Genome wide association study and phylogenetic analysis of novel SARS-COV-2 virus among different countries.

Corona Virus (COVID-19) outbreak has threatened the world, since it has become pandemic and spread all over the world. The causative agent SARS-COV2 has proved lethal caused serious public health concern worldwide. Our aims were to describe the SARS-COV-2 genetic connections and check for recombination of all genome. The recombination was investigated by RDP5 and conflicting phylogenetic clustering in individual genomic fragments was established by phylogenetic study by maximum likelihood and Bayesian methods. Our analysis suggests that the available sequences from currently genomes of various strain were retrieved from different countries including Japan, French Republic, Spain, Peru, China, Vietnam, Taiwan, Brazil, U.S.A., South Korea, Sweden, Australia, Nepal, India, Iran, and Italy. The phylogeny of SARS-COV-2 observed the largest number of genome is Vietnam 29891-bp, while France is the smallest member identified with 29679-bp. Using Recombination Detection program5 (RDP5) the china strains was taken as parental strain but there were no recombination in the all strains. In our study we identified the mutation in Pakistani strains in high conserved region of Corona nucleoca super family domain at the nucleotide position (394: C replace with T, Position: 858: C replace with T and Position: 997 G replace A).

Immunoinformatics approaches to explore B and T cell epitope-based vaccine designing for SARS-CoV-2 Virus.

SARS-CoV-2, a new world coronavirus belonging to class Nidovirales of Coronaviridae family causes COVID-19 infection which is the leading cause of death worldwide. Currently there are no approved drugs and vaccines available for the prevention of COVID-19 infection, although couples of immunizations are being tested in clinical trials. However, the present efforts are focused on computational vaccination technique for evaluating candidates to design multi-epitope-based vaccine against pathogenic mechanism of novel SARS-COV-2. Based on recent published evidence, we recognized spike glycoprotein and envelope small membrane protein are the potential targets to combat the pathogenic mechanism of SARS-CoV-2. Similarly, in the present study we identified epitope of both B and T cell associated with these proteins. Extremely antigenic, conserve, immunogenic and nontoxic epitope of B and T cell of Spike protein are WPWYVWLGFI, SRVKNLNSSEGVPDLLV whereas the CWCARPTCIK and YCCNIVNVSL are associated with envelope small membrane protein were selected as potential candidate for vaccine designing. These epitopes show virtuous interaction with HLAA0201 during molecular docking analysis. Under simulation protocol the predicted vaccine candidates show stability. Collectively, this work provides novel potential candidates for epitope-based vaccine designing against COVID-19 infection.

In Vitro Biomedical and Photo-Catalytic Application of Bio-Inspired Zingiber officinale Mediated Silver Nanoparticles.

To minimize the hazardous effect of physical and chemical synthesis of nanoparticles we focused on the green synthesis of nanoparticles. Nanotechnology is a research hotspot and catch great attention because of its versatile applications in medical, biosciences and engineering fields. Purpose of our recent study is to synthesize bio-inspired metallic silver NPs by root mediated Zingiber officianale extract. The synthesized Ag-NPs were further characterized by using UVVisible spectroscopy, XRD, EDX, SEM, TEM and DLS techniques. The extent of crystallites were confirmed by X-ray diffraction. SEM and TEM revealed the morphological features with size of nanoparticles between 17.3 and 41.2 nm. FTIR analysis confirmed the capping of nanoparticles by bio active constituents present in Zingiber officinale extract. Later EDX confirmed the elemental composition of nanoparticles. Zeta potential, PDI and hydrodynamic size of Ag-NPs were confirmed by DLS. The synthesize Ag-NPs possess eminent biological potency against bacterial and leishmanial strains. Moreover considerable anti-diabetic, anticancer, antioxidant and biocompatibility nature of Ag-NPs was elucidated. The highest antioxidant activity of 50.61± 1.12%, 38.22 ± 1.18% and 27.39 ± 0.92 at 200 g/mL for TAC, TRP DPPH and was observed respectively. Ag-NPs exhibit potent leishmanicidal activity of 80% ± 1.4 against promastigotes and 77% ± 1.6 against amastigotes cultures of L. tropica. Highest antidiabetic activity 30 ± 0.77% recorded at 200 µg/ml. Highest Brine shrimps cytotoxicity of Ag-NPs was 60 ± 1.18 at 200 g/ml. Maximum dye degradation for Ag-NPs was recorded as 94.1% at 140 minute. All UTI isolates were resistant to antibiotics not coated with Ag-NPs. By applying 1% of Ag-NPs highest activity was recorded as 25 ± 1.58 mm against K. pneumoniae. Maximum zone of inhibition for Ag-NPs coated with Imipenem antibiotics 26 ± 1.5 mm against K. pneumoniae and coated with Ciprofloxacin 26 ± 1.4 m against S. aureus were measured. Last but not least high biocompatible nature of Ag-NPs was observed against fresh RBCs making the ecofriendly biosynthesized silver NPs a multi-dimensional candidate in biomedical field.

Pattern of hepatitis C virus genotypes and subtypes circulating in war-stricken Khyber Pakhtunkhwa, Pakistan: Review of published literature.

