Shift in SARS-CoV-2 variants of concern from Delta to Omicron was associated with reduced hospitalizations, increased risk of breakthrough infections but lesser disease severity.

BACKGROUND: COVID-19 epidemiology changed with the emergence of SARS-CoV-2 variants of concern (VOC). Pakistan administered mostly inactivated vaccines. We investigated the association between VOC and breakthrough infections in a mixed-vaccination-status population of Karachi. METHODS: We investigated SARS-CoV-2 VOC tested in 392 respiratory specimens collected between May and December 2021. Data for age, sex, hospital admission, vaccinations, together with CT values of the diagnostic PCR test were analyzed. RESULTS: The median age of COVID-19 cases tested was 40 (27-57) years and 43.4% were female. Delta variants were most common (56.4%) followed by Alpha (15.9%), Omicron (12.2%), Beta/Gamma (11.3%), and others (4.3%). Eighteen percent of cases were hospitalized whereby, predominant VOC were Beta/Gamma (40.8%), Alpha (35.2%) and Delta (22.5%). Overall, 55.4% of individuals were fully vaccinated, 7.4% were partially vaccinated and 37.2% were unvaccinated. Most (74.6%) inpatients were unvaccinated. Vaccines comprised inactivated (85.34%), single-shot vector (8.62%), two-shot vector (3.02%) and mRNA (3.02%) types. Omicron variants showed lower viral loads as compared to Alpha, Beta/Gamma, and Delta (p = 0.017). The risk of infection with Delta and Omicron variants was higher, 8 weeks after vaccination. The majority of those with breakthrough infections after receiving inactivated vaccines acquired COVID-19 within 4 months of vaccination. CONCLUSION: Our data highlights the shifting of VOC from Delta to Omicron during 2021 and that COVID-19 vaccinations reduced both hospitalizations and viral transmission. It informs on the increased risk of breakthrough infection within 8 weeks of vaccination, indicating the need for booster vaccinations.

Wood ash application for crop production, amelioration of soil acidity and contaminated environments.

Agriculture is vital to human life and economic development even though it may have a detrimental influence on soil quality. Agricultural activities can deteriorate the soil quality, endangers the ecosystem health and functioning, food safety, and human health. To resolve the problem of soil degradation, alternative soil conditioners such as wood ash are being explored for their potential to improve soil-plant systems. This study provides an overview of the production, properties, and effects of wood ash on soil properties, crop productivity, and environmental remediation. A comprehensive search of relevant databases was conducted in order to locate and assess original research publications on the use of wood ash in agricultural and environmental management. According to the findings, wood ash, a byproduct of burning wood, may improve the structure, water-holding capacity, nutrient availability, and buffering capacity of soil as well as other physico-chemical, and biological attributes of soil. Wood ash has also been shown to increase agricultural crop yields and help with the remediation of polluted regions. Wood ash treatment, however, has been linked to several adverse effects, such as increased trace element concentrations and altered microbial activity. The examination found that wood ash could be a promising material to be used as soil conditioner and an alternative supply of nutrients for agricultural soils, while, wood ash contributes to soil improvement and environmental remediation, highlighting its potential as a sustainable solution for addressing soil degradation and promoting environmental sustainability in agricultural systems.

Pb uptake, accumulation, and translocation in plants: Plant physiological, biochemical, and molecular response: A review.

Lead (Pb) is a highly toxic contaminant that is ubiquitously present in the ecosystem and poses severe environmental issues, including hazards to soil-plant systems. This review focuses on the uptake, accumulation, and translocation of Pb metallic ions and their toxicological effects on plant morpho-physiological and biochemical attributes. We highlight that the uptake of Pb metal is controlled by cation exchange capacity, pH, size of soil particles, root nature, and other physio-chemical limitations. Pb toxicity obstructs seed germination, root/shoot length, plant growth, and final crop-yield. Pb disrupts the nutrient uptake through roots, alters plasma membrane permeability, and disturbs chloroplast ultrastructure that triggers changes in respiration as well as transpiration activities, creates the reactive oxygen species (ROS), and activates some enzymatic and non-enzymatic antioxidants. Pb also impairs photosynthesis, disrupts water balance and mineral nutrients, changes hormonal status, and alters membrane structure and permeability. This review provides consolidated information concentrating on the current studies associated with Pb-induced oxidative stress and toxic conditions in various plants, highlighting the roles of different antioxidants in plants mitigating Pb-stress. Additionally, we discussed detoxification and tolerance responses in plants by regulating different gene expressions, protein, and glutathione metabolisms to resist Pb-induced phytotoxicity. Overall, various approaches to tackle Pb toxicity have been addressed; the phytoremediation techniques and biochar amendments are economical and eco-friendly remedies for improving Pb-contaminated soils.

