Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications

SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on implications of emerging SARS-CoV-2 variants based on structural-function impact of crucial mutations occurring in its spike (S), ORF8 and nucleocapsid (N) proteins. While the N501Y mutation was observed in all three lineages, the 501Y.V1 and P.1 accumulated a different set of mutations in the S protein. The missense mutational effects were predicted through a COVID-19 dedicated resource followed by atomistic molecular dynamics simulations. Current findings indicate that some mutations in the S protein might lead to higher affinity with host receptors and resistance against antibodies, but not all are due to different antibody binding (epitope) regions. Mutations may, however, result in diagnostic tests failures and possible interference with binding of newly identified anti-viral candidates against SARS-CoV-2, likely necessitating roll out of recurring "flu-like shots" annually for tackling COVID-19. The functional relevance of these mutations has been described in terms of modulation of host tropism, antibody resistance, diagnostic sensitivity and therapeutic candidates. Besides global economic losses, post-vaccine reinfections with emerging variants can have significant clinical, therapeutic and public health impacts.

Could changes in the airborne pollutant particulate matter acting as a viral vector have exerted selective pressure to cause COVID-19 evolution?

Air pollution with particulate matter has been implicated in the incidence and the mortality due to COVID-19 infection. The levels of particulate matter have been shown to have decreased after regional and national lockdowns in a number of countries. COVID-19 possesses an elevated reproduction number (R₀) due to its high transmission rate. COVID-19 genes have been found adherent to particulate matter which has been suggested as a vector for this virus’ transmission. Following lockdown in China, the original viral Clade D steadily decreased mirroring the decline in particulate matter. Two months after the COVID-19 index case was reported in Wuhan early December 2019, a persistent mutation was noted at the D614 gene position of the viral spike protein establishing the Clade G variant. Clade G started to appear early in February and steadily attained predominance after lockdown in late February. It may be postulated that the changes in the source of airborne particulate matter, possibly derived from tobacco smoking (66% of Chinese males are smokers), may have contributed to the appearance of Clade G. Once the pandemic spread beyond China, in all countries affected except for Iceland, a consistent pattern arose whereby the initial viral Clade D outbreak was rapidly displaced by Clade G. It is hypothesized that changes in the source of COVID-19’s vector in the form of particulate matter may have contributed to natural selection favouring Clade G. The “open orientation” of Clade G spike protein’s three peptides as opposed to the “closed orientation” of the Clade D may have allowed easier adherence of the viral mutant to cells and as a corollary also to particulate matter. There may also have been differences between both viral Clades in the spike protein’s hydrophobic properties. Experimental research on the hypothesis that particulate matter may potentially act as a COVID-19 vector needs to be undertaken. Besides the potential vector effect, the deleterious effects of particulate matter on respiratory immunity and cardiovascular health are well known and consequently airborne pollution in all its forms should be addressed on a global scale.