Insights into the genetic characteristics, clustering patterns, and phylogeographic dynamics of the JC polyomavirus, 1993 to 2023.

The human JC polyomavirus (JCV) is a widespread, neurotropic, opportunistic pathogen responsible for progressive multifocal leukoencephalopathy (PML) as well as other diseases in immunosuppressed individuals, including granule cell neuronopathy, JCV-associated nephropathy, encephalitis, and meningitis in rare cases. JCV classification is still unclear, where the ICTV (International Committee on Taxonomy of Viruses) has grouped all the strains into human polyomavirus 2, with no classification on clade and subclade levels. Therefore, JCV strains were previously classified using different genomic regions, e.g., full-length, VP1, and the V-T intergenic region etc., and the strains were grouped into several types related to various geographic locations and human ethnicities. However, neither of these classifications and nomenclature contemplates all the groups described so far. Herein, we evaluated all the available full-length coding genomes, VP1, and large T antigen nucleotide sequences of JCV reported during 1993-2023 and classified them into four major phylogenetic clades, i.e., GI-GIV, where GI is further grouped into two types GI.1 and GI.2 with five sub-clades each (GI.1/GI.2 a-e), GII into three (GII a-c), GIII as a separate clade, and GIV into seven sub-clades (GIV a-g). Similarly, the phylogeographic network analysis indicated four major clusters corresponding to GI-GIV clades, each with multiple subclusters and mutational sub-branches corresponding to the subclades. GI and GIV clusters are connected via GI.1-e reported from Europe and America, GII, GIII and GIV clusters are connected by GII-b and GII-c strains reported from Africa, while GIV cluster strains are connected to the Russia-Italy JCV haplotype. Furthermore, we identified JCV-variant-GS/B-Germany-1997 (GenBank ID: AF004350.1) as an inter-genotype recombinant having major and minor parents in the GI.1-e and GII-a clades, respectively. Additionally, the amino acid variability analysis revealed high entropy across all proteins. The large T antigen exhibited the highest variability, while the small t antigen showed the lowest variability. Our phylogenetic and phylogeographic analyses provide a new approach to genotyping and sub-genotyping and present a comprehensive classification system of JCV strains based on their genetic characteristics and geographic distribution, while the genetic recombination and amino acid variability can help identify pathogenicity and develop effective preventive and control measures against JCV infections.

Seroprevalence and molecular detection of brucellosis among Pakistani women with spontaneous abortion.

Background: Human brucellosis is a neglected disease transmitted to humans from animals such as cattle, goats, dogs, and swine. The causative agents are bacteria of the genus Brucella, intracellular pathogens usually confined to the reproductive organs of their animal hosts causing sterility and abortions. The objective of the study was to determine the seroprevalence of brucellosis among women with spontaneous abortions (SAW) and compare this seroprevalence with that of healthy pregnant women (HPW). Methods: The case-control study was designed to determine the seroprevalence and molecular detection of brucellosis in women who suffered from spontaneous abortion and healthy pregnant women of the Haripur District of Pakistan. A total of 770 blood samples (n = 385 for each group) were collected from 9 public and 11 private hospitals in Haripur District from December 2021-March 2023. Data on demographic features, epidemiological variables, and risk factors were collected from each participant by structured questionnaires. Initial screening for brucellosis was performed by Rose Bengal Plate Test followed by qRT-PCR for molecular detection of the genus-specific BCSP-31 gene of Brucella. Results: The study showed that anti-Brucella antibodies were more found in SAW 23.63% (91/385) than in HPW 1.29% (5/385). Brucella specific DNA was amplified in 89.01% (81/91) seropositive samples of SAW. Demographic features and risk factors such as age, urbanicity, socioeconomic status, education, occupation, and animal contact were found significantly associated with brucellosis (p ≤ 0.05). Consumption of unpasteurized raw milk (OR = 18.28, 95%CI: 8.16-40.94) was found highly concomitant with seroprevalence. Conclusion: This study reports the first evidence of involvement of brucellosis in spontaneous abortions in women of Pakistan. The study can be used to develop strategies for risk management during pregnancy, to raise awareness for brucellosis, and develop control programs.

Human monkeypox: An updated appraisal on epidemiology, evolution, pathogenesis, clinical manifestations, and treatment strategies.

Monkeypox (Mpox) is a zoonotic viral disease caused by the monkeypox virus (MPXV), a member of the Orthopoxvirus genus. The recent occurrence of Mpox infections has become a significant global issue in recent months. Despite being an old disease with a low mortality rate, the ongoing multicountry outbreak is atypical due to its occurrence in nonendemic countries. The current review encompasses a comprehensive analysis of the literature pertaining to MPXV, with the aim of consolidating the existing data on the virus's epidemiological, biological, and clinical characteristics, as well as vaccination and treatment regimens against the virus.

Epidemiology of Staphylococcus aureus Non-Susceptible to Vancomycin in South Asia.

