Gene Reports

In the current study we analyzed the genomes of SARS-CoV-2 strains isolated from Italy, Sweden, Congo (countries in the same meridian) and Brazil, as outgroup country. Evolutionary analysis revealed codon 9628 under episodic selective pressure for all four countries, suggesting it as a key site for the virus evolution. Belonging to the P0DTD3 (Y14_SARS2) uncharacterized protein 14, further investigation has been conducted showing the codon mutation as responsible for the helical modification in the secondary structure. According to the predictions done, the codon is placed into the more ordered region of the gene (41-59) and close the area acting as transmembrane (54-67), suggesting its involvement into the attachment phase of the virus. The predicted structures of P0DTD3 mutated and not confirmed the importance of the codon to define the protein structure and the ontological analysis of the protein emphasized that the mutation enhances the binding probability.

Polycystic ovary syndrome (PCOS) is the most common form of endocrinopathy of women. Several studies have investigated the association of methylenetetrahydrofolate reductase (MTHFR) gene C677T polymorphism with PCOS risk but the results are contradictory. So, the aim of the present study was to carry out a meta-analysis of a published case control studies to find out exact association between MTHFR gene C677T polymorphism and PCOS susceptibility. Pubmed, Springer link, Science Direct and Google Scholar databases were searched for case-control studies. Odds ratios (ORs) with 95% confidence intervals (CIs) was used as association measure and meta-analysis was performed using MIX and MetaAnalyst programs. Meta-analysis of 24 studies showed strong significant association between C677T polymorphism and PCOS risk (for T vs. C: OR= 1.18, 95% CI=1.01-1.38, p=0.03; for TT vs. CC: OR= 1.37, 95% CI=1.0-1.89, p= 0.045; for TT + CT vs. CC: OR= 1.31, 95% CI= 1.07-1.62, p= 0.008; for CT vs. CC: OR= 1.31, 95% CI= 1.04-1.62, p= 0.01 and for TT vs. CT + CC: OR= 1.10, 95% CI= 0.82-1.47, p= 0.04). In subgroup analysis, MTHFR C677T polymorphism is significantly associated with PCOS risk with Asian individuallas but in Caucasian population MTHFR C677T polymorphism was not significantly associated with PCOS risk. In conclusion, C677T polymorphism is a risk factor for PCOS.

Estrogen (E2) is one of the most important signaling molecules that control cell-differentiation/early-embryogenesis/organogenesis in gender-independent manner. Nevertheless, during adolescence/adulthood it influences female reproductive-functions by delicate cellular proliferative-events via nongenomic (cellular-signaling)/genomic (transcriptional-signaling) pathways to recruit a number of genes/proteins. In case of post-menopausal-women high E2 may initiates tumors in breast/gynaecological-tissues. Impired estrogenic signaling may be the results from abnormal redox-regulations of estrogen-metabolizing-enzyme estrogen-sulfotransferase(SULT1E1), transcriptional-factors NF{kappa}{beta}, Nrf-2 and Matrixmetalloproteases (specially MMP 2/9) in the breast-tumor. Here, tumor and its surrounding tissues were obtained from the district-hospital. Intracellular redox-environment of tumors was screened with some in vitro-studies. RT-PCR for SULT1E1 expression and MMP 2/9-zymogram were conducted in lasoprazole (Nrf-2 inducer) or dexamethasone (SULT1E1 inducer) treted rat liver tissues. Immunohistochemistry was performed to analyze SULT1E1/NF{kappa}{beta} localization and MMP 2/9-zymogram in human breast-cancer versus its surrounding tissues. It can be hypothesized that transcription-factors (NF{kappa}{beta}/Nrf-2) imposes effect on MMPs expressions resulting in significant impacts on metastatic transition of breast-cancer. Breast tumor reveals higher (vs surrounding-tissue) expression/immunolocalization of NF{kappa}B/SULT1E1 paralleling to our previous finding of Nrf-2 induction. The relation between Nrf2/NF{kappa}B is determined by oxidative-stress and by CBP recruitment of HDAC3. Further, this relation is a determinant of MMP-regulations and SULT1E1-mediated E2 levels. Adaptively, augmented Nrf-2 may induce SULT1E1 resulting in lower active-estrogen. The triad regulations of NF{kappa}{beta}, SULT1E1 and Nrf2 are proposed here to execute MMPs function in the severity of human breast-carcinogenesis. Therapeutically this triad system may be effectively targeted for breast cancer treatment. Further studies are necessary in this regard.

