Occurrence of toxic elements in river areas along drains and groundwater resources: source of contamination and associated health risk.

The objective of the current research was to examine the water quality of the River Ravi and the River Sutlej, with a specific focus on potentially toxic elements (PTEs). Additionally, we sought to monitor the sources of pollution in these rivers by gathering samples from the primary drains that carry industrial and municipal waste into these water bodies. Furthermore, we aimed to evaluate the impact of PTEs in surface water on groundwater quality by collecting groundwater samples from nearby populated areas. A total of 30 samples were collected from these three sources: rivers (6 samples), drains (9 samples), and groundwater (15 samples). The analysis revealed that the levels of PTEs in the samples from these three resources having a mean value: arsenic (As) 23.5 µg/L, zinc (Zn) 2.35 mg/L, manganese (Mn) 0.51 mg/L, lead (Pb) 6.63 µg/L, and chromium (Cr) 10.9 µg/L, exceeded the recommended values set by the World Health Organization (WHO). Furthermore, PTEs including (As 84%), (Zn 65%), (Mn 69%), (Pb 53%), (Cr 53%), and (Ni 27%), samples were beyond the recommended values of WHO. The results of the Principal Component Analysis indicated that surface water and groundwater exhibited total variability of 83.87% and 85.97%, respectively. This indicates that the aquifers in the study area have been contaminated due to both natural geogenic factors and anthropogenic sources. These sources include the discharge of industrial effluents, wastewater from municipal sources, mining activities, agricultural practices, weathering of rocks, and interactions between rocks and water. Spatial distribution maps clearly illustrated the widespread mobilization of PTEs throughout the study area. Furthermore, a health risk assessment was conducted to evaluate the potential adverse health effects of PTEs through the ingestion of drinking groundwater by both children and adults. Health risk assessment result show the mean carcinogenic values for As, Cr, Pb and Ni in children are calculated to be (1.88E-04), (2.61E-04), (2.16E-02), and (5.74E-05), respectively. Similarly, the mean carcinogenic values for the above mentioned PTEs in adults were recorded to be (2.39E-05), (3.32E-05), (1.19E-03), and (7.29E-06) respectively. The total hazard index values for As, Zn, Cr, Pb, Mn, Cu, and Ni in children were observed to be (9.07E + 00), (9.95E-07), (4.59E-04), (5.75E-04), (4.72E-05), (2.78E-03), and (5.27E-05) respectively. The analysis revealed that As has an adverse effect on the population of the study area as compared to other PTEs investigated in this study.

A novel homozygous missense substitution p.Thr313Ile in the PDE6B gene underlies autosomal recessive retinitis pigmentosa in a consanguineous Pakistani family.

BACKGROUND: Retinitis pigmentosa (RP) is one of the most frequent hereditary retinal diseases that often starts with night blindness and eventually leads to legal blindness. Our study aimed to identify the underlying genetic cause of autosomal recessive retinitis pigmentosa (arRP) in a consanguineous Pakistani family. METHODS: Following a detailed ophthalmological examination of the patients by an ophthalmologist, whole-exome sequencing was performed on the proband's DNA to delineate the genetic cause of RP in the family. In-depth computational methods, in-silico analysis, and familial co-segregation study were performed for variant detection and validation. RESULTS: We studied an inbred Pakistani family with two siblings affected by retinitis pigmentosa. The proband, a 32 years old female, was clinically diagnosed with RP at the age of 6 years. A classical night blindness symptom was reported in the proband since her early childhood. OCT report showed a major reduction in the outer nuclear layer and the ellipsoid zone width, leading to the progression of the disease. Exome sequencing revealed a novel homozygous missense mutation (c.938C > T;p.Thr313Ile) in exon 12 of the PDE6B gene. The mutation p.Thr313Ile co-segregated with RP phenotype in the family. The altered residue (p.Thr313) was super conserved evolutionarily across different vertebrate species, and all available in silico tools classified the mutation as highly pathogenic. CONCLUSION: We present a novel homozygous pathogenic mutation in the PDE6B gene as the underlying cause of arRP in a consanguineous Pakistani family. Our findings highlight the importance of missense mutations in the PDE6B gene and expand the known mutational repertoire of PDE6B-related RP.

A Novel Intronic Deletion in PDE6B Causes Autosomal Recessive Retinitis Pigmentosa by Interfering with RNA Splicing.