Infection due to hepatitis C virus (HCV) is a major cause of fibrosis and hepatocellular carcinoma in Pakistan. In the current review, pattern of HCV genotypes and subtypes in Khyber Pakhtunkhwa province was ascertained in light of the available literature. After thorough analysis, genotype 3 (58.27%) was determined to be the leading HCV genotype, followed by genotypes 2 (12.39%), 1 (9.54%) and 4 (0.86%). The proportions of genotypes 5 and 6 were recorded as 0.09% and 0.22% respectively. Subtype wise, 3a accounted for 48.67%, followed by subtype 2a (10.91%), 3b (9.43%), 1a (5.84%), 1b (3.66%), 2b (1.45%) and genotype 4 with its undefined subtypes contributed a portion of 0.86%. The cumulative share of subtypes 1c, 2c, 3c, 5a and 6a was less than 1%. In 11.51% cases, the subtype was untypeable while in 7.17% cases mixed subtypes were recorded. Gender wise, proportions of most HCV subtypes were marginally higher among males as compared to females. On the basis of studied groups, 3a was pervasive among all groups except in intravenous drug users where 2a was the major HCV subtype. Similarly, based on various geographical locations (provincial divisions), subtype 3a revealed a ubiquitous distribution. Conclusively, HCV 3a persists to be the principal subtype across the province of Khyber Pakhtunkhwa. The considerable number of untypeable subtypes in most studies urges for an improved genotyping system on the basis of local sequence data and practice of sequencing for determination of underlying subtype in untypeable cases. Further, studies on identification of subtypes transmission pattern are imperative for assessment of transmission origin and reinforcement of efficient control strategies. In addition, the current review emphasizes the need of attention toward HCV risk groups and ignored southern side of Khyber Pakhtunkhwa province for better holistic understanding of HCV genotype distribution pattern in the province.

Untypeable hepatitis C virus subtypes in Pakistan: A neglected section.

Diagnostically untypeable subtypes contribute a considerable percent of hepatitis C virus (HCV) subtypes in Pakistan. In the present study, chronically infected HCV patients with known viremia were subjected to HCV genotyping. Among the total retrieved samples, 92.7% (64/69) were found typeable while 7.24% (5/69) were diagnostically untypeable. In conclusion, the presence of large number of untypeable HCV subtypes emphasizes the need of an updated type-specific genotyping assay and consideration of primers for proportionally rare subtypes to minimize the number of untypeable HCV subtypes.

Circulating serotypes of dengue virus and their incursion into non-endemic areas of Pakistan; a serious threat.

BACKGROUND: Dengue virus is circulating in Pakistan since 1994, which causes major and minor outbreaks in many areas of the country. The incidence of dengue in Pakistan in past years mainly restricted to parts of Sindh and Punjab provinces. As such, a severe dengue outbreak appeared in Pakistan in 2011, particularly in Punjab province with Lahore as the most hit city (290 deaths). In 2013, for the first time in the history of Pakistan, dengue outbreak erupted in Swat District, Khyber Pakhtunkhwa, which claimed more than 57 lives. Hence this study was conducted to document circulating serotypes of dengue virus in Pakistan in 2011 and 2013 dengue outbreaks in two different territories/areas of the country. METHODS: In total, 1340 blood samples from people having dengue (ELISA positive) and/or dengue like symptoms from various cities/areas of Punjab and Swat, Khyber Pakhtunkhwa (KP) were collected and analyzed by reverse transcription polymerase chain reaction (RT-PCR) using serotype specific primers. RESULTS: The results indicated that all the four dengue virus serotypes were circulating in Punjab Province with highest frequency of DENV-2 (41.64 %) and DENV-3 (41.05 %). Similarly, DENV-2 (41.66 %) and DENV-3 (35.0 %) were dominant serotypes detected in KP-based people lived in Punjab. On the other hand only DENV-2 (40.0 %) and DENV-3 (60.0 %) were detected in Swat District. Furthermore an important observation noted in this study was mixed infection of DENV-2 and DENV-3 in Punjab in 2011 (3.81 %) and in people from KP infected in Punjab (8.33 %) which may account for the high mortality and morbidity rates as compared to previous outbreaks. Over all male population was mostly infected as compared to females and people in the age group between 15 to 45 was the highest infected group. CONCLUSIONS: The findings of this study indicate that all four serotypes of dengue virus are circulating in Punjab whereas serotypes 2 and 3 introduced for the first time into Swat, KP in 2013; about 600 km away from Lahore, Punjab. Overall dengue virus serotypes 2 and 3 were the major outbreak-causing serotypes in Pakistan in 2011 and 2013. Dengue outbreak in Swat may be the continuation of previous dengue outbreaks in Punjab but it needs further research and investigation.

Molecular characterization of Hepatitis C virus 3a in Peshawar.

BACKGROUND: The purpose of this study was to explore molecular epidemiology of HCV genotype 3a in Peshawar based on sequencing and phylogenetic analysis of Core region of HCV genome. METHODS: Chronically infected Hepatitis C virus infected patients enrolled under the Prime Minister Hepatitis C control program at three Tertiary care units of Peshawar [Khyber Teaching Hospital Peshawar, Lady Reading Hospital Peshawar, Hayat Abad Medical Complex Peshawar] were included in this cross sectional observational study. Qualitative detection of HCV and HCV genotyping was carried out by a modified reverse transcription-polymerase chain reaction (RT-PCR) and type specific genotyping assay. The Core gene of HCV genotype 3a was amplified, cloned and sequenced. The sequences obtained were used for phylogenetic analysis using MEGA 6 software. RESULTS: Among the 422 (82.75 %) PCR positive samples, 192 (45.5 %) were identified as having HCV genotype 3a infection. HCV Core gene sequencing was carried out randomly for the characterization of HCV 3a. Nucleotide sequence analysis of the obtained viral genomic sequences based on partial HCV 3a Core gene sequences with reference sequences from different countries showed that our sequences clustered with some local and regional sequences with high bootstrap values. CONCLUSION: HCV 3a is highly prevalent in Peshawar, Pakistan and its phylogenetics based on Core gene sequences indicate the prevalence of different lineages of HCV 3a in Peshawar which may have consequences for disease management strategies causing more economic pressure on the impoverished population due to possible antiviral resistance.