Elucidating the origin and evolution of coronaviruses, as well as of other viruses, is critical to understanding the dynamics of future outbreaks and developing informed strategies to prevent subsequent global spread. Consequently, future zoonotic transmission of coronaviruses to human populations is inevitable. In particular, SARS-related coronaviruses appear frequently in bats 8, the likely proximal source of SARS-CoV-2 (see below). The prevalence of these coronaviruses, paired with the high number of human activities involving close contact with wild mammals harboring these viruses, provides abundant opportunities for future transfers between species. Many of these viruses have the potential to infect humans 7. Importantly, there is ample evidence indicating that coronaviruses related to those responsible for recent epidemic outbreaks are abundant in other mammals 3, 4, 5, 6. Second, these outbreaks exemplify the potential transmission of viruses from nonhuman animals to human populations. These incidences, coupled with the possibility that there may exist other coronavirus infections that went unrecognized, indicate that the spread of new coronaviruses among human populations is a relatively common phenomenon. Additionally, four strains of coronaviruses are known to cause milder symptoms of the common cold 2. These incidents include the first SARS outbreak in 2003 and the Middle East respiratory syndrome (MERS) in 2012, both of which induced severe human diseases 1.
First, outbreaks of coronavirus infection have occurred frequently over the last two decades, although previous episodes have remained relatively isolated at the regional level. Unfortunately, several aspects of the pandemic indicate that the current outbreak is not a singular event, nor will it be the last of its kind. The pervasiveness and detrimental impact of SARS-CoV-2 across the globe has established it among the most notorious pandemics that have ever been recorded in human history. Since then, this virus, named “severe acute respiratory syndrome coronavirus 2” (SARS-CoV-2), has emerged as the source of a global pandemic, with nearly 115 million confirmed cases reported worldwide and over 2.56 million fatalities as of early March 2021. Initially, the impact of the virus on humans was poorly understood. The global spread and explosive growth of the SARS-CoV-2 population (within human hosts) has contributed additional mutational variability into this genome, increasing opportunities for future recombination.Ī novel coronavirus (CoV) began to circulate among humans in Wuhan, China, around December 2019. The spike (S) protein of SARS-CoV-2, which enables the virus to enter host cells, exhibits signatures of both purifying selection and ancestral recombination events, leading to an effective S protein capable of infecting human and many other mammalian cells. Other regions of the SARS-CoV-2 genome show the impact of purifying selection. Consequently, the genome of SARS-CoV-2 harbors signatures of multiple recombination events, likely encompassing multiple species and broad geographic regions.
A key feature of SARS-CoV-2 is its propensity for genetic recombination across host species boundaries. Therefore, understanding the molecular origin and ongoing evolution of SARS-CoV-2 will provide critical insights for preparing for and preventing future outbreaks. The repetitive introduction of animal viruses into human populations resulting in disease outbreaks suggests that similar future epidemics are inevitable. SARS-CoV-2 has a zoonotic origin, similar to the causative viruses of these previous outbreaks. Other viruses in the same phylogenetic group have been responsible for previous regional outbreaks, including SARS and MERS. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global outbreak of a coronavirus disease (herein referred to as COVID-19).
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