 Ile105Val were observed in Han (0.253, 0.686, 0.312 and 0.188), Tibetan (0.186, 0.819, 0.192 and 0.173), Mongolian (0.198, 0.784, 0.228 and 0.235) and Uyghur (0.179, 0.858, 0.182 and 0.250) respectively. The allele frequency of CYP3A7*1C in Uyghur (0.019) was higher than that in Tibetan (0.002, p<0.01). There was a strong linkage disequilibrium between CYP3A4 rs2242480, CYP3A5 rs776746, and CYP3A7 rs2257401 among the four ethnic groups. The results might be useful for the precise medication in the Chinese populations.