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.

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.

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.

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.

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.

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.

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.

Integrated approach to hydrogeochemical appraisal of groundwater quality concerning arsenic contamination and its suitability analysis for drinking purposes using water quality index.

Arsenic (As), contamination in drinking groundwater resources is commonly environmental problem in many developing countries including Pakistan, with significant human health risk reports. In order to examine the groundwater quality concerning As contamination, its geochemical behavior along with physicochemical parameters, 42 samples were collected from community tube wells from District Bahawalpur, Punjab, Pakistan. The results showed the concentration of elevated As, its source of mobilization, and associated public health risk. The As concentration detected in groundwater samples varied from 0.12 to 104 µg/L with an average value of 34.7 µg/L. Among 42 groundwater samples, 27 samples were beyond the permitted limit of 10 µg/L recommended by World Health Organization (WHO), for drinking purposes. Statistical analysis result show that the groundwater cations values are in decreasing order such as: Na+ > Mg2+ > Ca2+ > K+, while anions were HCO3- > SO42- > Cl- > NO3-. Hydrochemical facies result depict that the groundwater samples of the study area, 14 samples belong to CaHCO3 type, 5 samples belong to NaCl type, 20 samples belong to Mixed CaMgCl type, and 3 samples belong to CaCl2 type. It can be accredited due to weathering and recharge mechanism, evaporation processes, and reverse ion exchange. Gibbs diagram shows that rock water interaction controls the hydrochemistry of groundwater resources of the study area. Saturation Index (SI) result indicated the saturation of calcite, dolomite, gypsum, geothite, and hematite mineral due their positive SI values. The principal component analysis (PCA) results possess a total variability of 80.69% signifying the anthropogenic and geogenic source of contamination. The results of the exposure-health-risk-assessment method for measuring As reveal significant potential non-carcinogenic risk (HQ), exceeding the threshold level of (> 1) for children in the study area. Water quality assessment results shows that 24 samples were not suitable for drinking purposes.

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.

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.

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.

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.

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.

Groundwater Quality, Health Risk Assessment, and Source Distribution of Heavy Metals Contamination around Chromite Mines: Application of GIS, Sustainable Groundwater Management, Geostatistics, PCAMLR, and PMF Receptor Model.

Groundwater contamination by heavy metals (HMs) released by weathering and mineral dissolution of granite, gneisses, ultramafic, and basaltic rock composition causes human health concerns worldwide. This paper evaluated the heavy metals (HMs) concentrations and physicochemical variables of groundwater around enriched chromite mines of Malakand, Pakistan, with particular emphasis on water quality, hydro-geochemistry, spatial distribution, geochemical speciation, and human health impacts. To better understand the groundwater hydrogeochemical profile and HMs enrichment, groundwater samples were collected from the mining region (n = 35), non-mining region (n = 20), and chromite mines water (n = 5) and then analyzed using ICPMS (Agilent 7500 ICPMS). The ranges of concentrations in the mining, non-mining, and chromite mines water were 0.02-4.5, 0.02-2.3, and 5.8-6.0 mg/L for CR, 0.4-3.8, 0.05-3.6, and 3.2-5.8 mg/L for Ni, and 0.05-0.8, 0.05-0.8, and 0.6-1.2 mg/L for Mn. Geochemical speciation of groundwater variables such as OH-, H+, Cr+2, Cr+3, Cr+6, Ni+2, Mn+2, and Mn+3 was assessed by atomic fluorescence spectrometry (AFS). Geochemical speciation determined the mobilization, reactivity, and toxicity of HMs in complex groundwater systems. Groundwater facies showed 45% CaHCO3, 30% NaHCO3, 23.4% NaCl, and 1.6% Ca-Mg-Cl water types. The noncarcinogenic and carcinogenic risk of HMs outlined via hazard quotient (HQ) and total hazard indices (THI) showed the following order: Ni > Cr > Mn. Thus, the HHRA model suggested that children are more vulnerable to HMs toxicity than adults. Hierarchical agglomerative cluster analysis (HACA) showed three distinct clusters, namely the least, moderately, and severely polluted clusters, which determined the severity of HMs contamination to be 66.67% overall. The PCAMLR and PMF receptor model suggested geogenic (minerals prospects), anthropogenic (industrial waste and chromite mining practices), and mixed (geogenic and anthropogenic) sources for groundwater contamination. The mineral phases of groundwater suggested saturation and undersaturation. Nemerow's pollution index (NPI) values determined the unsuitability of groundwater for domestic purposes. The EC, turbidity, PO4-3, Na+, Mg+2, Ca+2, Cr, Ni, and Mn exceeded the guidelines suggested by the World Health Organization (WHO). The HMs contamination and carcinogenic and non-carcinogenic health impacts of HMs showed that the groundwater is extremely unfit for drinking, agriculture, and domestic demands. Therefore, groundwater wells around the mining region need remedial measures. Thus, to overcome the enrichment of HMs in groundwater sources, sustainable management plans are needed to reduce health risks and ensure health safety.