INTRODUCTION: Retinitis pigmentosa (RP) is a rare degenerative retinal disease caused by mutations in approximately seventy genes. Currently, despite the availability of large-scale DNA sequencing technologies, ∼30-40% of patients still cannot be diagnosed at the molecular level. In this study, we investigated a novel intronic deletion of PDE6B, encoding the beta subunit of phosphodiesterase 6 in association with recessive RP. METHODS: Three unrelated consanguineous families were recruited from the northwestern part of Pakistan. Whole exome sequencing was performed for the proband of each family, and the data were analyzed according to an in-house computer pipeline. Relevant DNA variants in all available members of these families were assessed through Sanger sequencing. A minigene-based splicing assay was also performed. RESULTS: The clinical phenotype for all patients was compatible with rod cone degeneration, with the onset during childhood. Whole exome sequencing revealed a homozygous 18 bp intronic deletion (NM_000283.3:c.1921-20_1921-3del) in PDE6B, which co-segregated with disease in 10 affected individuals. In vitro splicing tests showed that this deletion causes aberrant RNA splicing of the gene, leading to the in-frame deletion of 6 codons and, likely, to disease. CONCLUSION: Our findings further expand the mutational spectrum of the PDE6B gene.

Hydrogeochemistry and prediction of arsenic contamination in groundwater of Vehari, Pakistan: comparison of artificial neural network, random forest and logistic regression models.

Arsenic contamination in the groundwater occurs in various parts of the world due to anthropogenic and natural sources, adversely affecting human health and ecosystems. The current study intends to examine the groundwater hydrogeochemistry containing elevated arsenic (As), predict As levels in groundwater, and determine the aptness of groundwater for drinking in the Vehari district, Pakistan. Four hundred groundwater samples from the study region were collected for physiochemical analysis. As levels in groundwater samples ranged from 0.1 to 52 µg/L, with an average of 11.64 µg/L, (43.5%), groundwater samples exceeded the WHO 2022 recommended limit of 10 µg/L for drinking purposes. Ion-exchange processes and the adsorption of ions significantly impacted the concentration of As. The HCO3- and Na+ are the dominant ions in the study area, and the water types of samples were CaHCO3, mixed CaMgCl, and CaCl, demonstrating that rock-water contact significantly impacts hydrochemical behavior. The geochemical modeling indicated negative saturation indices with calcium carbonate and other salt minerals, encompassing aragonite, calcite, dolomite, and halite. The dissolution mechanism suggested that these minerals might have implications for the mobilization of As in groundwater. A combination of human-induced and natural sources of contamination was unveiled through principal component analysis (PCA). Artificial neural networks (ANN), random forest (RF), and logistic regression (LR) were used to predict As in the groundwater. The data have been divided into two parts for statistical analysis: 20% for testing and 80% for training. The most significant input variables for As prediction was determined using Chi-squared analysis. The receiver operating characteristic area under the curve and confusion matrix were used to evaluate the models; the RF, ANN, and LR accuracies were 0.89, 0.85, and 0.76. The permutation feature and mean decrease in impurity determine ten parameters that influence groundwater arsenic in the study region, including F-, Fe2+, K+, Mg2+, Ca2+, Cl-, SO42-, NO3-, HCO3-, and Na+. The present study shows RF is the best model for predicting groundwater As contamination in the research area. The water quality index showed that 161 samples represent poor water, and 121 samples are unsuitable for drinking. Establishing effective strategies and regulatory measures is imperative in Vehari to ensure the sustainability of groundwater resources.

Potentially toxic metals contamination, health risk, and source apportionment in the agricultural soils around industrial areas, Firozabad, Uttar Pradesh, India: a multivariate statistical approach.

