Antigenic drift with typical 'ladder-like' phylogeny has been observed with multiple lineages in Influenza(Flu) which makes it more predictable and aids in vaccine development on a yearly basis . With Omicron variant also showing similar ladder like phylogeny with XE variant a hybrid of Omicron BA.1 and BA.2. Is it a good sign for the future implications and predictability?
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, millions of human cases have been reported globally (WHO 2020). COVID-19 is caused by the newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) (Li et al. 2020). By December 2020, >150 vaccine candidates are under development, and several vaccines have concluded phase III trials and licensed in several countries (Corum et al. 2020). Most of the COVID-19 vaccine candidates are mRNA-, subunit-, or vector-based vaccines encoding the spike (S) protein (Folegatti et al. 2020; Jackson et al. 2020; Mulligan et al. 2020; Zhu et al. 2020), which is the surface protein employed by coronaviruses for binding to and entry into the host cell. Thus, SARS-CoV-2 evolution engendering changes of the S protein can have an impact on long-term usability of COVID-19 vaccines.
Within the viral family Coronaviridae, viruses infecting humans belong to the genera Alpha- and Betacoronavirus. SARS-CoV-2 belongs to the SARS-related coronavirus species within the genus Betacoronavirus (Gorbalenya et al. 2020). All coronaviruses share an unusually long single-stranded RNA genome encompassing 27–32 kb and a similar genomic structure (Su et al. 2016). Error-prone RNA-dependent RNA polymerases (RdRp) of RNA viruses such as SARS-CoV-2 contribute to short generation times and high mutation rates (Domingo 1997; Duffy et al. 2008). However, differently from other RNA viruses, RdRp-driven mutation in coronaviruses is limited by a virus-encoded proofreading protein termed nsp14 (Denison et al. 2011).
Beyond the recently emerged SARS-CoV-2 and MERS-CoV, which emerged in 2012/2013 and causes zoonotic infections predominantly on the Arabian Peninsula, there are four endemic human coronaviruses (HCoV). HCoV-229E and HCoV-OC43 were identified already in the mid-1960s, whereas HCoV-NL63 and HCoV-HKU1 were identified more recently in 2004 and 2005 due to increased screening for HCoV in the aftermath of the SARS epidemic during 2003–2004 (Corman et al. 2018). The endemic HCoV and SARS-CoV-2 share several epidemiological and ecological traits. First, the endemic HCoV are comparable to SARS-CoV-2 in their high transmissibility and worldwide spread (Owusu et al. 2014; Corman et al. 2018; Goes et al. 2020). HCoV cause about 10 per cent of all common colds globally, predominantly during fall and winter seasons, and afford seroprevalence rates of up to 90 per cent already in young children (Corman et al. 2018; Edrige et al. 2020). Second, alike SARS-CoV-2 and many other respiratory viruses, repeated upper respiratory tract infections with HCoV are possible despite prior exposure and detectable systemic immune responses (Callow et al. 1990; Farag et al. 2015), as was exemplified by HCoV-229E re-infection within one year in an experimental infection study in humans (Callow et al. 1990). Third, alike SARS-CoV-2 that has likely evolutionary origins in bats, the endemic HCoV originated from an animal source, including bats, rodents and intermediate hosts (Vijgen et al. 2006; Pfefferle et al. 2009; Huynh et al. 2012; Corman et al. 2015; Jo et al., 2020).
Vaccines against COVID-19 provide a powerful mean to create herd immunity and control the pandemic, albeit long-term efficacy remains to be determined (Krammer 2020). No vaccine has yet been approved against any other HCoV. On the contrary, there are several vaccines against the major respiratory illness influenza, which is likely comparable to COVID-19 in the potential for pandemic spread and disease severity (Petersen et al. 2020). Influenza A viruses (IAV) have high evolutionary rates (Fitch et al. 1991) and evolve into antigenically distinct variants escaping community protective immunity within a few years, a process that is termed antigenic drift and requires evaluation and sometimes exchange of vaccine strains on an annual basis (Carrat and Flahault 2007; Rambaut et al. 2008). Among IAV, the endemic subtype H3N2 exhibits the strongest antigenic drift (Fitch et al. 1991; Bedford et al. 2015), largely influenced by its higher mutation rate (Pauly et al. 2017) and large effective population size (Rambaut et al. 2008). Once sufficient community immune responses against SARS-CoV-2 have been built either by wild-type infection or vaccination, a plausible post-pandemic scenario would be that the future trajectory of SARS-CoV-2 will be reminiscent of endemic HCoV and IAV (Petersen et al. 2020).