In this study, we evaluated the presence of early and late Human Papillomavirus (HPV) proteins in retinoblastoma Brazilian patients. For this, 8 formalin-fixed paraffin-embedded retinoblastoma tissue blocks were used. HPV DNA presence was determined by in situ hybridization (ISH). Immunohistochemistry were performed to verify HPV16/18 E6, E1^E4, and L1 proteins. HPV was detected in all retinoblastoma tumors and viral DNA was labeled in tumor cells, retinal layers and optical nerve structures. In addition, E1^E4, E6 and L1 proteins were detected in all samples in the same areas where HPV DNA was detected. Our data showed the presence and expression of early and late HPV proteins in retinoblastoma tumors from Brazilian children. However, further studies should be performed to clarify the role of HPV infection in retinoblastoma tumor.

IntroductionBreast cancer is one of the major and frequent tumors in the public health sector globally. The rising global prevalence of breast cancer has aroused attention in a viral etiology. Other than genetic and hormonal roles, viruses like Epstein - Barr virus (EBV) also participate in the development and advancement of breast cancer. AimThis study was conducted to detect the frequency of EBV genotypes in breast cancer patients and compare it with histopathological breast cancer changes. MethodsFormalin-fixed paraffin-embedded samples of breast cancer (N=60) ages ranged from 22-70 years were collected. EBV DNA was isolated, amplified, typed through PCR, and correlated with histopathological outcomes of breast cancer using SPSS software version 26. ResultsOur findings suggest that among breast cancer factors, Invasive ductal carcinoma (IDC) was the most common pathological pattern found among patients (90%), observed statistically significant (p= 0.01275). In regards to clinical staging, 8 (13.3 %) patients diagnosed with stage I, 39 (65 %) with stage II, and 13 (21.6 %) with stage III reported statistically significant association (p=0.0003). EBV DNA was detected in 68.3% (41/60) breast cancer patients, reported a statistically significant difference between the prevalence of EBV in breast cancer patients and normal samples (p = 0.001). Of 41 EBV-positive samples, 40 were EBV-1, while only 1 had EBV-2 infection (p < 0.001). No influence on cancer histology was observed. Regarding the association of breast cancer with EBV, histological type (P =0.209), tumor stage (P = 0.48), tumor grade (0.356), tumor sizes (p= 0.976), age (p= 0.1055), tumor laterality (p= 0.533) and ER/PR status (p=0.773) showed no significant association. ConclusionEBV-1 is prevalent in breast cancer patients and associated with IDC in the study area. For conclusive evidence, more studies are required based on a large sample size and by using more sensitive techniques.

Worldwide there are more than 273,000 deaths from cervical cancer each year and it accounts for 9% of female cancer deaths. The high-risk variants of human papillomavirus such as HPV 16 and 18 are major etiological agents of cervical cancer. The persistency of infection with HPV may due to inappropriate immune response due to SNPs interfering with the function of particular part of the immune system. Toll-like receptors (TLRs) play an important role in the signaling of many pathogen-related molecules and endogenous proteins associated with immune activation. The -196 to -174del polymorphism affects the TLR2 gene and alters its promoter activity. AimIn this study we investigated the presence and the influence of TLR2 -196 to - 174del polymorphism on the risk of cervical cancer development in Sudanese. The study was performed on 42 patients with cervical cancer and 27 healthy controls. Genotyping of -196 to -174del polymorphism of TLR2 was investigated using allele-specific polymerase chain reaction method in all subjects. We documented the presence of-196 to -174del polymorphism of TLR2 in Sudanese women with allele frequency 37% of control and 34% of patient sample although there was no observed association between this SNP and the risk of cervical cancer (p value. 394).Further studies are needed in a large and ethnically diverse population to determine the impact of the TLR2 polymorphism in the susceptibility of cervical cancer.

