Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

Abstract

COVID-19 has emerged as global pandemic with largest damage to the public health, economy and human psyche.The genome sequence data obtained during the ongoing pandemic are valuable to understand the virus evolutionary patterns and spread across the globe. Increased availability of genome information of circulating SARS-CoV-2 strains in India will enable the scientific community to understand the emergence of new variants and their impact on human health. The first case of COVID-19 was detected in Chambal region of Madhya Pradesh state in mid of March 2020 followed by multiple introduction events and expansion of cases within next three months. More than 5000 COVID-19 suspected samples referred to Defence Research and Development Establishment, Gwalior, Madhya Pradesh were analyzed during the nation -wide lockdown and unlock period. A total of 136 cases were found positive over a span of three months that included virus introduction to the region and its further spread. Whole genome sequences employing Oxford nanopore technology were generated for 26 SARS-CoV-2 circulating in 10 different districts in Madhya Pradesh state of India. This period witnessed index cases with multiple travel histories responsible for introduction of COVID-19 followed by remarkable expansion of virus. The genome wide substitutions including in important viral proteins were identified. The detailed phylogenetic analysis revealed the circulating SARS-CoV-2 clustered in multiple clades including A2a, A4 and B. The cluster-wise segregation was observed, suggesting multiple introduction links and subsequent evolution of virus in the region. This is the first comprehensive whole genome sequence analysis from central India, which revealed the emergence and evolution of SARS-CoV-2 during thenation-wide lockdown and unlock.

Molecular epidemiology of SARS‐CoV‐2 in Mongolia, first experience with nanopore sequencing in lower‐ and middle‐income countries setting

“…In developing countries setting, conventional next‐generation sequences are commonly challenging and requires extensive bioinformatics expertise. Moreover, the Oxford MinION, a third‐generation nanopore‐based platform has been used in several LMICs including India, Bangladesh, Indonesia, and others for SARS‐CoV‐2 nationwide surveillance studies 31–38 . This study represents a pioneering genomic surveillance effort, involving systematic sampling in Mongolia for respiratory viral pathogens.…”

“…Moreover, the Oxford MinION, a third‐generation nanopore‐based platform has been used in several LMICs including India, Bangladesh, Indonesia, and others for SARS‐CoV‐2 nationwide surveillance studies. 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 This study represents a pioneering genomic surveillance effort, involving systematic sampling in Mongolia for respiratory viral pathogens. In Armenia, a molecular surveillance study of SARS‐CoV‐2 was conducted using nanopore sequencing, in addition to the Illumina sequencing platform.…”

Nanopore sequencing technology and its applications

“…The turnover of the SARS‐CoV‐2 lineage within the region may have resulted from viral evolution 168 or the continuous introduction of foreign dominant mutants. 191 Sequencing samples at different times in the region is beneficial to understand the dynamic replacement process of the SARS‐CoV‐2 lineage in the region 168 (Table 5 ).…”

In silico screening of phenylethanoid glycosides, a class of pharmacologically active compounds as natural inhibitors of SARS-CoV-2 proteases

“…In addition to protease activity, PL pro also exhibits deubiquitinase and deISGylase activities, which makes it relevant for virus-induced changes in the cell signaling process [13] . Indeed, several authors have explored the potential of these enzymes as targets for antiviral development [14] , [15] , [16] , [17] , [18] .…”

“…Another class of pharmaceutically interesting polyphenols are the phenylethanoid glycosides (or phenylpropanoid glycosides), which are compounds with phenylethyl alcohol, caffeic acid and glycosyl moieties in their structures. Previous literature demonstrated their potential antiviral activity against SARS-CoV-2 proteases, such as forsythoside, verbascoside (or acteoside) and calceolarioside B [16] , [17] , [18] , [22] , [23] , [24] , [25] .…”