Potentially toxic metals (PTMs) contamination in the soil poses a serious danger to people's health by direct or indirect exposure, and generally it occurs by consuming food grown in these soils. The present study assessed the pollution levels and risk to human health upon sustained exposure to PTM concentrations in the area's centuries-old glass industry clusters of the city of Firozabad, Uttar Pradesh, India. Soil sampling (0-15 cm) was done in farmers' fields within a 1 km radius of six industrial clusters. Various environmental (geo-accumulation index, contamination factor, pollution load index, enrichment factor, and ecological risk index) and health risk indices (hazard quotient, carcinogenic risk) were computed to assess the extent of damage caused to the environment and the threat to human health. Results show that the mean concentrations of Cu (33 mg kg-1), Zn (82.5 mg kg-1), and Cr (15.3 mg kg-1) were at safe levels, whereas the levels of Pb, Ni, and Cd exceeded their respective threshold limits. A majority of samples (88%) showed considerable ecological risk due to the co-contamination of these six PTMs. Health risk assessment indicated tolerable cancer and non-cancer risk in both adults and children for all PTMs, except Ni, where adults were exposed to potential threat of cancer. Pearson's correlation study revealed a significant positive correlation between all six metal pairs and conducting principal component analysis (PCA) confirmed the common source of metal pollution. The PC score ranked different sites from highest to lowest according to PTM loads that help to establish the location of the source. Hierarchical cluster analysis grouped different sites into the same cluster based on similarity in PTMs load, i.e., low, medium, and high.

The occurrence of geogenic fluoride in shallow aquifers of Kenya Rift Valley and its implications in groundwater management.

Widespread concerns about high-fluoride groundwater and their health risks have been raised worldwide. Weathering of volcanic minerals is regarded as a principal source of groundwater fluoride in regions with volcanic bedrocks. However, how does the volcanic minerals control fluoride occurrence, if it induces other hydrogeochemical processes participating in and how this relates to human health still remain unclear. This study takes Kenya Rift Valley, which has volcanic geological formations, as an example to delineate the occurrence and origins of high-fluoride shallow groundwater with analysis of hydrochemistry, graphical and multivariate statistical methods. Over 40% of shallow groundwater (F-: up to 23.5 mg/L) show elevated fluoride values over the WHO standards of 1.5 mg/L. High fluoride groundwater are generally Na-rich and Ca-poor with high pH and HCO3¯ concentrations. Hydrogeochemical and principal component analysis indicate that weathering of hyper-alkaline volcanic rocks could release accumulated fluoride in melts and volatile fractions, as well as in clay minerals. Alkaline condition and high HCO3- contents lead to the competitive desorption of F- from clay minerals and Fe-hydroxides into groundwater. Clay minerals also provide abundant exchange sites where cation exchange happens and promotes the release of F- from the sediments by controlling the dissolution/precipitation of calcite and fluorite. Health risk assessment results show that chronic health risks by groundwater geogenic fluoride ingestion are identified to various individuals, with highest threats in children. Finally, a conceptual model has been developed to demonstrate the formations of high geogenic fluoride groundwater in regions with volcanic bedrocks and its relation with human health.

Synthesis and Characterizations of PdNi Carbon Supported Nanomaterials: Studies of Electrocatalytic Activity for Oxygen Reduction in Alkaline Medium.

Electrocatalytic materials offer numerous benefits due to their wide range of applications. In this study, a polyol technique was used to synthesize PdNi nanoparticles (NPs) with different percent atomic compositions (Pd = 50 to 90%) to explore their catalytic efficiency. The produced nanoparticles were characterized using X-ray diffraction (XRD) and electrochemical investigations. According to XRD measurements, the synthesized NPs were crystalline in nature, with crystallite sizes of about 2 nm. The electrochemical properties of the synthesized NPs were studied in alkaline solution through a rotating ring-disk electrode (RRDE) technique of cyclic voltammetry. The PdNi nanoparticles supported on carbon (PdNi/C) were used as electrocatalysts and their activity and stability were compared with the homemade Pd/C and Pt/C. In alkaline solution, PdNi/C electrocatalysts showed improved oxygen reduction catalytic activity over benchmark Pd/C and Pt/C electrocatalysts in all composition ratios. Furthermore, stability experiments revealed that PdNi 50:50 is more stable in alkaline solution than pure Pd and other PdNi compositions.

Protective effects of phyllanthus emblica leaf extract on sodium arsenite-mediated adverse effects in mice.