Pseudomonas fluorescens and L-tryptophan application triggered the phytoremediation potential of sunflower (Heliantus annuus L.) in lead-contaminated soil.

Lead, a toxic heavy metal present in soil, hampers biological activities and affects the metabolism of plants, animals, and human beings. Its higher concentration may disturb the various physio-chemical processes, which result in stunted and poor plant growth. An interactive approach of plant growth promoting rhizobacteria (PGPR) and L-tryptophan can be used to mitigate the lethal effects of lead. A pot experiment was conducted, and two weeks before sowing, the level of lead (300 mg kg-1) was maintained by spiking the PbCl2 salt. Pseudomonas fluorescens and L-tryptophan were applied individually as well as in combination to segregate the effect of both in contaminated soil under a completely Randomized Design (CRD). Statistical analysis revealed that plant growth was significantly reduced up to 22% due to lead contamination. However, the interactive approach of PGPR and L-tryptophan significantly improved the plant growth, physiology, and yield with relative productive index (RPI) under a lead-stressed environment. Moreover, integrated use of PGPR and L-tryptophan demonstrated a considerable increase (22%) in lead removal efficiency (LRE) by improving bioconcentration factor (BCF) and translocation factor (TF) for shoot without increasing the lead concentration in achenes. The reduced lead concentration in achene was due to its immobilization in shoot and root by negatively charged particles and improved the lead sequestration in vegetative parts which abridged the translocation of lead into achenes.

Impact Assessment of Lead-Tolerant Rhizobacteria to Improve Soil Health Using Indian Mustard (Brassica juncea) as an Indicator Plant.

Due to ongoing human activities, heavy metals are heavily accumulated in the soil. This leads to an increase in the discharge and the quick spread of heavy metal pollution in human settlements and natural habitats, having a disastrous effect on agricultural products. The current experiment was planned to evaluate the effect of lead-tolerant-plant-growth-promoting rhizobacteria (LTPGPR) on growth, yield, antioxidant activities, physiology, and lead uptake in the root, shoot, and seed of Indian mustard (Brassica juncea) in lead-amended soil. Three pre-isolated well-characterized lead-tolerant rhizobacterial strains-S10, S5, and S2-were used to inoculate seeds of Indian mustard grown at three different levels of lead (300 mg kg-1, 600 mg kg-1, 900 mg kg-1) contaminated soil. The experiment was designed following a completely randomized design (CRD) under factorial arrangements. Lead nitrate was used as a source of lead contamination. At harvesting, data regarding growth, physiology, yield per plant, antioxidant activities, malondialdehyde and proline content, and lead uptake in the root, shoot, and seed of Indian mustard were recorded. Results demonstrated that lead contamination at all levels significantly reduced the plant growth, yield, and physiological processes. Plants inoculated with lead-tolerant rhizobacteria showed a significant improvement in plant growth, yield, antioxidant activities, and physiological attributes and cause a valuable reduction in the malondialdehyde contents of Indian mustard in lead-contaminated soil. Moreover, plants inoculated with lead-tolerant rhizobacteria also showed an increment in lead uptake in the vegetative parts and a significant reduction of lead contents in the seed of Indian mustard.

A Rare Occurrence of Ectopic Parathyroid Carcinoma Presenting as a Case of Recurrent Fractures.

