Research Article Temporal data series and logistic models reveal the dynamics of SARS-CoV-2 spike protein D614G variant in the COVID-19 pandemic

Wang L., Guzman M., Muñoz-Santos D., Honrubia J.M., Ripoll-Gomez J., Delgado R., Sola I., Enjuanes L., Zuñiga S.

Engineering of reverse genetics systems for newly emerged viruses allows viral genome manipulation, being an essential tool for the study of virus life cycle, virus-host interactions and pathogenesis, as well as for the development of effective antiviral strategies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent human coronavirus that has caused the coronavirus disease (COVID-19) pandemic. The engineering of a full-length infectious cDNA clone and a fluorescent replicon of SARS-CoV-2 Wuhan-Hu-1, using a bacterial artificial chromosome, is reported. Viral growth and genetic stability in eleven cell lines were analyzed, showing that both VeroE6 cells overexpressing transmembrane serin protease 2 (TMPRSS2) and human lung derived cells resulted in the optimization of a cell system to preserve SARS-CoV-2 genetic stability. The recombinant SARS-CoV-2 virus and a point mutant expressing the D614G spike protein variant were virulent in a mouse model. The RNA replicon was propagation-defective, allowing its use in BSL-2 conditions to analyze viral RNA synthesis. The SARS-CoV-2 reverse genetics systems developed constitute a useful tool for studying the molecular biology of the virus, the development of genetically defined vaccines and to establish systems for antiviral compounds screening.

Sarkar P., Banerjee S., Saha S.A., Mitra P., Sarkar S.

AbstractIndia had witnessed unprecedented surge in SARS-CoV-2 infections and its dire consequences during the second wave of COVID-19, but the detailed report of the epidemiological based spatiotemporal incidences of the disease is missing. In the manuscript, we have applied various statistical approaches (correlation, hierarchical clustering) to decipher the pattern of pathogenesis of the circulating VoCs responsible for surge in the incidences. B.1.617.1 (Kappa) was the predominant VoC during the early phase of the second wave, whereas, Delta (B.1.617.2) or Delta-like (AY.x) VoC constitutes majority ($$>90.17$$ > 90.17 %) of the cases during the peak of the second wave. The correlation plot of Delta/Delta-like lineage demonstrates inverse correlation with other lineages including B.1.617.1, B.1.1.7, B.1, B.1.36.29 and B.1.36. The spatiotemporal analysis shows that most of the Indian states were affected during the peak of the second wave due to the Delta surge, and fall under the same cluster. The second cluster populated mostly by north-eastern states and the islands of India were minimally affected. The presence of signature mutations (T478K, D950N, E156G) along with L452K, D614G and P681R within the spike protein of Delta or Delta-like might cause elevation in the host cell attachment, increased transmission and altered antigenicity which in due course of time has replaced the other circulating variants.The timely assessment of new VoCs including Delta-like will provide a rationale for updating the diagnostic, vaccine development by medical industries and decision making by various agencies including government, educational institutions, and corporate industries.

Sarkar P., Banerjee S., Saha S.A., Mitra P., Sarkar S.

India had witnessed unprecedented surge in SARS-CoV-2 infections and the dire consequences during the second wave of COVID-19, but the detailed report of the epidemiological based spatiotemporal incidences of the disease is missing. Here in, we have applied various statistical methods like correlation, hierarchical clustering to know the pattern of pathogenesis of the circulating VoCs. B.1.617.1 (Kappa) was the predominant VoC during the early phase of second wave. Delta (B.1.617.2) or Delta-like (AY.x) VoC constitutes majority (>90.17) of the cases during the peak of second wave. The correlation plot showed Delta/Delta-like lineage is inversely correlated with other lineages including B.1.617.1 (kappa), B.1.1.7, B.1, B.1.36.29 and B.1.36. Delta/Delta-like surge coincided with second wave whereas all other lineages (B.1.617.1, B.1.36.29, etc.) occurred during the prior phase of the second wave. The spatiotemporal analysis showed that most of the Indian states were affected during the peak of the second wave due to delta surge and fall under the same cluster. The second cluster populated mostly by north-eastern states and islands of India were minimally affected. The presence of signature mutations (T478K, D950N, E156G) along with L452K, D614G and P681R within the spike protein of Delta or Delta-like might cause elevation in host cell attachment, increased transmission and altered antigenicity which in due course of time has replaced the other circulating variants. The timely assessment of new VoCs will provide a rationale for updating the diagnostic, vaccine development by medical industries and decision making by various agencies including government, educational institutions, and corporate industries.