Core amino acid substitutions in HCV-3a isolates from Pakistan and opportunities for multi-epitopic vaccines.

Hepatitis C virus (HCV), which infected 71 million worldwide and about 5%-6% are from Pakistan, is an ssRNA virus, responsible for end-stage liver disease. To date, no effective therapy is available to cure this disease. Hence, it is important to study the most prevalent genotypes infecting human population and design novel vaccine or small molecule inhibitors to control the infections associated with HCV. Therefore, in this study clinical samples (n = 35; HCV-3a) from HCV patients were subjected to Sanger sequencing method. The sequencing of the core gene, which is generally considered as conserved, involved in the detection, quantitation and genotyping of HCV was performed. Multiple mutations, that is, R46C, R70Q, L91C, G60E, N/S105A, P108A, N110I, S116V, G90S, A77G and G145R that could be linked with response to antiviral therapies were detected. Phylogenetic analysis suggests emerging viral isolates are circulating in Pakistan. Using ab initio modelling technique, we predicted the 3D structure of core protein and subjected to molecular dynamics simulation to extract the most stable conformation of the structure for further analysis. Immunoinformatic approaches were used to propose a multi-epitopes vaccine against HCV by using core protein. The vaccine constructs consist of nine CTL and three HTL epitopes joined by different linkers were docked against the two reported Toll-like receptors (TLR-3 and TLR-8). Docking of vaccine construct with TLR-3 and TLR-8 shows proper binding and in silico expression of the vaccine resulted in a CAI value of 0.93. These analyses suggest that specific immune responses may be produced by the proposed vaccine.Communicated by Ramaswamy H. Sarma.

Genetic Defects in DNAH2 Underlie Male Infertility With Multiple Morphological Abnormalities of the Sperm Flagella in Humans and Mice.

Asthenozoospermia accounts for over 80% of primary male infertility cases. Reduced sperm motility in asthenozoospermic patients are often accompanied by teratozoospermia, or defective sperm morphology, with varying severity. Multiple morphological abnormalities of the flagella (MMAF) is one of the most severe forms of asthenoteratozoospermia, characterized by heterogeneous flagellar abnormalities. Among various genetic factors known to cause MMAF, multiple variants in the DNAH2 gene are reported to underlie MMAF in humans. However, the pathogenicity by DNAH2 mutations remains largely unknown. In this study, we identified a novel recessive variant (NM_020877:c.12720G > T;p.W4240C) in DNAH2 by whole-exome sequencing, which fully co-segregated with the infertile male members in a consanguineous Pakistani family diagnosed with asthenozoospermia. 80-90% of the sperm from the patients are morphologically abnormal, and in silico analysis models reveal that the non-synonymous variant substitutes a residue in dynein heavy chain domain and destabilizes DNAH2. To better understand the pathogenicity of various DNAH2 variants underlying MMAF in general, we functionally characterized Dnah2-mutant mice generated by CRISPR/Cas9 genome editing. Dnah2-null males, but not females, are infertile. Dnah2-null sperm cells display absent, short, bent, coiled, and/or irregular flagella consistent with the MMAF phenotype. We found misexpression of centriolar proteins and delocalization of annulus proteins in Dnah2-null spermatids and sperm, suggesting dysregulated flagella development in spermiogenesis. Scanning and transmission electron microscopy analyses revealed that flagella ultrastructure is severely disorganized in Dnah2-null sperm. Absence of DNAH2 compromises the expression of other axonemal components such as DNAH1 and RSPH3. Our results demonstrate that DNAH2 is essential for multiple steps in sperm flagella formation and provide insights into molecular and cellular mechanisms of MMAF pathogenesis.

Evaluation of hematological parameters as an indicator of disease severity in Covid-19 patients: Pakistan's experience.

BACKGROUND: The severity of COVID-19 could be evaluated by examining several blood parameters mainly white blood cell (WBC) count, granulocytes, platelet, and novel hemocytometric markers neutrophils to lymphocyte ratio (NLR), platelet-to-lymphocyte (PLR), and lymphocyte to monocyte ratio (LMR). The current study was conducted to investigate alteration in blood parameters and their association with the severity and mortality of COVID-19 patients. METHODOLOGY: An observational cross-sectional study was conducted retrospectively, a total of 101 COVID-19 positive patients were examined: 52 were mild, 24 were moderate, 09 were severe, and 16 were critically diseased patients. We also recorded 16 deaths associated with the critical group. The overall mean age observed in our study was 48.94 years, where the mean age for critical individuals was 62.12 ± 14.35 years. RESULTS: A significant association between the disease severity and elevation in blood parameters were observed. The WBC's and granulocyte count were significantly increased (p value <0.001) while the mean platelet count (165.0 × 109 /L) and red blood cell volume distribution width (RDW) were decreased in the critical group (57.86%) compared to mild group's patients (177.3%) (p = 0.83). The lymphocytes count was decreased in critical patients (1.40 × 109 /L) compared to mild patients (1.92 × 109 /L) (p = 0.28). A significant association was observed in platelet-lymphocyte ratio (p < 0.001), Neutrophil-Lymphocyte ratio (p = <0.001), and Lymphocyte-Monocyte ratio (0.011). CONCLUSION: These blood parameters could be used as a suitable biomarker for the prognosis and severity of COVID-19. Evaluating novel hemograms NLR, PLR, and LMR can aid clinicians to identify potentially severe cases at early stages, initiate effective management in time, and conduct early triage which may reduce the overall mortality of COVID-19 patients.