Groundwater contamination of arsenic is the major cause of a serious health hazard in Bangladesh. No specific treatment is yet available to manage the large number of individuals exposed to arsenic. In this study, we evaluated the protective effects of Phyllanthus emblica (Indian gooseberry or Amla) leaf extract (PLE) on arsenic-mediated toxicity in experimental mice. Male Swiss albino mice were divided into three different groups (n=6/group). 'Control' mice received arsenic free water together with normal feed. Mice in the remaining two groups designated 'SA' and 'SA+PLE' were exposed to sodium arsenite (SA, 10 µg/g body weight/day) through drinking water in addition to receiving normal feed and PLE-supplemented feed, respectively. The weight gain of SA-exposed mice was decreased compared with the controls; however, this decrease in body weight gain was prevented when the feed was supplemented with PLE. A secondary effect of arsenic was enlargement of the liver, kidney and spleen of SA-group mice. Deposition of arsenic in those organs was demonstrated by ICP-MS. When PLE was supplemented in the feed the enlargement of the organs was minimized; however, the deposition of arsenic was not significantly reduced. These results indicated that PLE may not block arsenic deposition in tissue directly but rather may play a protective role to reduce arsenic-induced toxicity. Therefore, co-administration of PLE in arsenic-exposed animals might have a future therapeutic application for protecting against arsenic-mediated toxicity.

Hydrogeochemical characteristics, stable isotopes, positive matrix factorization, source apportionment, and health risk of high fluoride groundwater in semiarid region.

Chronic exposure to high fluoride (F-) levels in groundwater causes community fluorosis and non-carcinogenic health concerns in local people. This study described occurrence, dental fluorosis, and origin of high F-groundwater using δ2H and δ18O isotopes at semiarid Gilgit, Pakistan. Therefore, groundwater (n = 85) was collected and analyzed for F- concentrations using ion-chromatography. The lowest F- concentration was 0.4 mg/L and the highest 6.8 mg/L. F- enrichment is linked with higher pH, NaHCO3, NaCl, δ18O, Na+, HCO3-, and depleted Ca+2 aquifers. The depleted δ2H and δ18O values indicated precipitation and higher values represented the evaporation effect. Thermodynamic considerations of fluorite minerals showed undersaturation, revealing that other F-bearing minerals viz. biotite and muscovite were essential in F- enrichment in groundwater. Positive matrix factorization (PMF) and principal component analysis multilinear regression (PCAMLR) models were used to determine four-factor solutions for groundwater contamination. The PMF model results were accurate and reliable compared with those of the PCAMLR model, which compiled the overlapping results. Therefore, 28.3% exceeded the WHO permissible limit of 1.5 mg/L F-. Photomicrographs of granite rocks showed enriched F-bearing minerals that trigger F- in groundwater. The community fluorosis index values were recorded at > 0.6, revealing community fluorosis and unsuitability of groundwater for drinking.

Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan.

The objective of this study was to characterize a novel circulating recombinant form of human immunodeficiency virus type 1 (HIV-1) among people living with HIV in Karachi, Pakistan. We conducted near-full-length genome (NFLG) sequencing on eight samples exhibiting D/G recombination signals in the pol gene region. We successfully obtained NFLG sequences (790-9,614; with reference to the HXB2 genome) from four of the eight samples and then conducted phylogenetic and recombination analyses on them. The four NFLG sequences from our study and one DG unique recombinant form previously identified in the United Kingdom (GenBank accession: MF109700) formed a distinct monophyletic cluster with an Shimodaira-Hasegawa approximate likelihood ratio test node support value of 100%. Bootscan analyses of the five NFLG sequences of DG recombinants showed that all five NFLGs shared the same unique mosaic pattern of recombination breakpoints between D and G clades, with two D fragments in the pol and vif regions inserted into a G backbone. Subregion phylogenetic analyses confirmed these sequences to be a novel circulating recombinant form (CRF) composed of subtypes D and G. The DG recombinant sequences were eventually designated as CRF152_DG by the Los Alamos HIV Sequence Database staff. IMPORTANCE: In Pakistan, the genetic diversity of human immunodeficiency virus type 1 (HIV-1) is becoming increasingly complex, compared to the early years of the epidemic that started after the detection of the first cases of HIV-1 in 1987 in Karachi. Based on the available molecular studies, two dominant HIV-1 clades, sub-subtype A1 and CRF02_AG, have been found to co-circulate with other clades, namely B, C, D, G, CRF01_AE, CRF35_A1D, and CRF56_cpx, in various urban areas of Pakistan. Several novel recombinant forms have also been detected. This first report of CRF152_DG highlights the complex nature of the HIV epidemic in Pakistan and emphasizes the importance of continual molecular surveillance (ideally based on whole-genome sequences) of HIV.

