The world is currently face to face with a pandemic which is spreading rapidly across the globe caused by SARS-CoV-2, a strain of Coronaviruses (CoVs) belonging to subgenus Sarbecovirus of genus Betacoronavirus. World Health Organisation (WHO) on 11 Feb 20 named this disease caused by SARS-CoV-2 as Covid-19. This pandemic is spreading rapidly and more than 20,00,000 cases have occurred globally. The human Coronaviruses discovered in 1960s were considered potentially harmless endemic viruses with seasonal distribution before late 2002. The CoVs are found in a large number of domestic and wild animals and birds. The first pandemic caused by Coronavirus caused by SARS-CoV was recognized in the late 2002 in Guangdong Province and resulted in widespread morbidity and mortality. This was followed by MERS-CoV which began in 2012 in the Arabian peninsula with multiple outbreaks related to it in various parts of the globe. Various studies have suggested how these viruses made their entry from their natural reservoir bats via intermediate host like civets and camels in case of SARS-CoV and MERS-CoV respectively. The intermediate host of the SARS-CoV-2 still needs to be established. The SARS-CoV-2 has 96.2% similarity to the bat Severe Acute Respiratory Syndrome related-Coronavirus (SARSr-CoV RaTG13). SARS-CoV-2 has been found to be more distant in relation to SARS-CoV (79%) and MERS-CoV (50%). At the whole genome sequence level pangolin CoV and SARSr-CoV RaTG13 show 91.02% and 96.2% similarity with SARS-CoV-2 but the S1 subunit of spike protein of pangolin CoV is more closely related to SARS-CoV-2 than SARSr-CoV RaTG13. The genetic analysis of the currently circulating strains of the pandemic have shown 99.98-100% similarity in their genomes implying a recent shift to humans. The animal source of SARS-CoV-2 needs to be identified to implement control measures in the present pandemic. Also, how the virus moves interspecies will help predict and prevent future pandemics.

India has become the third worst-hit nation by the COVID-19 pandemic caused by the SARS-CoV-2 virus. Here, we investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in western India, the most affected region of the country. A total of 90 genomes were sequenced. Four nucleotide variants, namely C241T, C3037T, C14408T (Pro4715Leu), and A23403G (Asp614Gly), located at 5'UTR, Orf1a, Orf1b, and Spike protein regions of the genome, respectively, were predominant and ubiquitous (90%). Phylogenetic analysis of the genomes revealed four distinct clusters, formed owing to different variants. The major cluster (cluster 4) is distinguished by mutations C313T, C5700A, G28881A are unique patterns and observed in 45% of samples. We thus report a newly emerging pattern of linked mutations. The predominance of these linked mutations suggests that they are likely a part of the viral fitness landscape. A novel and distinct pattern of mutations in the viral strains of each of the districts was observed. The Satara district viral strains showed mutations primarily at the 3′ end of the genome, while Nashik district viral strains displayed mutations at the 5′ end of the genome. Characterization of Pune strains showed that a novel variant has overtaken the other strains. Examination of the frequency of three mutations i.e., C313T, C5700A, G28881A in symptomatic versus asymptomatic patients indicated an increased occurrence in symptomatic cases, which is more prominent in females. The age-wise specific pattern of mutation is observed. Mutations C18877T, G20326A, G24794T, G25563T, G26152T, and C26735T are found in more than 30% study samples in the age group of 10-25. Intriguingly, these mutations are not detected in the higher age range 61-80. These findings portray the prevalence of unique linked mutations in SARS-CoV-2 in western India and their prevalence in symptomatic patients.

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Although the overall burden of resistance against first-line ART agents remained steady over the study decade, periodic monitoring is essential. There is the need to develop an HIV-1 subtype C-specific resistance database in India.

Background The first dose of the ChAdOx1 nCoV- 19 Corona Virus Vaccine (Covishield) was administered to the eligible beneficiaries of tertiary care institute of Western Maharashtra on 16 Jan 21 and in the past three months almost 97% of the staff has been vaccinated. The present study analyses the incidence of COVID cases in the unvaccinated and vaccinated population of the institute. Methods All Covid 19 infections (RT-PCR positive) from 01 February 21 to 25 April 21 were included in the study and analyzed as per their vaccination status. To assess the COVID 19 transmission in contacts, Secondary Attack Rates (SAR) of the pre-vaccination period (Jun–Oct 20) was compared with the present SAR. Results A total of 113 cases occurred in the study period (01 Feb to 25 Apr 21). Lower number of infections were observed among the fully vaccinated as compared to partially vaccinated and non-vaccinated. The overall vaccine effectiveness was found to be 88.6% (81.55–92.37) and 44.1% (4.55–67.3) in completely and partially vaccinated individuals respectively. Hazard Ratios for getting infected dropped significantly after 28 days of the second dose. The SAR in high risk contacts (HRCs) was found to be 4.25%, which was lower than SAR (20.6%) of pre-vaccination period. Conclusion This is one of the earliest studies in India to report the impact of COVID-19 vaccination. The results indicate that the vaccine provides effective protection against COVID-19 infection. However, given the complex dynamics of vaccination, the role of NPIs and implementation of COVID appropriate behavior cannot be undermined.

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The pandemic spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has affected 188 countries and territories. Altered physiological status during pregnancy makes a mother vulnerable to severe SARS-CoV-2 infection. The virus may be transmitted from mother to baby during antenatal period or postnatal period. Although the primary mode of transmission of the virus is by respiratory droplets, there is emerging evidence of in utero transmission from mother to foetus. In this rare case report, we describe one such episode of probable vertical transmission. To the best of our knowledge, this is the second systematically investigated Indian case, indicating in utero transmission of SARS-CoV-2 from mother to foetus.

Since the introduction of varicella vaccination in India, surveillance of circulating VZV strains has gained significance. Differentiating wild-type VZV strains from the Oka vaccine strain can be achieved only by molecular genotyping methods. The development of PCR methods for VZV strain differentiation has been hampered by the fact that the VZV genome is highly conserved. We used VZV ORF 62 PCR-RFLP analysis to identify and differentiate wild-type VZV strains in India from the Oka vaccine strain. Digestion of VZV ORF 62 amplicons with SmaI, enabled accurate strain differentiation; the Oka strain was positive for three SmaI sites, compared to two SmaI sites in the wild-type VZV strains that we tested.