Recently the first genome sequence for a Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 isolate from Bangladesh became available. The sequencing was carried out by the Child Health Research Foundation and provided the first insight into the genetic details of the viral strain responsible for the SARS-CoV-2 infections in Bangladesh. Here we carried out a comparative study were we explored the phylogenetic relationship between the Bangladeshi isolate with other isolates from different parts of the world. Afterwards we identified single nucleotide variants in the Bangladeshi isolate, using the Wuhan virus reference sequence. We found a total of 9 variants in the Bangladeshi isolate using 2 separate tools. Barring 2, the rest of these variants were also observed in other isolates from different countries. Most of the variants occurred in the ORF1ab gen. Another noteworthy finding was a sequence of three consecutive variants in the N protein gene that were observed in other isolates as well. Lastly the phylogenetic analysis revealed a close relationship between the Bangladeshi isolate and those from Taiwan, Kazakhstan, Greece, California, Spain, Israel, and Sri Lanka.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a highly infectious and pathogenic virus has claimed lot of lives globally since its outbreak in December 2019 posing dire threat on public health, global economy, social and human interaction. At moderate rate, mutations in the SARS-CoV-2 genome are evolving which might have contributed to viral genome variability, transmission, replication efficiency and virulence in different regions of the world. The present study elucidated the mutational landscape in SARS-CoV-2 genome among the African population, which may have contributed to the virulence, pathogenicity and transmission observed in the region. Multiple sequence alignment of the SARS-CoV-2 genome (356 viral protein sequences) was performed using ClustalX version 2.1 and phylogenetic tree was built using Molecular Evolutionary Genetics Analysis (MEGA) X software. ORF1ab polyprotein, spike glycoprotein, ORF3, ORF8 and nucleocapsid phosphoprotein were observed as mutational hotspots in the African population and may be of keen interest in the adaptability of SARS-CoV-2 to the human host. While, there is conservation in the envelope protein, membrane glycoprotein, ORF6, ORF7a, ORF7b and ORF10. The accumulation of moderate mutations (though slowly) in the SARS-CoV-2 genome as revealed in our study, could be a promising strategy to develop drugs or vaccines with respect to the viral conserved domains and host cellular proteins and/or receptors involved in viral invasion and replication to avoid a new viral wave due to drug resistance and vaccine evasion.

The present study developed a review and exploration of data in public and already validated repositories. The main objective is to identify the pathways involved in ruminants cervical dilatation, which are conserved between cattle and sheep in the follicular and luteal phases of the reproductive cycle. In cattle, 1961 genes were found to be more expressed in the follicular phase and 1560 in the luteal phase. 24 genes were considered exclusively expressed from these 18 genes were in the follicular phase and 6 genes were in the luteal phase. In sheep, 2126 genes are more expressed in the follicular phase and 2469 genes are more expressed in the luteal phase. Hoxb genes were identified in both species and are correlated with the PI3K/Akt pathway. PI3K/Akt was also found in both cattle and sheep, appearing prominently in the follicular and luteal phases of both species. Our analyzes have pointed out that the PI3K/Akt pathway and the Hoxb genes appear in prominence, in modulating mechanisms that involve estrus alterations in the cervix. PI3K/Akt appears to be an important pathway in the cervical relaxation process.

Toll like receptors are expressed by variety of cells, mainly immune cells and also found to have role in the tumor microenvironment. Among them, Toll like receptors-4 is found to modulate tumor progression. But definitive action of TLR4 in tumor progression is not well understood. In the present study, in breast tumor samples, expression of TLR4 was studied by immunohistochemistry method while MMP2 and MMP9 expression were studied by gelatin zymography. Kaplan Meier plotter was used to test survivability. Breast cancer cells - MCF7, MDA MB 231, T47D were studied in the presence of TLR4 lignd LPS, with the help of MTT assay, BrdU incorporation assay, scratch wound healing assay and invasion assay. Activation of TLR4 in MCF7 which is TP53 wild type has no significant effect in proliferative rate, adhesiveness and invasiveness. While in MDA-MB-231 and T47D which are TP53 mutant, there were a significant increase in adhesiveness and migratory ability, observed., TLR4 had been expressed in breast tumor of invasive ductal carcinoma (IDC) and was found to be significantly correlated with lymph node involvement. Kaplan Meier plotter analysis revealed that high TLR4 expression might serve as an immune-protectant in invading cancer cells of TP53 wild state. It has been revealed that activation of TLR4 in breast cancer cells leads to higher expression of EMT related genes along with matrix metalloproteinases helping in migration and invasion of cells. Kaplan Meier plotter analysis revealed that TP53 wild status of the patient along with high TLR4 expression has a good overall survival of the patients.

