As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being used to investigate its transmission and evolution. Against the backdrop of the global emergence of “variants of concern” (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches were undertaken to identify possible new variants and gauge the fitness of the current circulating strains. Phylogenetic analysis revealed that newly identified lineages B.1.617.1 and B.1.617.2 were predominantly circulating. The signature mutations possessed by these strains were L452R, T478K, E484Q, D614G and P681R in the spike protein, including within the receptor-binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R, T478K and E484Q revealed that these may possibly result in increased ACE2 binding while P681R in the furin cleavage site could increase the rate of S1-S2 cleavage, resulting in better transmissibility. The two RBD mutations, L452R and E484Q, indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Further in vitro/in vivo studies would help confirm the phenotypic changes of the mutant strains. Overall, the study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra. Lineage B.1.617.2 has been designated as a VOC delta and B.1.617.1 as a variant of interest kappa, and they are being widely reported in the rest of the country as well as globally. Continuous monitoring of these and emerging variants in India is essential.

This study aims to describe the demographic and clinical profile and ascertain the determinants of outcome among hospitalised COVID-19 adult patients enrolled in the National Clinical Registry for COVID-19 (NCRC). NCRC is an on-going data collection platform operational in 42 hospitals across India. Data of hospitalized COVID-19 patients enrolled in NCRC between 1^st September 2020 to 26^th October 2021 were examined. Analysis of 29,509 hospitalised, adult COVID-19 patients [mean (SD) age: 51.1 (16.2) year; male: 18752 (63.6%)] showed that 15678 (53.1%) had at least one comorbidity. Among 25715 (87.1%) symptomatic patients, fever was the commonest symptom (72.3%) followed by shortness of breath (48.9%) and dry cough (45.5%). In-hospital mortality was 14.5% (n = 3957). Adjusted odds of dying were significantly higher in age-group ≥60 years, males, with diabetes, chronic kidney diseases, chronic liver disease, malignancy, and tuberculosis, presenting with dyspnea and neurological symptoms. WHO ordinal scale 4 or above at admission carried the highest odds of dying [5.6 (95% CI: 4.6, 7.0)]. Patients receiving one [OR: 0.5 (95% CI: 0.4, 0.7)] or two doses of anti-SARS CoV-2 vaccine [OR: 0.4 (95% CI: 0.3, 0.7)] were protected from in-hospital mortality. WHO ordinal scale at admission is the most important independent predictor for in-hospital death in COVID-19 patients. Anti-SARS-CoV2 vaccination provides significant protection against mortality.

Objectives: This study aims to describe the demographic and clinical profile and ascertain the determinants of outcome among hospitalised COVID-19 adult patients enrolled in the National Clinical Registry for COVID-19 (NCRC). Methods: NCRC is an on-going data collection platform operational in 42 hospitals across India. Data of hospitalized COVID-19 patients enrolled in NCRC between 1 ^st September 2020 to 26 ^th October 2021 were examined. Results: Analysis of 29,509 hospitalised, adult COVID-19 patients [mean (SD) age: 51.1 (16.2) year; male: 18752 (63.6%)] showed that 15678 (53.1%) had at least one comorbidity. Among 25715 (87.1%) symptomatic patients, fever was the commonest symptom (72.3%) followed by shortness of breath (48.9%) and dry cough (45.5%). In-hospital mortality was 14.5% (n=3957). Adjusted odds of dying were significantly higher in age-group ≥60 years, males, with diabetes, chronic kidney diseases, chronic liver disease, malignancy, and tuberculosis, presenting with dyspnea and neurological symptoms. WHO ordinal scale 4 or above at admission carried the highest odds of dying [5.6 (95% CI: 4.6, 7.0)]. Patients receiving one [OR: 0.5 (95% CI: 0.4, 0.7)] or two doses of anti-SARS CoV-2 vaccine [OR: 0.4 (95% CI: 0.3, 0.7)] were protected from in-hospital mortality. Conclusions: WHO ordinal scale at admission is the most important independent predictor for in-hospital death in COVID-19 patients. Anti-SARS-CoV2 vaccination provides significant protection against mortality.