Integrated Approach to Hydrogeochemical Assessment of Groundwater Quality in Major Industrial Zone of Punjab, Pakistan.

Groundwater contamination with arsenic (As) is a significant concern in Pakistan's Punjab Province. This study analyzed 69 groundwater samples from Faisalabad, Gujranwala, Lahore, and Multan to understand hydrogeochemistry, health impacts, contamination sources, and drinking suitability. Results revealed varying as concentrations across districts, with distinctive cation and anion orders. Faisalabad exhibited Na+ > Mg2+ > Ca2+ > K+ > Fe2+ for cations and SO42- > Cl- > HCO3- > NO3- > F- for anions. Gujranwala showed Na+ > Ca2+ > Mg2+ > K+ for cations and HCO3- > SO42- > Cl- > NO3- > F- for anions. In Lahore, demonstrated: Na+ > Ca2+ > Mg2+ > Fe > K+ for cations and HCO3- > SO42- > Cl- > NO3- > F- for anions. Multan indicated K+ > Ca2+ > Mg2+ > Na+ > Fe for cations and HCO3- > SO42- > Cl- > F- > NO3- ) for anions. Hydrochemical facies were identified as CaHCO3 and CaMgCl types. Principal Component Analysis (PCA), highlighted the influence of natural processes and human activities on groundwater pollution. Water Quality Index (WQI) result reveal that most samples met water quality standards. The carcinogenic risk values for children exceeded permissible limits in all districts, emphasizing a significant cancer risk. The study highlights the need for rigorous monitoring to mitigate (As) contamination and protect public health from associated hazards.

Human Immunodeficiency Virus Type-1 Genetic Diversity and Drugs Resistance Mutations among People Living with HIV in Karachi, Pakistan.

The human immunodeficiency virus type-1 epidemic in Pakistan has significantly increased over the last two decades. In Karachi, Pakistan, there is a lack of updated information on the complexity of HIV-1 genetic diversity and the burden of drug resistance mutations (DRMs) that can contribute to ART failure and poor treatment outcomes. This study aimed to determine HIV-1 genetic diversity and identify drug-resistance mutations among people living with HIV in Karachi. A total of 364 HIV-positive individuals, with a median age of 36 years, were enrolled in the study. The HIV-1 partial pol gene was successfully sequenced from 268 individuals. The sequences were used to generate phylogenetic trees to determine clade diversity and also to assess the burden of DRMs. Based on the partial pol sequences, 13 distinct HIV-1 subtypes and recombinant forms were identified. Subtype A1 was the most common clade (40%), followed by CRF02_AG (33.2%). Acquired DRMs were found in 30.6% of the ART-experienced patients, of whom 70.7%, 20.7%, and 8.5% were associated with resistance to NNRTIs, NRTIs, and PIs, respectively. Transmitted DRMs were found in 5.6% of the ART-naïve patients, of whom 93% were associated with resistance against NNRTIs and 7% to PIs. The high prevalence of DRMs in ART-experienced patients poses significant challenges to the long-term benefits and sustainability of the ART program. This study emphasizes the importance of continuous HIV molecular epidemiology and drug resistance surveillance to support evidence-based HIV prevention, precise ART, and targeted AIDS care.

Distinct genetic clusters in HIV-1 CRF01_AE-infected patients induced variable degrees of CD4+ T-cell loss.