A loss-of-function variant in DNA mismatch repair gene MLH3 underlies severe oligozoospermia.

Male infertility pertains to male's inability to cause pregnancy in a fertile female. It accounts for 40-50% of infertility in human. In the study, presented here, a large consanguineous family of Pakistani origin segregating male infertility in autosomal recessive manner was investigated. Exome sequencing revealed a homozygous frameshift variant [NM_001040108: c.3632delA, p.(Asn1211Metfs*49)] in DNA mismatch repair gene MLH3 (MutL Homolog) that segregated with male infertility within the family. This is the first loss-of-function homozygous variant in the MLH3 gene causing severe oligozoospermia leading to male infertility. Previous studies have demonstrated association of infertility with gene knockout in the mice.

Epidemiological features of cutaneous leishmaniasis endemic in hilly areas of district Karak, Khyber-Pakhtunkhwa province of Pakistan.

Cutaneous leishmaniasis is a vector borne infection caused by flagellated parasitic protozoans of the genus Leishmania. This is an emergent threat and endemic in areas of tropic and sub-tropics and has a wider geographical distribution. This study was aimed to find the epidemiological aspects of cutaneous leishmaniasis during the recent epidemic in district Karak in 2018-2019. The suspected patients of leishmaniasis from different areas of district Karak were examined. We came across 803 cases during six-month period from August 2018 to January 2019. A major portion (> 37%; n = 299) of these patients were in age 11-20 years. The infection rate was higher in female (55.3%; n = 803) compared to males (44.6%; n = 803). Both gender and age showed a significant effect on the occurrence of infection. It is concluded that cutaneous leishmaniasis has appeared as a major health issue in district Karak. The current study report CL outbreak in Karak district which need immediate response from the healthcare authorities. In addition, extensive awareness campaigns are needed for timely prevention of such outbreaks.

Expanding the clinical and genetic spectrum of G6PD deficiency: The occurrence of BCGitis and novel missense mutation.

Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme in the pentose phosphate pathway that ensures sufficient production of coenzyme nicotinamide adenine dinucleotide phosphate (NADPH) by catalyzing the reduction of NADP+ to NADPH. Noteworthy, the latter mediates the production of reactive oxygen species (ROS) by phagocytic cells such as neutrophils and monocytes. Therefore, patients with severe forms of G6PD deficiency may present impaired NADPH oxidase activity and become susceptible to recurrent infections. This fact, highlights the importance to characterize the immunopathologic mechanisms underlying the susceptibility to infections in patients with G6PD deficiency. Here we report the first two cases of G6PD deficiency with Bacille Calmette-Guérin (BCG) adverse effect, besides jaundice, hemolytic anemia and recurrent infections caused by Staphylococcus aureus. The qualitative G6PD screening was performed and followed by oxidative burst analysis using flow cytometry. Genetic and in silico analyses were carried out by Sanger sequencing and mutation pathogenicity predicted using bioinformatics tools, respectively. Activated neutrophils and monocytes from patients displayed impaired oxidative burst. The genetic analysis revealed the novel missense mutation c.1157T>A/p.L386Q in G6PD. In addition, in silico analysis indicated that this mutation is pathogenic, thereby hampering the oxidative burst of neutrophils and monocytes from patients. Our data expand the clinical and genetic spectrum of G6PD deficiency, and suggest that impaired oxidative burst in this severe primary immune deficiency is an underlying immunopathologic mechanism that predisposes to mycobacterial infections.

Expanding the clinical and genetic spectrum of G6PD deficiency: the occurrence of BCGitis and novel missense mutation

Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme in the pentose phosphate pathway that ensures sufficient production of coenzyme nicotinamide adenine dinucleotide phosphate (NADPH) by catalyzing the reduction of NADP-F to NADPH. Noteworthy, the latter mediates the production of reactive oxygen species (ROS) by phagocytic cells such as neutrophils and monocytes. Therefore, patients with severe forms of G6PD deficiency may present impaired NADPH oxidase activity and become susceptible to recurrent infections. This fact, highlights the importance to characterize the immunopathologic mechanisms underlying the susceptibility to infections in patients with G6PD deficiency. Here we report the first two cases of G6PD deficiency with Bacille Calmette-Guerin (BCG) adverse effect, besides jaundice, hemolytic anemia and recurrent infections caused by Staphylococcus aureus. The qualitative G6PD screening was performed and followed by oxidative burst analysis using flow cytometry. Genetic and in silico analyses were carried out by Sanger sequencing and mutation pathogenicity predicted using bioinformatics tools, respectively. Activated neutrophils and monocytes from patients displayed impaired oxidative burst. The genetic analysis revealed the novel missense mutation c.1157T>A/p.L386Q in G6PD. In addition, in silico analysis indicated that this mutation is pathogenic, thereby hampering the oxidative burst of neutrophils and monocytes from patients. Our data expand the clinical and genetic spectrum of G6PD deficiency, and suggest that impaired oxidative burst in this severe primary immune deficiency is an underlying immunopathologic mechanism that predisposes to mycobacterial infections.