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

Abstract

The COVID-19 pandemic is caused by the worldwide spread of the RNA virus SARS-CoV-2. Because of its mutational rate, wide geographical distribution, and host response variance this coronavirus is currently evolving into an array of strains with increasing genetic diversity. Most variants apparently have neutral effects for disease spread and symptom severity. However, in the viral spike protein, which is responsible for host cell attachment and invasion, the D614G variant, containing the amino acid substitution D to G in position 614, was suggested to increase viral infection capability. Here we propose a novel method to test the epidemiological impact of emergence of a new variant, by a combination of epidemiological curves (for new cases) and the temporal variation of relative frequencies of the variants through a logistic regression model. We applied our method to temporal distributions of SARS-CoV-2 D614 or G614, in two geographic areas: USA (East Coast versus West Coast) and Europe-Asia (East Countries versus West Countries). Our analysis shows that the D614G prevalence and the growth rates of COVID-19 epidemic data curves are correlated at the early stages and not correlated at the late stages, in both the USA and ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 20 (4): gmr18960 F. Antoneli et al. 2Europe-Asia scenarios. These results show that logistic models can reveal the potential selective advantage of D614G, which can explain, at least in part, the impact of this variant on COVID-19 epidemiology.

Cell type dependent stability and virulence of a recombinant SARS-CoV-2, and engineering of a propagation deficient RNA replicon to analyze virus RNA synthesis

“…The genomes of these two viruses were identical except for the two genetic markers and three-point mutations: the silent mutation C3037>T and two missense mutations C14408>T (affecting nsp12) and A23403>G (leading to D614G in S protein). Interestingly, the S protein D614G mutation became prevalent in SARS-CoV-2 isolates early during the global pandemic and it has been maintained in all SARS-CoV-2 variants since then ( Antoneli et al., 2021 ; Chakraborty et al., 2021 ). To further characterize the cell culture system for SARS-CoV-2, based on our previous observation and given its rapid rise in human isolates and enhanced transmission, we engineered rSARS-CoV-2-D614G mutant virus as a more representative virus compared with the parental one.…”

Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India

“…Earlier studies have suggested that this D614G mutation provides a certain replication advantage to the virus. Thus, D614G was associated to increased human transmission of SARS-CoV-2 infections [24][25][26] ) appeared with 21 signature and 5 overlapping mutations within its spike protein (Fig. 5).…”

“…Earlier studies have suggested that this D614G mutation provides a certain replication advantage to the virus. Thus, D614G was associated to increased human transmission of SARS-CoV-2 infections 24 – 26 . The spike protein mutation (L452R) which is found in B.1.617.1, B.1.617.2 and AY.4/AY.x is very important for the pathogenicity of the virus.…”

Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India

“…Earlier studies have suggested that the mutation gives a certain replication advantage to the virus. Thus, D614G was associated to increased human transmission and infectivity events (25–27). The spike protein mutation L452R which is found in B.1.617.1, B.1.617.2 and AY.4/AY.x is very important for the pathogenicity of the virus.…”