CRF01_AE strains have been shown to form multiple transmission clusters in China, and some clusters have disparate pathogenicity in Chinese men who have sex with men. This study focused on other CRF01_AE clusters prevalent in heterosexual populations. The CD4+ T-cell counts from both cross-section data in National HIV Molecular Epidemiology Survey and seropositive cohort data were used to evaluate the pathogenicity of the CRF01_AE clusters and other HIV-1 sub-types. Their mechanisms of pathogenicity were evaluated by co-receptor tropisms, predicted by genotyping and confirmed with virus isolate phenotyping, as well as inflammation parameters. Our research elucidated that individuals infected with CRF01_AE clusters 1 and 2 exhibited significantly lower baseline CD4+ T-cell counts and greater CD4+ T-cell loss in cohort follow-up, compared with other HIV-1 sub-types and CRF01_AE clusters. The increased pathogenesis of cluster 1 or 2 was associated with higher CXCR4 tropisms, higher inflammation/immune activation, and increased pyroptosis. The protein structure modeling analysis revealed that the envelope V3 loop of clusters 1 and 2 viruses is favorable for CXCR4 co-receptor usage. Imbedded with the most mutating reverse transcriptase, HIV-1 is one of the most variable viruses. CRF01_AE clusters 1 and 2 have been found to have evolved into more virulent strains in regions with predominant heterosexual infections. The virulent strains increased the pressure for early diagnosis and treatment in HIV patients. To save more lives, HIV-1 surveillance systems should be upgraded from serology and genotyping to phenotyping, which could support precision interventions for those infected by virulent viruses. IMPORTANCE: Retroviruses swiftly adapt, employing error-prone enzymes for genetic and phenotypic evolution, optimizing survival strategies, and enhancing virulence levels. HIV-1 CRF01_AE has persistently undergone adaptive selection, and cluster 1 and 2 infections display lower counts and fast loss of CD4+ T cells than other HIV-1 sub-types and CRF01_AE clusters. Its mechanisms are associated with increased CXCR4 tropism due to an envelope structure change favoring a tropism shift from CCR5 to CXCR4, thereby shaping viral phenotype features and impacting pathogenicity. This underscores the significance of consistently monitoring HIV-1 genetic evolution and phenotypic transfer to see whether selection bias across risk groups alters the delicate balance of transmissible versus toxic trade-offs, since virulent strains such as CRF01_AE clusters 1 and 2 could seriously compromise the efficacy of antiviral treatment. Only through such early warning and diagnostic services can precise antiviral treatments be administered to those infected with more virulent HIV-1 strains.

Arsenic Contamination, Water Toxicity, Source Apportionment, and Potential Health Risk in Groundwater of Jhelum Basin, Punjab, Pakistan.

Potable groundwater (GW) contamination through arsenic (As) is a commonly reported environmental issue in Pakistan. In order to examine the groundwater quality for As contamination, its geochemical behavior, and other physicochemical parameters, 69 samples from various groundwater sources were collected from the mining area of Pind Dadan Khan, Punjab, Pakistan. The results showed the concentration of elevated As, its source of mobilization, and linked public health risk. Arsenic detected in the groundwater samples varied from 0.5 to 100 µg/L, with an average value of 21.38 µg/L. Forty-two samples were beyond the acceptable limit of 10 µg/L of the WHO for drinking purposes. The statistical summary showed that the groundwater cation concentration was in decreasing order such as Na+ > Ca2+ > Mg2+ > K+, while anions were as follows: HCO3- > SO42- > Cl- > NO3-. Hydrochemical facies results depicted that groundwater samples belong to CaHCO3 type. Rock-water interactions control the hydrochemistry of groundwater. Saturation indices' results indicated the saturation of the groundwater sources for CO3 minerals due to their positive SI values. Such minerals include aragonite, calcite, dolomite, and fluorite. The principal component analysis (PCA) findings possess a total variability of 77.36% suggesting the anthropogenic and geogenic contributing sources of contaminant. The results of the Exposure-health-risk-assessment model for measuring As reveal significant potential carcinogenic risk exceeding the threshold level (value > 10-4) and HQ level (value > 1.0).

HIV-1 Disease Progression and Drug Resistance Mutations among Children on First-Line Antiretroviral Therapy in Ethiopia.