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.

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).

Survival and Predictors of Mortality among Adults Initiating Highly Active Antiretroviral Therapy in Ethiopia: A Retrospective Cohort Study (2007-2019).

Background: Studies have shown high early mortality after initiation of highly active antiretroviral therapy (HAART). We examined change in three-year survival and predictors of mortality of patients initiating HAART in Ethiopia since 2007 to 2019. Methods: A retrospective cohort study was conducted in 47 health facilities (HFs) using records of 11,013 adult patients initiating HAART from 2007 to 2019. Study subjects were stratified as four different cohorts based on their calendar year of HAART initiation: 2007-2010, 2011-2013, 2014-2016, and 2017-2019. HFs were selected using probability proportional to size of patients. Survival rate and predictors of mortality were estimated by the calendar year using the Kaplan-Meier and Cox proportional hazard, respectively. We generated a pooled estimate of survival rate and predicators of mortality. Results: Data from 1881, 3868, 3004, and 2260 patients were retrieved from each of the cohorts. Overall mortality for all cohorts at all times was 10.3%. A gradual decline of mortality was observed in the first three years of follow-up since 2007-2016 which were 21.37%, 10.03%, and 4.34% among patients who initiated HAART in 2007, 2011, and 2014 respectively. A mortality jump of 9.25% was observed among patents initiating HAART in 2017, which coincided with political instability happened in the country. Of the 21,638 person-years of follow-up among 11,013 adults, mortality was 5.23/100 person-years, while disaggregated by the cohorts, it was 14.77, 5.06, 2.12, and 4.17 per 100 person-years, respectively. Among all the cohorts, patients with CD4 count of ≤200 cells/mm3, unsuppressed viral load, poor adherence, and drug resistance in all cohorts, respectively, have overall 2.0 (95%CI = 1.35 - 2.69), 4.66 (95%CI = 2.53 - 6.72), 6.78 (95%CI = 3.4 - 10.3), and 10.02 (95%CI = 6.91 - 13.82) times of mortality risk than those without. Patients with bedridden for cohort initiating HAART during 2007 and 2011 were 2.0 (95%CI = 1.35 - 2.69) times of mortality risk than those without. Conclusion: Patients initiating HAART from 2007 to 2016 have continuously improved their survival during three-year cohort follow-up in Ethiopia. The significant decline of survival among those who initiate HAART as of 2017 calls for program intervention. Low CD4 counts, unsuppressed viral load, poor adherence, and drug resistance could be used as predictors for increased mortality to monitor the quality of HAART and improve clinical management of HIV/AIDS patients.

Unique profile of predominant CCR5-tropic in CRF07_BC HIV-1 infections and discovery of an unusual CXCR4-tropic strain.

CRF07_BC is one of the most prevalent HIV-1 strains in China, which contributes over one-third of the virus transmissions in the country. In general, CRF07_BC is associated with slower disease progression, while the underlying mechanisms remain unclear. Our study focused on envelope proteins (Env) and its V3 loop which determine viral binding to co-receptors during infection of cells. We studied a large dataset of 3,937 env sequences in China and found that CRF07_BC had a unique profile of predominantly single CCR5 tropism compared with CCR5 and CXCR4 dual tropisms in other HIV-1 subtypes. The percentages of the CXCR4-tropic virus in B (3.7%) and CRF01_AE (10.4%) infection are much higher than that of CRF07_BC (0.1%), which is supported by median false-positive rates (FPRs) of 69.8%, 25.5%, and 13.4% for CRF07_BC, B, and CRF01_AE respectively, with a cutoff FPR for CXCR4-tropic at 2%. In this study, we identified the first pure CXCR4-tropic virus from one CRF07_BC-infected patient with an extremely low CD4+T cell count (7 cells/mm3). Structural analysis found that the V3 region of this virus has the characteristic 7T and 25R and a substitution of conserved "GPGQ" crown motif for "GPGH". This study provided compelling evidence that CRF07_BC has the ability to evolve into CXCR4 strains. Our study also lay down the groundwork for studies on tropism switch, which were commonly done for other HIV-1 subtypes, for the long-delayed CRF07_BC.