key: cord-1023890-yfg8lbyt
authors: Shastri, Jayanthi; Yadav, Pragya D.; Agrawal, Sachee; Shete, Anita M.; Nyayanit, Dimpal A.; Parikh, Swapneil; Gomare, Mangala; Sahay, Rima R.; Patil, Deepak Y.; Dudhmal, Manisha; Kadam, Neelam
title: Community transmission of SARS-CoV-2 with B.1.1.7 lineage in Mumbai, India
date: 2021-11-03
journal: J Microbiol Immunol Infect
DOI: 10.1016/j.jmii.2021.10.004
sha: 113005393eb47f4803316ece6144763f9006d246
doc_id: 1023890
cord_uid: yfg8lbyt

The B.1.1.7 (Alpha) variant has been detected in Mumbai, India during February 2021. Subsequently, we retrieved 43 sequences from specimens of 51 COVID-19 cases from Mumbai. The sequence analysis revealed that the cases were mainly affected with Alpha variant which suggests its role in community transmission of SARS-CoV-2 in Mumbai, India.

Over the course of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic, multiple variants have emerged across the globe. During late December 2020, a new variant of concern (VOC) B.1.1.7 (Alpha) was identified in the United Kingdom which has spread to more than 135 countries in the world including Europe, Asia, USA. 1 This variant has about 17 mutations, including N501Y, P681H, HV 69-70 deletion in the spike protein and various other mutations. It has been designated as variant of concern due to its high transmissibility, with estimates ranging from 40-80% higher transmissibility. 2, 3 During the first wave of pandemic in India, SARS-CoV-2 cases showed downward trend Genomic characterization of the referred clinical specimens was carried out with the quantified RNA using next generation sequencing (NGS). Briefly, the ribosomal RNA depletion was performed using NebnextrRNA depletion kit (Human/mouse/rat) followed by cDNA synthesis using the first strand and second synthesis kit. The RNA libraries were prepared using TruSeq Stranded Total RNA library preparation kit. The amplified RNA libraries were quantified and loaded on the Nexseq Illumina sequencing platform after normalization. 5 Reference-based mapping was performed to retrieve the genomic sequence of the SARS-CoV-2 from clinical samples using the CLC genome workbench v20.0.4 and submitted to the public repository i.e., GISAID. A phylogenetic tree was generated using the MEGA software version 7.

Out of 51 SARS-CoV-2 cases, the clinical details of 37 cases (18 male, 19 female) were available. The cases were distributed amongst all the age groups including <14 years (n=3); 15-45 years (n=14), 46-60 years (n=8), and >60 years (n=17). Out of 37 cases, 70%

were asymptomatic while 27.03% had cough, 21.62% had fever, 18.92% had mild breathlessness and 13.51% had runny nose. The cases were followed till 14 days to check for the development of any kind of symptoms. The cases didn't develop disease severity and recovered completely. The COVID-19 vaccination drive has started in India from 16 J o u r n a l P r e -p r o o f January 2021. However, only health care and frontline workers were vaccinated during the initial phase of vaccination. All the study participants were not vaccinated against SARS-CoV-2 during the study period.

SARS-CoV-2 sequences (n=43) were retrieved with more than 98% genome length from the clinical specimens of the COVID-19 cases. The details of the total read mapped, percent relevant reads and genome length is given in Table 

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