Background: High rates of disease progression and HIV drug resistance (HIVDR) among adults taking highly active antiretroviral treatment (HAART) in Sub-Saharan Africa were previously documented. However, children were generally not considered despite their greater risk. Hence, this study was aimed to evaluate HIV-1 disease progression and drug resistance mutation among children on first-line antiretroviral therapy in Ethiopia. Method: A longitudinal study was conducted among 551 HIV-positive children (<15 years old) recruited between 2017 and 2019 at 40 antiretroviral treatment delivery sites in Ethiopia. Disease progression was retrospectively measured over a 12-year (2007-2019) follow-up as the progress towards immunosuppression. Two consecutive viral load (VL) tests were conducted in 6-month intervals to assess virologic failure (VF). For children with VF, HIV-1 genotyping and sequencing was performed for the pol gene region using in-house assay validated at the Chinese Center for Disease Control and Prevention, and the Stanford HIVDB v9.0 algorithm was used for identification of drug resistance mutations. The Kaplan-Meier analysis and Cox proportional hazards regression model were used to estimate the rate and predictors of disease progression, respectively. Results: The disease progression rate was 6.3 per 100 person-years-observation (95% CI = 4.21-8.53). Overall immunosuppression (CD4 count < 200 cells/mm3) during the 12-year follow-up was 11.3% (95% CI = 7.5-15.1). Immunosuppression was significantly increased as of the mean duration of 10.5 (95% CI = 10.1-10.8) years (38.2%) to 67.8% at 12 years (p < 0.001). Overall, 14.5% had resistance to at least one drug, and 6.2% had multi-drug resistance. A resistance of 67.8% was observed among children with VF. Resistance to non-nucleotide reverse transcriptase inhibitors (NNRTI) and nucleotide reverse transcriptase inhibitors (NRTI) drugs were 11.4% and 10.1%, respectively. Mutations responsible for NRTI resistance were M184V (30.1%), K65R (12.1%), and D67N (5.6%). Moreover, NNRTI-associated mutations were K103N (14.8%), Y181C (11.8%), and G190A (7.7%). Children who had a history of opportunistic infection [AHR (95% CI) = 3.4 (1.8-6.2)], vitamin D < 20 ng/mL [AHR (95% CI) = 4.5 (2.1-9.9)], drug resistance [AHR (95% CI) = 2.2 (1.4-3.6)], and VF [AHR (95% CI) = 2.82 (1.21, 3.53)] had a higher hazard of disease progression; whereas, being orphan [AOR (95% CI) = 1.8 (1.2-3.1)], history of drug substitution [(AOR (95% CI) = 4.8 (2.1-6.5), hemoglobin < 12 mg/dL [AOR (95% CI) = 1.2 (1.1-2.1)] had higher odds of developing drug resistance. Conclusions: Immunosuppression was increasing over time and drug resistance was also substantially high. Enhancing routine monitoring of viral load and HIVDR and providing a vitamin-D supplement during clinical management could help improve the immunologic outcome. Limiting HAART substitution is also crucial for children taking HAART in Ethiopia.

Characterization of HIV-1 CRF02_AG/A3/G unique recombinant forms identified among children in Larkana, Pakistan.

Co-circulation of different human immunodeficiency virus type 1 HIV-1 subtypes among infected populations can lead to the generation of new recombinants. In Pakistan, subtype A1 and CRF02_AG are the dominant strains circulating among key populations. The high prevalence of new HIV infections among the key populations highlights the possibility of recombination between the dominant strains, which can lead to the generation of new recombinants. Here, we identified a recombinant cluster composed of CRF02_AG, sub-subtype A3, and subtype G among HIV-infected children in Larkana. For the study, 10 retrospectively collected samples, with recombination signals in the pol gene, were used to perform a near full-length genome NFLG sequencing. Of the 10 samples, NFLG was successfully sequenced from seven samples. Phylogenetic analysis of the seven NFLGs showed that all recombinants formed a distinct monophyletic cluster and were distinct from known HIV-1 circulating recombinant forms CRFs. Recombination analyses showed that all seven NFLGs shared a similar recombinant structure consisting of CRF02_AG, sub-subtype A3, and subtype G, with a sub-subtype A3 fragment inserted into pol and vif regions spanning from (HXB2: 4218-5518), and a subtype G fragment inserted into vpu, rev, tat and env regions spanning from (HXB2: 5957-8250) of the CRF02_AG backbone. The identification of unique recombinant forms may indicate the presence and transmission of several co-circulating lineages in Larkana, giving rise to newer CRFs. This study also highlights the importance of continuous molecular surveillance to fully understand HIV-1 genetic diversity in Pakistan, particularly in Larkana, which is the epicenter of HIV outbreaks.

The spectrum of opportunistic infections and malignancies among women on antiretroviral therapy in Ethiopia.

ABBREVIATIONS: AIDS: acquired immune deficiency syndrome; CI: confidence interval; EPHI: Ethiopian Public Health Institute; HAART: highly active antiretroviral therapy; HIV: human immunodeficiency virus; HR: hazard ratio; Mg/dl: milligram per deciliter; TB: tuberculosis; PCP: pneumocystis carinii pneumonia; ZJU: Zhejiang University.