Ectopic parathyroid tumors are uncommon, accounting for only 6% of parathyroid adenomas, and even fewer cases are attributed to parathyroid carcinomas. While ectopic parathyroid carcinoma in the anterior mediastinum is a rare condition, the occurrence of recurrent skeletal fractures in the presence of mild hypercalcemia is even rarer. In this report, we present the case of a 52-year-old man with a medical history of hypertension, chronic kidney disease, and a previous right-sided intertrochanteric fracture of the femur one year earlier. He presented to the emergency room with left-sided hip pain and shortness of breath due to volume overload. Laboratory tests revealed mild hypercalcemia and hyperparathyroidism, with normal vitamin D levels. An X-ray showed a left neck of femur fracture. Further evaluation with a three-phase skeletal scintigraphy indicated the presence of metabolic bone disease. A contrast-enhanced computed tomography of the chest revealed a solitary soft tissue nodule in the anterior mediastinum, representing an ectopic parathyroid adenoma. The lesion was successfully removed using video-assisted thoracic surgery, and the histopathological analysis confirmed the diagnosis of parathyroid carcinoma. The combination of mild hypercalcemia and recurrent fractures is an unusual presentation of ectopic parathyroid carcinoma, underscoring the importance of considering this condition as a potential cause in similar cases to ensure timely and appropriate treatment.

COVID-19 encephalopathy: an unusual presentation with new-onset seizure causing convulsive status epilepticus.

Although neurological manifestations such as headache and myalgias have been observed with COVID-19, presentation with more serious neurological illness is uncommon and rare. We report a case of a middle-aged woman who presented to the emergency department of a tertiary care hospital. Her clinical presentation was primarily neurological rather than the more common presentation with respiratory manifestations. She presented with generalised tonic-clonic seizures, along with history of undocumented low-grade fever and generalised body aches. The positive SARS-CoV-2 RT-PCR nasal swab, the cerebrospinal fluid analysis (lymphocytic pleocytosis) and electroencephalogram were consistent with viral encephalitis; brain imaging was unremarkable. This case highlights the variable presenting features of COVID-19 infection as patients can primarily present with neurological manifestations in the absence of significant respiratory symptoms. We believe it is important to recognise neurological disease associated with SARS-CoV-2 in patients with asymptomatic respiratory infection.

Low performance of internal medicine senior residents in in-service examinations.

We observed an unprecedented and consistent low performance of senior residents as compared with juniors in monthly examinations. This compelled us to evaluate systematically and compare the scores of senior residents with their junior colleagues. This retrospective observational study was conducted in April 2020 among internal medicine residents. Residents in first and second year of their training were labelled as junior residents. Residents in third or fourth year of their training were labelled as senior residents. Comparison of mean scores of each resident level was done separately both for monthly formative multiple-choice questions tests, and summative yearly end of term examinations. We discussed the possible reasons as well. There were 67 residents in year 2018 and 69 in 2019. There is no significant difference between scores of monthly examinations of years 2018 and 2019 among residents of each level. Rather, in March and December 2018, junior residents perform better than senior residents with p values of 0.01 and 0.04, respectively. In February and September 2019, senior residents performed better than junior residents with p value of 0.02. Similarly, there is no significant difference in scores of residents of each level in end-of-term examinations of years 2018 and 2019 with p values 0.18 and 0.25, respectively. Performance of senior residents in our residency programme in in-service examinations is relatively low as compared with their junior colleagues. There is a need to evaluate reasons for this relatively low performance of senior residents.

Frequency and risk factors of non-alcoholic fatty liver disease in Helicobacter pylori-infected dyspeptic patients: A cross-sectional study.

