Despite the continued vaccination efforts, there had been a surge in breakthrough infections, and the emergence of the B.1.1.529 omicron variant of SARS-CoV-2 in India. There is a paucity of information globally on the role of newer XBB variants in community transmission. Here, we investigated the mutational patterns among hospitalised patients infected with the XBB omicron sub-variant, and checked if there was any association between the rise in the number of COVID-19 cases and the observed novel mutations in Tamil Nadu, India. Nasopharyngeal and oropharyngeal swabs, collected from symptomatic and asymptomatic COVID-19 patients were subjected to real-time PCR followed by Next Generation Sequencing (NGS) to rule out the ambiguity of mutations in viruses isolated from the patients (n = 98). Using the phylogenetic association, the mutational patterns were used to corroborate clinico-demographic characteristics and disease severity among the patients. Overall, we identified 43 mutations in the S gene across 98 sequences, of which two were novel mutations (A27S and T747I) that have not been reported previously with XBB sub-variants in the available literature. Additionally, the XBB sequences from our cohort had more mutations than omicron B.1.1.529. The phylogenetic analysis comprising six major branches clearly showed convergent evolution of XBB. Our data suggests that age, and underlying conditions (e.g., diabetes, hypertension, and cardiovascular disease) or secondary complications confers increased susceptibility to infection rather than vaccination status or prior exposure. Many vaccinated individuals showed evidence of a breakthrough infection, with XBB.3 being the predominant variant identified in the study population. Our study indicates that the XBB variant is highly evasive from available vaccines and may be more transmissible, and potentially could emerge as the ‘next’ predominant variant, which likely could overwhelm the existing variants of SARS-CoV-2 omicron variants. National Health Mission (India), 10.13039/100004441 SIDA 10.13039/100020422 SARC , VINNMER (Sweden), 10.13039/100016958 ORIP / 10.13039/100000002 NIH (USA).

Chronic kidney disease of unknown cause (CKDu) has been reported in “hotspots” around the world and linked to occupational heat stress, exposure to agrochemicals and environmental toxins. This was a systematic, statewide, population-based, observational study of agricultural workers in Tamil Nadu, to estimate the prevalence of chronic kidney disease (CKD) and CKDu. The state of Tamil Nadu was divided into five agroclimatic zones and stratified multi-stage cluster sampling was performed to select a representative study population. All participants underwent clinical evaluation and laboratory testing (Phase 1). Repeat sampling was performed after 3 months for all individuals with an eGFR <60 mL/min per 1.73 m² during initial sampling (Phase 2). Among 3350 participants who were screened, the number of participants with eGFR ≤60 mL/min per 1.73 m² at the end of Phase 1 and Phase 2 were 584 and 178, respectively. The overall prevalence of CKD was therefore 5.31% (95% CI 4.58–6.13), with the prevalence of CKDu being 2.66% (95% CI 2.14–3.26). The factors that were significantly associated with CKD were increased age, diabetes, hypertension, absence of formal education, anaemia, smokeless tobacco use, and weekly hours of outdoor work. Notably, 406 participants with an eGFR ≤60 mL/min per 1.73 m² during Phase 1 had a normal eGFR when re-measured during Phase 2. These episodes of transient subclinical AKI could potentially contribute to CKD. The prevalence of CKD among agricultural workers in Tamil Nadu is 5.31%, with about half of these due to CKDu. The effect of transient subclinical AKI on CKD progression needs further study. Tamil Nadu Health System Reform Program, Department of Health and Family Welfare, Government of Tamil Nadu.