Geochemical control, water quality indexing, source distribution, and potential health risk of fluoride and arsenic in groundwater: Occurrence, sources apportionment, and positive matrix factorization model.

Fluoride (F-), and arsenic (As) in the groundwater cause health problems in developing countries, including Pakistan. We evaluated the occurrence, distribution, sources apportionment, and health hazards of F-, and As in the groundwater of Mardan, Pakistan. Therefore, groundwater samples (n = 130) were collected and then analyzed for F-, and As by ion-chromatography (IC) and Inductively-coupled plasma mass-spectrometry (ICP-MS). The F-, and As concentrations in groundwater were 0.7-14.4 mg/L and 0.5-11.2 µg/L. Relatively elevated F-, and As coexists with higher pH, Na+, HCO3-, SO4-2, and depleted Ca+2 due to fluoride, sulfide-bearing minerals, and anthropogenic inputs. Both F-, and/or As are transported in subsurface water through adsorption and desorption processes. Groundwater samples 45%, and 14.2% exceeded the WHO guidelines of 1.5 mg/L and 10 µg/L. Water quality indexing (WQI-model) declared that 35.7% samples are unfit for household purposes. Saturation and undersaturation of minerals showed precipitation and mineral dissolution. Groundwater contamination by PCA-MLR and PMF-model interpreted five factors. The fitting results and R2 values of PMF (0.52-0.99)>PCA-MLR (0.50-0.95) showed high accuracy of PMF-model. Human health risk assessment (HHRA-model) revealed high non-carcinogenic and carcinogenic risk for children than adults. The percentile recovery of F- and As was recorded 98%, and 95% with reproducibility ± 5% error.

Universal HIV testing and the impact of late diagnosis on disease stage among adults in urban Ethiopia.

BACKGROUND: Treatment as prevention evolved into the universal HIV test-and-treat (UTT) strategy, which entails testing to the general population and treatment to every people living with HIV. We investigated universal testing (UT) performance and its determinants in urban Ethiopia and explore magnitude of late diagnosis and its impact on disease stages. METHOD: We used data from the Ethiopia Population Based HIV Impact assessment (EPHIA), conducted in 2017/2018 which was a cross-sectional and household-based study. For current analysis, we considered self-report first diagnosis to estimate universal testing irrespective of their serostatus and also consider HIV LAg avidity vs viral load vs plasma antiretroviral drug level algorithm to categorize the late diagnosis. We finally evaluate disease stages using CD4 count and viral load. A 2-level multilevel mixed-effect logistic regression model was employed. The effects of individual-level predictors were quantified by the estimates from the fixed-effect part of the model with p-value < 0.05. RESULT: Data were collected from 18,926 adults among those 29.4% of people living in Urban Ethiopia were never tested for HIV. Never tested females was 26.4% (95% CI = 25.3; 27.5). Never tested among divorced and widowed were 19.4% (95% CI: 17.3; 21.8) and 28.3% (95% CI: 24.6; 32.2), respectively. Never tested among elderly and youth were high (28.3% among 45-54 years old) to (41.2% among 55-64 years old) to 47.8% among 15-24 years old. Overall, late HIV diagnosis among adults in urban Ethiopia was 25.9% (95% CI: 21.7, 30.2). Late diagnosis varies by region ranged from 38.1% in the Gambella to 5.8% in Benishangul Gumuz. Advanced immune suppression (CD4 count < 350 cells/µl) among newly diagnosed long-term infection were significantly higher compared to those who were recently infected which accounted 47.8% (95%CI = 33.2-52.1) and 30.9% (95%CI = 21.3-32.2), respectively. Moreover, Viral load suppression were significantly lower among those who were late diagnosed 26.1% (95%CI = 13.6-33.8) compared to those of newly infected 89.6% (95%CI = 76.2; 93.4). CONCLUSION: With the aim of UT for high risk and priority population, the low rate of HIV testing among widowed, elderly, young adolescent and women in urban Ethiopia calls for enhanced HIV testing. Moreover, the low HIV testing and high late diagnosis among the high-burden regions calls for region-specific intervention. Advanced disease stages as a result of the high proportion of late diagnosis may impact on fueling community transmission and hinder treatment outcome among PLHIV.