Phylogeny and evolution of SARS-CoV-2 during Delta and Omicron variant waves in India.

SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was reported in patients without comorbidity (97%), while Omicron BA.2 was reported in patients with comorbidity (77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2. Higher propensity of Omicron variants to bronchial tissue, probably ensured increased transmission while Omicron BA.2 became the prevalent variant possibly due to evolutionary trade-off. Virus evolution continues to shape the epidemic and its culmination.Communicated by Ramaswamy H. Sarma.

A rare case of complicated pancreatitis due to leptospirosis.

The COVID-19 pandemic and the actions taken to combat it have greatly impacted the health infrastructure of all nations. Here we present a rare case of leptospirosis with severe acute pancreatitis, bilateral peripheral gangrene, disseminated intravascular coagulopathy and multiorgan failure. This is a rare presentation of leptospirosis wherein the patient had no history suggestive of acquisition of leptospires. The patient was started on doxycycline but still could not be saved due to the multisystem involvement.

Antibiotic susceptibility patterns of urinary pathogens in female outpatients.

BACKGROUND: Urinary tract Infection (UTI) is among the most common infections described in outpatient setting and hospital patients. In almost all cases empirical antimicrobial treatment initiates before the laboratory results of urine culture are available; thus antibiotic resistance may increase in uropathogens due to frequent use of antibiotics. AIMS: The study was designed to find the prevalence of UTI in females with urinary tract symptoms, to determine the causative organism (s) of UTI, and to determine the antibiotic susceptibility pattern of microbial agents isolated from urine culture (antibiogram). MATERIALS AND METHODS: The prospective, observational study involved 139 females, aged 15 years and above clinically suspected for UTI attending outpatient Departments of Vivekananda Polyclinic and Institute of Medical Sciences, Lucknow. A structured questionnaire was used to interview the study subjects. A chi-square test and Fisher Exact test were used to analyze data. RESULTS: The overall prevalence of UTI was found to be 45.32% (63/139). Escherichia coli (33.1%) and Klebsiella pneumoniae (7.9%) were the most common organisms isolated. The most effective antibiotic for both was Nitrofurantoin. CONCLUSIONS: Regular monitoring is required to establish reliable information about susceptibility pattern of urinary pathogens for optimal empirical therapy of patients with UTI.