Background & objectives: COVID-19 cases have been rising rapidly in countries where the SARS-CoV-2 variant of concern (VOC), Omicron (B.1.1.529) has been reported. We conducted a study to describe the epidemiological and clinical characteristics and outcomes of COVID-19 patients with ‘S’ gene target failure (SGTF, suspected Omicron). Furthermore, their clinical outcomes with COVID-19 patients with non-SGTF (non-Omicron) were also compared. Methods: This study was conducted in Tamil Nadu, India, between December 14, 2021 and January 7, 2022 among patients who underwent reverse transcription-PCR testing for SARS-CoV-2 in four laboratories with facilities for S gene screening. Consecutively selected COVID-19 patients with SGTF were telephonically contacted, seven and 14 days respectively after their date of positive result to collect information on the socio-demographic characteristics, previous history of COVID-19, vaccination status and clinical course of illness along with treatment details. To compare their outcomes with non-SGTF patients, one randomly suspected non-Omicron case for every two suspected Omicron cases from the line-list were selected, matching for the date of sample collection and the testing laboratory. Results: A total of 1175 SGTF COVID-19 patients were enrolled for this study. Almost 6 per cent (n=72) reported a history of previous infection. 141 (13.5%) suspected Omicron cases were non-vaccinated, while 148 (14.2%) and 703 (67.4%) had received valid one and two doses of COVID-19 vaccines, respectively. Predominant symptoms reported included fever (n=508, 43.2%), body pain (n=275, 23.4%), running nose (n=261, 22.2%) and cough (n=249, 21.2%). Five (0.4%) of the 1175 suspected Omicron cases required oxygen supplementation as compared to ten (1.6%) of the 634 suspected non-Omicron cases. No deaths were reported among omicron suspects, whereas there were four deaths among suspected non-Omicron cases. Interpretation & conclusions: Majority of the suspected Omicron cases had a mild course of illness. The overall severity of these cases was less compared to the suspected non-Omicron cases.

In December 2023, we observed a notable shift in the COVID-19 landscape, when JN.1 omicron emerged as the predominant SARS-CoV-2 variant with a 95% incidence. We characterized the clinical profile, and genetic changes in JN.1, an emerging SARS-CoV-2 variant of interest. Whole genome sequencing was performed on SARS-CoV-2 positive clinical specimens, followed by sequence analysis. Mutations within the spike protein sequences were analysed and compared with the previously reported lineages and sub-lineages, to identify the potential impact of the unique mutations on protein structure and possible alterations in the functionality. Several unique and dynamic mutations were identified herein. Molecular docking analysis showed changes in the binding affinity, and key interacting residues of wild-type and mutated structures with key host cell receptors of SARS-CoV-2 entry viz., ACE2, CD147, CD209L and AXL. Our data provides key insights on the emergence of newer variants and highlights the necessity for robust and sustained global genomic surveillance of SARS-CoV-2.

Healthcare workers (HCWs) are at high risk of tuberculosis (TB) infection due to their continued occupational exposure to patients with active TB disease. The prevalence of latent TB infections (LTBI) among the HCWs of primary healthcare centers (PHCs) has seldom been investigated. PHCs provide effective and preventive medical care largely for the rural population. Comparatively, the HCWs of PHCs are likely to have an increased risk of occupational exposure and reactivation of LTBI. A cross-sectional study (March–April 2024) was carried out to assess the prevalence of LTBI among the HCWs of 64 PHCs across Thiruvallur district, India. Blood samples (n = 392) were analyzed using a commercial QuantiFERON-TB Gold Plus assay. A comprehensive hematological, biochemical, and immunological workup was performed, including cell count, blood glucose determination, liver/renal function tests, and serum ferritin concentration estimation, which were subsequently correlated with LTBI status using multivariate logistic regression analysis. The study revealed an LTBI prevalence of 25.3% (n = 99) among HCWs of PHCs. The red cell distribution width (RDW) was significantly associated (p = 0.002) with LTBI positivity among the different parameters analyzed. Factors such as individuals’ age (p = 0.029), underlying comorbid conditions (30.3%; p = 0.035), and longer employment duration (28%; p = 0.034) were significantly associated with IGRA positivity. Further, IGRA positivity was significantly associated with decreased RDW standard deviation (RDW-SD). This phenomenon was observed especially among females, the obese, and participants with the ‘O’ blood group. Although the exact prevalence of LTBI in the general population is not known, it is estimated to range from 20-48%. The study reported the prevalence of LTBI among HCWs of PHCs (25.3%) and factors associated with IGRA positivity including age, underlying comorbid conditions, and years of employment. Our findings will aid in developing and establishing an appropriate framework for TB screening and clinical testing guidance for HCWs.