BACKGROUND: In dyspeptic patients with Helicobacter pylori contributes to non-alcoholic fatty liver disease. However, little evidence available from Pakistan. OBJECTIVE: The study aims to determine the frequency and risk factors of non-alcoholic fatty liver disease in dyspeptic patients with Helicobacter pylori. METHODS: This cross-sectional study was conducted between 22 November 2016 and 30 June 2018. Adults of age between 18 and 90 years who attended the out-patient department due to abdominal discomfort, pain, fullness, and bloating who underwent upper gastrointestinal tract endoscopy were enrolled after taking informed consent. Patients with celiac disease, inflammatory bowel disease, taking alcohol, pregnant women and lactating mothers, known cases of hepatitis B and C, and history of recent antibiotic use were excluded. Data on age, gender, smoking, alcohol use, dyslipidemia, hypertension, type 2 diabetes mellitus, and ischemic heart disease were collected. Non-alcoholic fatty liver disease was diagnosed through ultrasonography. Helicobacter pylori infection was detected using a carbon urea breath test. RESULTS: A total of 698 patients were screened for eligibility, and 399 (57.2%) had Helicobacter pylori infection and were enrolled in the study after consent. The median age was 50.1 (interquartile range = 14.5) years and 209 (52.4%) were males. Frequency of non-alcoholic fatty liver disease in patients with Helicobacter pylori dyspeptic patients was 153 (38.3%). Factors associated with non-alcoholic fatty liver disease in the presence of Helicobacter pylori were dyslipidemia 7.38 (95% confidence interval = 2.4-22.71), type 2 diabetes mellitus 5.96 (95% confidence interval = 1.86-19.07), hypertension 3.0 (95% confidence interval = 1.21-7.45), and moderate gastritis 2.81 (95% confidence interval = 1.2-6.59). CONCLUSION: The frequency of non-alcoholic fatty liver disease in Helicobacter Pylori dyspeptic patients was 38.3%. Male gender, dyslipidemia, hypertension, ischemic heart disease, and moderate gastritis were associated with non-alcoholic fatty liver disease.

Acuity level of care as a predictor of case fatality and prolonged hospital stay in patients with COVID-19: a hospital-based observational follow-up study from Pakistan.

OBJECTIVES: To determine if there is an association between acuity level of care (ALC), case fatality and length of stay in patients admitted to hospital due to COVID-19. DESIGN: A hospital-based observational follow-up study. SETTING: Internal Medicine Service of the Aga Khan University Hospital, Pakistan, from 26 February 2020 to 30 June 2020. PARTICIPANTS: Adult patients with confirmed COVID-19, aged ≥18 years. METHODS: ALC was categorised into low, intermediate and high level and patients were triaged using the standard emergency severity illness score. All patients were followed until the end of hospital admission for the outcome of case fatality and length of stay. RESULTS: A total of 822 patients with COVID-19 were admitted during the study period and 699 met inclusion criteria. The mean age was 54.5 years and 67% were males; 50.4% were triaged to low, 42.5% to intermediate and 7.2% to high acuity care. The overall case-fatality rate was 11.6%, with the highest (52%) in high acuity level followed by 16.2% in intermediate and 2% in low acuity care. Acuity level was associated with case fatality, with an HR (95% CI) of 5.0 (2.0 to 12.1) for high versus low acuity care and an HR of 2.7 (1.2, 6.4) for intermediate versus low acuity care, after adjusting for age, sex and common comorbidities including diabetes, hypertension, ischaemic heart disease and chronic lung disease. Similarly, acuity level was also associated with length of hospital stay. CONCLUSION: High and intermediate acuity level is associated with higher case fatality rate and prolonged length of hospital stay in patients admitted with COVID-19. In resource-limited settings where the provision of high acuity care is limited, the intermediate care acuity could serve as a useful strategy to treat relatively less critical patients with COVID-19.

Comparative growth analysis of okra (Abelmoschus esculentus) in the presence of PGPR and press mud in chromium contaminated soil.

Chromium is a toxic heavy metal. Plants, animals and human metabolic processes are disturbed due to higher levels of chromium. PGPR are involved in seed germination, growth improvement, metabolic process and in most of the physiological processes of plants. Press mud in soil provides substrate to the microbes. PGPR can convert the more toxic form of Cr (VI) into less toxic form Cr (III). This study was conducted to find out the reduction potential of pre-isolated rhizobacteria and their role in strengthening of plant growth and physiological attributes. Soil collected from the research area was spiked with 20 mg kg-1 of Cr (VI) by using potassium dichromate (K2Cr2O7) salt before sowing. Results revealed that Cr (VI) significantly suppressed the shoot length, root length and photosynthetic rate of okra up to 19, 37 and 31%, respectively. However, inoculation decreases the uptake of Cr (VI) in root and shoot up to 37 and 31% and by press mud 33 and 20%, respectively. Combined application of inoculation and press mud significantly recovered the negative impact of chromium and plant growth was almost at par compared with contaminated treatment without inoculation.