BackgroundAmong common cancers in women, ovarian cancer has the lowest incidence; however, mortality rates are more than other gynecological cancers due to the lack of specific symptoms during early stages and absence of diagnostic markers. Golgi integral membrane protein 4 (GOLIM4) is a member of transporter complex which is located to the cis/medial of Golgi, and its role in tumor is unknown. In this study we aimed to assess the expression of Golim4 (GPP130) in epithelial ovarian cancer (EOC) patients. MethodsThe expression levels of Golim4 in 58 malignant EOC specimens and 11 benign and normal control tissues were determined by real-time RT-PCR. Clinicopathological characteristics were analyzed. Non-parametric survival analysis was estimated by using Kaplan-Meier and log-rank test. Parametric survival analysis was evaluated through multivariate Cox regression analysis and generalized Gamma survival model. ResultOur findings showed that Golim4 was significantly down-regulated in Serous Papillary type of EOC tissue specimens than in non-cancerous tissues (P<0.001); however; the expression of Golim4 in total EOC tissue specimens revealed non-significant up-regulation. Kaplan-Meier analysis and log-rank test have suggested that EOC patients with low Golim4 expression have shorter overall survival when compared with patients with other expression groups (log-rank test P<0.05). Semi-parametric Cox proportional hazards model indicated that the status of Golim4 were independent predictor of overall survival in patients with EOC. Correlation analysis has been done by Spearman Rank correlation coefficient.

The last decade has witnessed great progresses regarding the molecular basis of breast cancer with discovery of different nuclear susceptibility genes; in addition investigations and researches regarding mitochondrial DNA (mtDNA) mutations in breast cancer have been started. Mitochondrial haplogroup determinants (single nucleotide polymorphism SNP) and somatic mitochondrial mutations have recently been studied as possible risk factors for carcinogenic processes in different tissues, hence in order to identify breast cancer related SNPs and haplogroups among the population of Sulaimaniyah city/Iraq, the entire mitochondrial genome of 20-breast cancer samples and comparable controls were sequenced. Haplogrep 2.0 was used for haplogroup identification; Chi-square and Fishers exact test were applied to assess relational significance. HV haplogroup in the cancer samples appeared to be a risk factor for breast cancer compared to the most common H haplogroup in control samples with a p-values of 0.002 and 0.006 respectively and an Odd Ratio (OR) = 28.00. Besides, SNP (A8860G) was also identified as a risk factor for breast cancer as compared to other randomly selected SNPs (A750G, A1438G and C7028T) with p values {square}0.05 and OR >1.

PurposeDiabetic retinopathy (DR) is a neurovascular complication of diabetes (DM) causing the loss of neurons (ganglion cells) in the retina. The disease etiology and potential pathogenic mechanisms in this disease remains unclear. In the present study, we aimed to further understand the key and novel pathogenic mechanisms involved in DR pathogenesis by taking cues from our global proteomics data. MethodologyThe study was approved by the institutional review board (IRB) of LVPEI, Hyderabad, India. Vitreous humour samples (PDR; n=3, DM; n=3, Control; n=3) were collected from patients undergoing vitrectomy and subjected to LC-MS-MS analysis. The acquired raw data were searched against the human vitreous proteome and was further analysed by various bioinformatic and proteomic tools. Western blotting and IHC was performed to validate crucial pathways. Blood samples from patients (DM, PDR & NPDR) and controls (n=50); cadaveric retinas from diabetic and non-diabetic donors (n=10) and epiretinal membranes (ERM, n=10) from DR cases and controls were collected and RNA was isolated. Quantitative expression of genes involved in autophagy were performed. CT was compared across different categories and significance estimated using a student t-test. ResultA total of 1079 proteins were identified with 16 completely novel proteins in eye proteome. Top pathways identified were autophagy, inflammation, LXR/RXR activation (lipid metabolism), ROS generation by macrophages, apoptosis and protein degradation. Regulatory proteins identified were associated with cell death, phagocytic activation, angiogenesis and apoptosis. Autophagy inducers such as ROS was found to be accumulated in the DR vitreous. TREM2, microglial receptor was identified as a novel protein in PDR vitreous. The expression of TREM2, an autophagy-associated gene was significantly (p-value = 0.05) upregulated in all categories as compared to control (NDM and/or NDM/No-DR). TREM2 protein also seemed to colocalise with microglial marker F4/80 in retinal tissues and intense expression was observed near the blood vessels in case of PDR retina. Other autophagy-associated markers were also differentially regulated in DR as compared to controls. ConclusionThis study emphasises on the strong role of autophagy pathways and its associated genes in the development of DR.

