Coronavirus: Epidemiology, Origin, and Evolution

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Since original reports in Wuhan, China, COVID-19 has spread very quickly across the globe, prompting the World Health Organization to declare a pandemic. With no vaccines nor antiviral drugs, and the presence of carriers without apparent symptoms, traditional public health intervention measures are significantly less effective.

But, when and how did the SARS-CoV-2 virus emerge? What is or are the natural and intermediate host species for COVID-19? What is the distribution of the SARS-CoV-2 virus in different mammalian species?

In this article, we discuss the epidemiology, origin, and evolution of the SARS-CoV-2 virus and the disease it causes, COVID-19.

COVID-19 Epidemiology

As of March 31, 2020, there are a total of 784,392 confirmed cases, including 37,780 fatalities worldwide. The epidemiology curve of the COVID-19 disease can approximately be divided into three phases.

  1. The first phase is marked by the local outbreak by exposure in a wet seafood market in Wuhan City, Hubei Province of China. From the first case in December 2019 to the appearance of new cases outside Wuhan by January 2020, a total of 41 cases were confirmed. Epidemiologic analysis revealed that in this initial phase, person-to-person transmission had already occurred through close contact[1].
  2. The second phase started on January 2020, marked by the rapid expansion and spread of the virus within hospitals (nosocomial infection) and by family transmission (close-contact transmission). In this phase, COVID-19 spread from Wuhan to other areas. The first case outside of China was reported in Thailand on January 13 – it was caused by a Wuhan resident who traveled to this country. On January 19, COVID-19 cases were reported outside Wuhan – cases were reported in the Guangdong Province and in Beijing City, showing that the virus has spread within China. In this phase, the total number of confirmed cases rose to 205. By January 23, 29 provinces and 6 foreign countries had reported a total of 846 confirmed COVID-19 cases. Meanwhile, Wuhan implemented a lock-down. Unfortunately, this period overlapped with the traditional mass movement of people, a type of homecoming before the Chinese New Year and thus, over 5 million people had already left Wuhan.
  3. The third phase began on January 26, which was marked by the rapid increase of cluster cases. On February 10, retrospective analysis revealed that the number of clustered cases was responsible for about 50-80% of all confirmed cases in Shanghai, Shandong, Jiangsu, and Beijing. On January 30, the total number of confirmed cases rose to 9,826 and the World Health Organization (WHO) declared this epidemic a Public Health Emergency of International Concern (PHEIC). By February 11, the total number of confirmed cases rose to 44,730 and 16,067 suspected cases were reported in about 1,386 counties and districts in China. However, there were only about 441 confirmed cases in 24 countries outside of China. Fatality rate stayed high in China and one fatality outside China was reported in the Philippines. Due to the implementation of a new clinical definition for diagnosis in Hubei province by February 12, the total number of confirmed cases rose to 14, 840; of these cases, 13,332 were only based on clinical diagnosis. By that time, 25 countries had reported 60,329 infections, with 1,471 times the original number. Of note, February 3 seems to be a tipping point of the COVID-19 epidemic, from which time the daily number of confirmed cases outside Hubei started to decline. Whether this reflects the success of the Wuhan lock-down and other public health measures, or virus transmission reduced for other reasons, still remains unclear.

Origin and Evolution of SARS-CoV-2

As animal markets had been involved in the SARS-CoV outbreak of 2002-2003, and initial COVID-19 infections are also linked to the wet seafood market with wildlife trading, it was assumed that wild animals were also responsible for the emergence of the SARS-CoV-2 virus. However, from which type and what circumstance the virus crossed the species barrier to infect humans still needs to be clarified.

Early investigations about the origin of COVID-19 suggested that the SARS-CoV-2 virus may have jumped from bats to humans[2]. This is not unprecedented because bat viruses have been shown to jump from one species to another. However, since bats were in hibernation when the COVID-19 outbreak occurred, and it was uncertain whether bats were sold at the wet market in China, the virus is more likely to have been transmitted through other species on the market.  

Genomic analyses of the SARS-CoV-2 virus demonstrate a 96% nucleotide identity with a CoV isolated from a bat – RaTG13. Previous reports revealed that species from the bat genera Rhinolophus in southern China are a high source of SARS-like-CoVs. The viruses exhibit frequent recombination events and rich genetic diversity, which increases the potential for cross-species transmission. Based on phylogenetic trees and recombination analysis, researchers found that the SARS-CoV-2 virus shares a most recent common ancestor with BetaCoV-RaTG13 because both viruses are in the same cluster. However, these results indicate that this cluster may be due to complex recombination events or convergent evolution concerning at least two virus species with different evolutionary histories.

Further studies show the existence of multiple lineages of pangolin CoVs with a genetic similarity to the SARS-CoV-2 virus. This further supports the hypothesis that pangolins served as a potential intermediate host[3].  Current data do not fully clarify if the SARS-CoV-2 virus was directly transmitted from bats to humans or indirectly through an intermediate host. Current data also does not rule out convergent evolution as an alternative hypothesis to recombination to explain the conflicting phylogenetic trees.

Scientists also compared the available genome sequence data for known coronavirus strains. The results of their studies reveal that the SARS-CoV-2 virus originated through natural processes. Two features of the virus – its distinct backbone and the mutations in the RD portion of the spike protein – rules out laboratory engineering as a potential origin for the SARS-CoV-2 virus.

With laboratory engineering ruled out, some scientists propose two viable hypotheses regarding the origin of the SARS-CoV-2 virus. First, that the natural selection took place in an animal host before the virus was transmitted to humans. The second hypothesis is that the natural selection took place in humans after the virus was transmitted from an animal host. In the second scenario, scientists propose that the SARS-CoV-2 virus crossed from animals into humans before it became capable of causing human disease. Then, as a result of evolutionary changes over years, the virus gradually gained the ability to spread from one person to another and cause serious, often life-threatening disease.

The Bottom Line

More sequence data are necessary to confirm the specific source and origin of the SARS-CoV-2 virus. Currently, there are several hypotheses regarding the origin and source of the virus, but further research is necessary.

With no vaccines nor antiviral drugs currently available, slowing the spread of COVID-19 is highly important. So, make sure to stay home, wash your hands, and help with the effort of flattening the curve.

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