Coronavirus outbreak in France did not come directly from China: Institut Pasteur’s scientists

PARIS, May 6, 2020, SCMP. The coronavirus outbreak in France was not caused by cases imported from China, but from a locally circulating strain of unknown origin, according to a new study by French scientists at the Institut Pasteur in Paris, South China Morning Post reported.

Genetic analysis showed that the dominant types of the viral strains in France belonged to a clade – or group with a common ancestor – that did not come from China or Italy, the earliest hotspot in Europe.
“The French outbreak has been mainly seeded by one or several variants of this clade… we can infer that the virus was silently circulating in France in February,” said researchers led by Dr Sylvie van der Werf and Etienne Simon-Loriere in a non-peer reviewed paper released on bioRxiv.org last week.

The Covid-19 pandemic has infected more than 128,000 people in France and caused more than 23,000 deaths.

France detected the virus in late January, before any other country in Europe. A few patients with a travel history that included China’s Hubei province were sampled on January 24 and tested positive.

The French government took quick and decisive measures to trace contacts of the infected people and shut down the chance of further infection.

However, these strains were not found in patients tested after the initial imported cases, suggesting “the quarantine imposed on the initial Covid-19 cases in France appears to have prevented local transmission”, the researchers said.

The Pasteur institute collected samples from more than 90 other patients across France and found the strains all came from one genetic line. Strains following this unique path of evolution had so far only been detected in Europe and the Americas.

The earliest sample in the French clade was collected on February 19 from a patient who had no history of travel and no known contact with returned travellers.

Several patients had recently travelled to other European countries, the United Arab Emirates, Madagascar and Egypt but there was no direct evidence that they contracted the disease in these destinations.

To the researchers’ surprise, some of the later strains collected were genetically older – or closer to the ancestral root – than the first sample in this clade.

A possible explanation, according to the authors, was that local transmission had been occurring in France for some time without being detected by health authorities.

The French government may have missed detecting the transmission. According to the researchers, a large proportion of those patients might have had mild symptoms or none at all.

The researchers also found that three sequences later sampled in Algeria were closely related to those in France, suggesting that travellers from France might have introduced the virus to the African country and caused an outbreak.

Benjamin Neuman, professor and chair of biological sciences with the Texas A&M University-Texarkana, said the French strains might have come from Belgium, where some sequences most closely related to the original strain from China were clustered.

“Since the earliest European strains of [the coronavirus] Sars-CoV-2 seem to be associated with Belgium, the idea that the virus spread from Belgium to both Italy and France at around the same time seems plausible, as this paper contends,” he said.

France is the latest in a growing number of countries and areas where no direct link between China and local outbreaks could be established.

The dominant strains in Russia and Australia, for instance, came from Europe and the United States, respectively, according to some studies.

These findings have drawn fire from some politicians who have tried to deflect domestic anger over their handling of the crisis by blaming China.

US President Donald Trump lashed out on social media after two separate teams in the US found the strains devastating New York came from Europe.

“So now the Fake News @nytimes is tracing the CoronaVirus origins back to Europe, NOT China. This is a first!” he tweeted on April 11, referring to a story about the studies in the The New York Times’ science section.

The findings also highlight the difficulties governments face in tracing the source of coronavirus outbreaks.

Less-developed countries may never know where their strains came from due to inadequate testing and sequencing capability.

India, for example, has released the genetic sequence of fewer than 40 samples to the public so far, a small number considering its huge population.

Most of the strains sampled in 35 early cases came from clades that could be traced to Italy and Iran, with only a few from China, according to a recent study. But researchers were not able to track further because of the lack of data.

A scientist on the study, Dr Mukesh Thakur, of the Zoological Survey of India, said it was too early to rule out China as the source of outbreaks in India because the number of samples at hand was limited.
A 20-year-old student studying medicine in Wuhan, for instance, might have come in contact with many people on the way home before she was tested positive on January 30.

Thakur said local media reported that the Indian government quarantined 3,500 people possibly linked to three positive cases imported from Wuhan.

“God knows how many of them tested positive in the subsequent stages,” Thakur said in an email response to the Post’s queries on Tuesday.

Some prominent scientists, including Francis Collins, director of the US National Institutes of Health, said the virus might have been spreading quietly in humans for years, or even decades, without causing a detectable outbreak.

The virus had thus adapted well to the human body. Some genes regulating its binding to host cells were similar, or even identical, to those found in some other highly infectious human viruses, such as HIV and Ebola.

According to some estimates, the ancestor of Sars-CoV-2, the virus causing Covid-19, might have left bats between 50 and 70 years ago. A recent study by a team of geneticists in Oxford University estimated the first outbreak of the current pandemic could have occurred as early as September last year.

They found that the dominant strains circulating in China and Asia were genetically younger than some popular strains in the United States.