BackgroundImmunohistochemical expression of p53 protein in tumor nephrectomy specimens of patients with nephroblastoma has been associated with an adverse clinical outcome. SV40 is a known tumorigenic virus associated with inflammatory kidney diseases. This study aimed to evaluate the role in clinical outcome of p53 and SV40 immunopositivity in formalin-fixed paraffin-embedded (FFPE) tissue blocks of children with nephroblastoma. Materials and methodsThis was a retrospective study of 24 nephroblastoma patients managed in a tertiary hospital. FFPE tumor tissue blocks from the patients were subjected to immunohistochemical staining for p53 and SV40, and their relationship to clinical outcome was analyzed using the methods of Kaplan - Meier. Statistical significance was set at p [&le;]0.05. ResultsThe p53 immunopositivity rate in the study was 20.80% (5/24). None of the patient had a positive SV40 stain. There was a significant association between p53 immunoreactive and gender (p=0.021). The study showed a statistically significant poorer overall survival (OS) for those who showed p53 immunopositivity (p=0.05). ConclusionThe study provides preliminary evidence that p53 immunopositivity is associated with a poor survival. This may thus be used in the detection of patients with a poor prognostic tumor.

Mitochondria possess 37 genes of its own, helpful for carrying out various functions including oxidative phosphorylation. But the mitochondria is neither independent in terms of its structure, nor its function, it depend upon nuclear gene for its functionality and replication. Our lab has earlier reported the role of mitochondrial genome in controlling health and reproduction in animal model. Reports also indicate that mitochondria have role in immune response against bacterial infection. In our current study, we depict the role of two polypeptide coding mitochondrial gene as cytochrome B and cytochrome C in providing host immunity against bacterial disease (Duck Pasteurellosis). We further observe that the mechanism was governed by cascade of mechanisms mediated through nuclear genes NRLP3, IL18 and Sting. In the first phase of the study, we have characterized Cytochrome B and Cytochrome C genes from Bengal duck and quantified through the assesment of the expression profiling with respect to healthy and Pasteurella infected ducks following a natural challenge with Pasteurella multocida. In the next phase of our study, we have characterized the above nuclear genes in Bengal duck and attempted to correlate the expression with mitochondrial genes. We attempted to explore the mechanism of pathway how mitochondrial DNA triggers the nuclear immune response leading to destruction of bacterial pathogen. Molecular docking revealed how IL18 directly binds with the pathogen. This is the first report in animal model.

Retinoblastoma is a pediatric neoplasia with a high incidence in non-developed countries. Nowadays the diagnosis is clinical and unfortunately in advanced stages of the diseases, which puts the childs life risk. The search for molecular diagnosis on retinoblastoma is necessary. Due to their location and tendency to migrate, biopsies of retinoblastoma are not recommended then, peripheral blood samples can be a good source for the search of biomarker. RT qPCR is a sensitive method for gene expression quantification; in order to achieve optimal results, a crucial step is the reference gene choice that cannot be neglected under any circumstance. Six of the most commonly used housekeeping genes; GAPDH, HPRT1, B2M, TBP, RPL13a and 18S, were tested in the blood samples of patients diagnosed with retinoblastoma and healthy controls. The HPRT and TBP were found the most reliable genes whereas GAPDH, that is one of the most commonly used genes for normalisation, together with B2M, RPL13a and 18S have to be avoided. Using the selected reference genes, the Rb mRNA showed significant differences between patients and healthy children whereas no differences were found using to control groups. In the present study, we validate blood samples of patients with retinoblastoma.

We have previously reported that ovarian cancer G protein-coupled receptor 1 (OGR1) is a new metastasis suppressor gene. We have also reported for the first time that a new intronless gene for casein kinase 2 (CSNK2A3) is expressed in human cells. The promoter of the well-known casein kinase 2 (CSNK2A1) displays characteristics of housekeeping gene whereas CSNK2A3 has a characteristic of a regulated promoter with two TATA boxes and a CAAT box. In this study, we found that OGR1 up-regulates expression of CSNK2A3 by about 3 folds in A549 cells but not CSNK2A1. OGR1 also up-regulates expression of neutral endopeptidase (NEP). The OGR1 induced inhibition of A549 cell migration is completely abrogated by inhibition of casein kinase 2 activity, whereas partial abrogation (~ 30%) was observed in the presence of NEP inhibition. The results also revealed that OGR1 regulates CSNK2A3 via activation of Rac1/cdc42 and MAPKs pathways. CK2 is ubiquitously expressed and in contrast it is believed to be a constitutively active enzyme and its regulation appears to be independent of known second messengers. There is no previous report on how expression of CK2 in cancer cells is regulated although many studies have report of aberrant expression of the kinase in cancer. In the current study, we are reporting for the first time the regulation of intronless casein kinase 2 gene, CSNK2A3 in cancer cells. Our findings suggest that the aberrantly casein kinase 2 expression found in various cancer cells may the due to CSNK2A3 expression which is potentially regulated by several master regulators of the developmental pathways rather than well-known casein kinase 2 gene, CSNK2A1.