Staphylococcus aureus is one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens among which multidrug resistance has emerged. Resistance to methicillin has resulted in clinicians using the antibiotic of last resort, vancomycin, to treat infections caused by methicillin-resistant S. aureus (MRSA). However, excessive use and misuse of vancomycin are major causes of resistance among S. aureus strains. South Asia encompasses ~25% of the world's population, and countries in South Asia are often characterized as low- and middle-income with poor healthcare infrastructure that may contribute to the emergence of antibiotic resistance. Here, we briefly highlight the mechanism of vancomycin resistance, its emergence in S. aureus, and the molecular epidemiology of non-susceptible S. aureus to vancomycin in the South Asian region.

Epidemiology and molecular characterization of Staphylococcus aureus causing bovine mastitis in water buffaloes from the Hazara division of Khyber Pakhtunkhwa, Pakistan.

Buffalo represent a major source of milk in Pakistan. However, production is impacted by the disease bovine mastitis. Mastitis causes significant economic losses, with Staphylococcus aureus (S. aureus) being one of its major causative agents. While much work has been done understanding the epidemiology of bovine mastitis in Pakistan, detailed molecular characterization of the associated S. aureus is unavailable. In the current study both the epidemiological and molecular characterization of S. aureus from bovine mastitis in the Hazara division of Pakistan are examined. S. aureus was isolated from 18.41% of the animals, and left quarters more prone to infection (69.6%) than right quarters (30.4%). Sub-clinical mastitis (75.31%) was more prevalent than clinical mastitis (24.69%), with infections evenly distributed amongst the eight districts. Molecular characterization revealed that only 19.6% of the isolates were methicillin-resistant, and four strains types identified, including ST9-t7867-MSSA, ST9-MSSA, ST101-t2078-MSSA, and ST22-t8934-MRSA-IVa. Antiseptic resistance genes were not detected in the isolates, and low levels of antibiotic resistance were also noted, however the methicillin-resistant strains had higher overall antibiotic resistance. This study represents the most complete molecular typing data for S. aureus causing bovine mastitis in the Hazara district of Pakistan, and the country as a whole.

A novel, eco-friendly bio-nanocomposite (Alg-Cst/Kal) for the adsorptive removal of crystal violet dye from its aqueous solutions.

Herein, we report the synthesis of a novel bio-nanocomposite (Alg-Cst/Kal) for the effective removal of the dye "Crystal Violet" from its aqueous solutions. In order to observe the surface morphology and functional groups, the bio-nanocomposite was characterized using various techniques such as SEM, EDX, TEM, FTIR, XRD, and TGA. The effect of parameters like contact time, pH, concentration and temperature on the adsorption of the dye over adsorbent has been studied in detail. The dye - adsorbent system has been tested over various isotherm models and found to follow the Freundlich adsorption isotherm model at 303 K. The developed bio-nanocomposite material exhibits an excellent adsorption toward Crystal Violet with a maximum adsorption capacity of 169.49 mg.g-1. The experimental data has been further validated by applying various kinetic models and the pseudo-second order kinetic model was the best suited model. The calculated rate constant values ranged from 0.0046 to 0.0204 g.mg-1.min-1 for different dye concentrations. The positive values of change in enthalpy, ΔH° (9.765 kJ.mol-1) and change in entropy, ΔS° (0.0565 kJ.mol-1.K-1) obtained through thermodynamic studies demonstrate the endothermic nature and spontaneity of the adsorption process, respectively. The adsorption capacity of the adsorbent for the removal of the Crystal Violet dye was also compared with other adsorbents and found maximum. Novelty statement A novel bio-nanocomposite is synthesized by modifying the biopolymer alginate, cysteine and mixing the clay, kaolinite (Kal). The adsorption abilities of the material was tested the on the cationic hazardous dye, Crystal Violet. The material is novel and no attempt has so far been made to examine its batch adsorption abilities to remove hazardous dyes from the wastewater. The results are highly encouraging as out of all the adsorbents tested so far highest adsorption of the dye is observed in the present studies.

COVID-19 third wave: a challenge for overburdened and underdeveloped healthcare system of Pakistan.

BACKGROUND: To the Editor, Countries around the globe have observed the dynamic pattern of COVID-19 associated morbidity and mortality in which the first wave was observed in spring 2020 that considerably moderated during the summer. The second wave emerged in fall 2020, which subsequently decreased in early 2021. But now COVID-19 third wave is on the line with an inclined rate and is considered more infectious in some of the countries [1]. In Pakistan, COVID-19 has caused 630,471 confirmed cases with about 13,863 deaths by 21 March 2021 as shown in Figure (a). The rate of positive cases was highest (23%) in June 2020, which dropped to 1.7% by September 2020. Later, it began to rise, reaching 7.45% in January 2021 and 3% in February 2021. Now it is on the rise again and already reached 8% by 19 March 2021 Figure (b). According to the National Command and Operating Center (NCOC) of Pakistan, COVID-19 cases rose to 22,018 in the last 10 days, which is a 68% increase in the cases from the proceeding 10 days, as shown in Figure c. DISCUSSION: The author declares there is no conflict of interest.