Dengue is the most common mosquito-borne viral infection in tropical and sub-tropical countries. In recent years, India has reported increased incidences of concurrent infection with multiple serotypes of dengue viruses (DENV). In the present study, we have characterized DENV circulating during a single season of 2016 in Pune, India. A total of 64 serum samples from NS1 ELISA positive dengue patients were used for PCR amplification of CprM region of the viral genome and sequencing. Phylogenetic analysis documented circulation of all the four DENV serotypes with predominance of DENV-2 (40.6%). DENV genotyping classified DENV-1 to Genotype V, DENV-2 to Genotype IV, DENV-3 to Genotype III and DENV-4 to Genotype I. Further analysis revealed emergence of a novel clade (D) of genotype I of DENV-4. Subsequent isolation of three DENV-4 viruses in cell culture followed by complete genome sequence analysis confirmed this observation. Additionally, a new genotype within serotype-4 with >6.7% sequence variation from other genotypes was identified. This first report of significant co-circulation of all the four serotypes in a single outbreak in Pune reconfirms need for molecular monitoring of DENV.

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The emergence of novel variants of SARS-CoV-2 in several countries has been associated with increased transmissibility or reduced neutralization potential of antibodies against the Wuhan virus (wild type). From August 2021 onwards, India experienced a progressive decline in the number of active SARS-CoV-2 infections, indicative of a downward trend in the explosive second wave. This prospective study was conducted quarterly for one year (May 2020 to June 2021) at a tertiary care hospital in the city of Pune in western India. Receptor-binding domain (RBD, n = 319) and full genome (n = 20) sequences from viral-RNA-positive nasopharyngeal swabs of COVID-19 patients representing the first and second waves were used for analysis. No Brazilian, South African, or California variants were detected in this study. Until December 2020, only the wild-type strain was prevalent. Concurrent with the upsurge of the second wave in March 2021, 73% (33/45) of RBD sequences harboured L452R/E484Q mutations characteristic of the Kappa variant. In April 2021, co-circulation of Kappa (37%) and Delta (L452R/T478K, 59%) variants was recorded. During May and June 2021, the Delta variant became the predominant circulating variant, and this coincided with a significant decline in the number of COVID-19 cases. Of the 20 full genome sequences, six isolates each exhibited signature mutations of the Kappa and Delta variant. With several states witnessing a reduction in the number of COVID-19 cases, continuous monitoring of newer mutations and assessment of their effect on virus transmissibility and their impact on vaccinated or previously exposed individuals is necessary. Supplementary Information The online version contains supplementary material available at 10.1007/s00705-021-05320-7.

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Background: Coronavirus disease 2019 (COVID-19) is a global health issue. Healthcare workers (HCWs) are especially vulnerable to infection by SARS-CoV-2. The present study was conducted to determine the proportion of HCWs infected with COVID 19 in a tertiary care centre with emphasis on the epidemiological and clinical aspectMethods: HCWs (symptomatic and asymptomatic contacts) who tested positive for COVID-19 by SARS-CoV-RTPCR or COVID-19 rapid antigen test were included in the study. Demographic and clinical data of the infected HCWs was obtained through a detailed telephonic interview with structured questionnaire.Results: Out of total 921 HCWs tested for COVID-19 (SARS-CoV-2 RT-PCR and Rapid antigen test), 323 (35%) HCWs were positive. Proportion of COVID-19 positive HCWs among all HCWs was 13.67% (323/2362). Most COVID-19 positive HCWs (88%) were symptomatic. Majority of infected HCWs (62.23%) were between the age group of 21-30 years. Nurses were the most predominantly affected among various categories of HCWs (42.41%). Fever was the most common presenting symptom, seen in 160 (49.50%) HCWs. Comorbidities were found in 28 (8.66%) of infected HCWs. Majority of HCWs (86%) suffered from mild infection.Conclusions: HCWs, especially nurses, face a high risk of COVID-19 infection while providing care for suspected or confirmed COVID-19 patients. It is important to characterize the epidemiological and clinical profile of HCWs regarding COVID-19 for formulation of prevention and management strategies.

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