The emergence of the virus and its propagation

At the end of 2019, the city of Wuhan reported cases of atypical pneumonia of unknown origin. Scientists then discovered that these cases were due to a new coronavirus, called SARS-CoV-2. The illness that resulted was named COVID-19, and it spread rapidly throughout the world, causing more than 5 million deaths in some 238 million cases. Chinese researchers (at the Academy of Medical Sciences of Tai’an) have worked on a synthesis of current knowledge relating to the emergence of the virus and its propagation.

Firstly, the researchers summarised what we know about the origin of the epidemic. The 1^st hypothesis, which has not been completely discounted, was that the virus escaped from a virology laboratory in Wuhan. But it is the 2^nd hypothesis that seems the most probable: that the virus spread to humans from animals (that is, jumped the species barrier). SARS-CoV-2 does appear to be very similar to viruses found in bats and pangolins. The discovery of animal viruses that are increasingly close to SARS-CoV-2 seems to confirm the hypothesis of zoonosis. In terms of location, numerous early cases of COVID-19 seemed to originate from Wuhan market. Although there were concurrent cases from other locations, the market was the source of one of the first large chains of contamination (also known as a cluster).

The authors of this study then looked at the genetic diversity of SARS-CoV-2. Like all viruses with an RNA genome, errors in the replication of its genome occur randomly when the virus multiplies. Some of these mutations give a selective advantage to the virus and enable its proliferation: more effective entry into cells, for example, or better antibody resistance. The more a virus is transmitted, the more it reproduces and the more mutations appear. On average, 2 mutations per month occur in the SARS-CoV-2 genome. In order to be considered as a variant, the virus must have acquired a certain number of mutations compared to the original Wuhan strain.

In order to know which mutations have occurred in a virus and to be able to monitor the emergence of new variants, unprecedented levels of sequencing have taken place in recent months (more than 2,8 million SARS-CoV-2 genomes were sequenced during August 2021). Several variants have already emerged since the beginning of the epidemic. Some, such as the Alpha (UK) and Delta (Indian) variants, have become dominant for a period of time.

Finally, the scientists summarised the worldwide spread of the virus following the first cases localised in Wuhan province.  The virus first spread in this region before lockdown measures were enacted on the 23^rd of January 2020. Propagation then slowed due to the lockdown and other measures such as a massive testing programme and transport restrictions. SARS-CoV-2 was then detected in other Chinese provinces. International travel spread the virus worldwide, notably in Asia, Europe and North America in the 2 weeks preceding the Wuhan lockdown. Restrictions placed on travel by the Chinese authorities then greatly reduced the spread of the virus from China.

France was the 1^st European country to declare a case of COVID-19. During the 1^st wave, Europe was a major source of SARS-CoV-2 propagation. Then, at the end of March, the first cases were detected in the United States, the epicentre of the epidemic on the American continent where, by the end of 2020, there had been more than 20 million cases and about 350 000 deaths. But South America was not spared, notably Brazil. Numerous African countries also had their first transmission clusters during May, mostly imported from Europe and the United States. Cases in Africa were undoubtedly largely under-estimated, due to limitations in testing and care facilities.

In conclusion, this new coronavirus probably came from an animal reservoir. It adapted to humans, then spread rapidly through international travel in our hyper-connected world. These conclusions underline the necessity of setting up, on a worldwide level, a coordinated and effective system of genomic monitoring of emerging new pathogens.