(1) Background: This study aimed to explore temporal changes in the transcriptome of oocytes in an adolescent-onset polycystic ovarian syndrome (PCOS) mouse model. (2) Methods: An adolescent-onset PCOS mouse model was established using DHEA. Genes with a similar expression trend over time were identified using trend analysis. KEGG pathway enrichment analysis and gene regulatory network diagrams were examined for signaling pathways to identify potential hub genes related to the pathogenesis of PCOS. (3) Results: Four main trends of gene expression were extracted, of which six combinations of Venn diagrams were generated. Differentially expressed genes were mainly enriched in oxidative phosphorylation, cell cycle, P53 signaling pathway. Cell cycle-related genes (Skp1, Ccnb1, Orc1 and 5, Wee2, Mapk3, Cdc20) were abnormally down-regulated in the DHEA group. Ptges3 was the top1 DEGs at the initial stage of PCOS modeling. (4) Conclusion: This study provides a novel insight into the altered transcriptome of oocytes from PCOS mice. mtDNA-related genes and Cell cycle-related genes play the most important role in the development of PCOS. Ptges3 was the one of the top DEGs which was up-regulated in DHEA group at the initial stage of modeling, which suggested it may play an important role in the early stage of PCOS.

Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) gene plays a vital role in the activation of T-cells as a down regulator. CTLA-4 gene polymorphisms have implicated a potential risk factor for autoimmune disorders like arthritis. Therefore the current study was designed to determine the association of CTLA-4 gene polymorphism in the onset of rheumatoid and osteoarthritis in Pakistani individuals. Genotyping was performed on 300 RA, 316 OA, and 412 control subjects by direct sequencing method as well as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. It was observed that allelic and genotypic frequency of rs5742909, rs231775, rs4553808, rs733618, and rs3087243 were significantly varied among patients and controls and considered as a significant risk factor in the onset of RA as well as OA. However, no mutation was identified on the rs11571317 polymorphic site. Haplotype CAGTCA and CAG TCG act as a protectant against disease onset whereas CAACCG was significant in disease onset. Mutation on rs231775 polymorphic site lead to the change of threonine into alanine It was concluded that CTLA-4 gene polymorphism is a significant risk factor in the onset of RA as well as OA. Large scale survey is required for the screening of the genetic markers for pre-diagnosis of the disease. SUMMARY STATEMENTThe study summarized that CTLA-4 gene polymorphism plays a key role in the arthritis onset in Pakistani population.

The first case of severe acute respiratory syndrome 2 (SARS CoV2) was imported to Pakistan in February 2020 since then 10,258 deaths have been witnessed. The virus has been mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS CoV2 have been defined globally. In this study, the epidemiology of SARS CoV2 was studied and locally transmitted SARS CoV2 isolates from Karachi were sequenced to compared and identify any possible variants.The real time PCR was performed on nasopharyngeal specimen to confirm SARSCoV2 with Orf 1ab and E gene as targets. The viral sequencing was performed through oxford nanopore technology MinION platform. Isolates from first and second wave of COVID-19 outbreak in Karachi were compared. The overall positivity rate for PCR was 26.24% with highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from second wave of COVID-19. Based on the present findings it is suggested that the locally transmitted virus from Karachi vary from those reported from other parts of Pakistan. Slight variability was also observed between viruses from first and second wave. Variability in any potential vaccine target may result in failed trials therefore information on any local viral variants is always useful for effective vaccine design and/or selection. Authors summaryDespite precautionary measures the COVID-19 pandemic is causing deaths all over the world. The continuous mutations in viral genome is making it difficult to design vaccines. Variability in genome is host dependent and data sharing has revealed that variant for different geographical locations may harbor different mutations. Keeping this in mind the current study was focused on the epidemiology of SARS CoV2 in symptomatic and asymptomatic COVID -19 suspected cases with impact of age and gender. The locally transmitted SARS CoV2 isolates from Karachi were sequenced to compared and identify any possible variants. The sequenced viral genome varied from the already submitted sequences from Pakistan thereby confirming that slightly different viruses were causing infections during different time periods in Karachi. All belonged to GH clade with D614G, P323L and Q57H mutations. The virus from second wave had A222V mutation making it more different. This information can be useful in selecting or designing a vaccine.