Outbreak in France not caused by cases imported from China: Pasteur Institute

0 Comment(s)Print E-mail Science and Technology Daily, May 4, 2020
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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 study by scientists at the Pasteur Institute in Paris.

The Pasteur Institute published the results of the study on the early spread of the virus in France on bioRxiv.org, according to its press release on April 28.

Also according to the press release, France strengthened surveillance of COVID-19 cases on Jan. 10, and made the Pasteur Institute and the National Reference Center for Respiratory Viruses (NRC) responsible for initiating a close watch on potential cases.

On Jan. 24, the first case of COVID-19 in Europe was identified in France. Two other imported cases from China were soon diagnosed and treated in hospital. The French government took quick and decisive steps to trace contacts of the infected people and block the spread of infection.

The coronavirus samples were collected from confirmed cases in France from Jan. 24 to March 24. During this period, the country reported 22,302 confirmed cases, including 1,100 deaths, and the outbreak was mainly occurring in the country's north.

The samples, mainly nasal swab and sputum, were stored at the NRC. The Pasteur Institute conducted gene sequencing and comparison on 97 samples, and included information in the comparison such as country of origin, travel history, time of onset, viral load, and sampling position. The study also included three samples from Algeria.

A map of main regions affected in France in March.
Comparison of single nucleic acid polymorphism of virus strains from different regions in France.

Ju Liya, chief scientist of the European precision medicine platform, gave her interpretations on the traceability study:

1. The virus strains (GE1583, B2340) from southeastern France with a history of travel to Italy are different from those of northern France and not prevalent in France, but similar to those prevalent in northern Italy;

2. The virus strain sampled from the first patient in France from Wuhan (IDF0372) has a unique single nucleic acid polymorphism (G22661T) different from all the others sampled in France;

3. The representative virus genes in northern France are GE1973, IDF2849, and N2223;

4. The representative gene of virus strains with European travel history is IDF2792;

5. The three virus strains were homologous with the prevalent strains from northern France.

The Pasteur Institute compared sequences of samples tested in France with the 338 COVID-19 sequences released by GISAID, and established the virus evolution tree map.

Genetic analysis shows 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 earliest sample in the French clade was collected on Feb. 19 from a patient who had no history of travel and no known contact with returned travelers. The patient died on Feb. 25, followed by a major outbreak in France.

Evolution of virus strains from different regions.

Ju said that the picture tells that:

1. Strains from the Asia-Pacific region (including Wuhan, Hubei) are not associated with those in France;

2. Strains from the U.S. have little association with those in France;

3. Prevalent strains in northern France (marked in different colors for different regions) are derived from the same original strain.

The researchers concluded that the virus was silently circulating in France and other European countries before the virus broke out in February, and a large proportion of those patients might have had mild symptoms or none at all without being detected by health authorities.

They also pointed out that it is not possible to nail down the origin or the import time of the virus in France yet, since the virus sampling in many countries is still incomplete.

One of the research leaders said that the sequencing of the coronavirus from different regions is important for understanding the outbreak in France.

(The article was published in Chinese on Science and Technology Daily and translated by Zhang Jiaqi from China.org.cn.)

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