The past, current and future epidemiological dynamic of SARS-CoV-2

Abstract

SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron Variants of Concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterised by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunisation are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good—circulation of a fifth endemic ‘common cold’ coronavirus of potentially low virulence, the bad—a situation roughly comparable to seasonal flu, and the ugly—extensive diversification into serotypes with long-term high-level endemicity. Lay Summary SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 and spread globally causing the COVID-19 pandemic. When SARS-CoV-2 jumped into humans, it had essentially no genetic diversity, but as the viral population expanded, it diversified into myriad genetically distinct lineages through the acumulation of approximately two mutations a month. The vast majority of those lineages are now extinct. The most successful lineages so far were the Alpha, Delta and Omicron variants which all reached global prevalence and replaced each other in the process. Alpha and Delta emerged in late 2020 and spread at a time when immunisation of the human population was still low and reached global prevalence primarily by being more transmissible. Omicron started expanding in late 2021, at a time when a large proportion of the human population had already been vaccinated and/or exposed to SARS-CoV-2. Omicron was so successful mainly due to its ability to (re-)infect hosts with prior immunity. In this review, we provide an overview of the evolution of SARS-CoV-2 and put it in context of what is known about other coronaviruses infecting humans. We conclude by delineating plausible scenarios for the ‘endemic’ future of SARS-CoV-2.

Impact of vaccination on the presence and severity of symptoms of hospitalised patients with an infection by the Omicron variant (B.1.1.529) of the SARS-CoV-2 (subvariant BA.1)

“…Interestingly, if Omicron infection is less associated with severe COVID-19, it was also shown to be more contagious than Delta infection (Syed et al 2022;Cui et al 2022); this explains why many deaths were still observed during the BA-1 and BA-2 waves, the low frequency of severe form being counterbalanced by the massive number of infections. This observation undermines the statements describing Omicron as a step of SARS-CoV-2 toward a more "banal" coronavirus (Balloux et al 2022;Callaway 2021;Gudina, Ali, et Froeschl 2022), such as 229E, NL63, OC43 and HKU1, and is an argument to maintain high During the second quarter of 2022, new Omicron subvariants, BA.4 and BA.5, progressively became predominant in Europe. Studies showed a decrease in the neutralisation activities of antibodies elicited by vaccination (Wang et al 2022) and of therapeutic monoclonal antibodies (Takashita et al 2022) toward them.…”

“…Interestingly, if Omicron infection is less associated with severe COVID-19, it was also shown to be more contagious than Delta infection (Syed et al 2022; Cui et al 2022); this explains why many deaths were still observed during the BA-1 and BA-2 waves, the low frequency of severe form being counterbalanced by the massive number of infections. This observation undermines the statements describing Omicron as a step of SARS-CoV-2 toward a more “banal” coronavirus (Balloux et al 2022; Callaway 2021; Gudina, Ali, et Froeschl 2022), such as 229E, NL63, OC43 and HKU1, and is an argument to maintain high vaccine coverage. Moreover, divalent mRNA vaccines have received market authorisation by the European medicines agency (EMA 2022 for Wuhan SARS-CoV-2 and Omicron BA.1 SARS-CoV-2 on 01/09/2022), and by the Food and Drug Administration (FDA) of the USA (FDA 2022 Wuhan SARS-CoV-2 and Omicron BA.4/5 on 31/08/2022); our results suggest that patients with risk factors for severe Covid-19 should not wait for such vaccines before receiving a boosting injection (such an injection being recommended 3 to 6 months after the previous one), as currently available vaccines, targeting the Wuhan SARS-CoV-2 viral sequence, still retain efficacy.…”

Evolutionary Challenges to Humanity Caused by Uncontrolled Carbon Emissions: The Stockholm Paradigm

“…On the basis of their modeling, the authors deduced the retro-colonization of humans by this strain from an unidentified mammal that was initially infected by humans. This result was subsequently grounded by additional empirical data obtained by other researchers [ 120 , 121 , 122 ]. Within their model, Boeger et al proved the presence of host oscillations for SARS-CoV-2, one of the core elements of the SP’s theoretical framework.…”

Recent developments in the immunopathology of COVID-19

“…New variants of SARS-CoV-2 emerged sequentially, becoming the predominant strains during the pandemic. These variants have distinct ACE2 binding affinity, virulence, transmissibility and host immune responses [88][89][90][91][92][93][94][95][96][97][98][99][100] (Figure 1). Currently, the most pronounced risk factor for SARS-CoV-2 infection is the emergence of new variants or subvariants that are resistant to neutralizing antibodies and with higher transmissibility 101 .…”