The French Ministry of Health reported on 24 January 2020 the first three cases of Wuhan coronavirus-affected patients. The French Institute of Pasteur for Respiratory Viruses (IPV) sequenced the entire coronavirus genome branded as “2019-nCoV” on 29 January 2020 and became the first European organization to sequence the virus since the outbreak.
In December 2019 in the town of Wuhan, in the Chinese province of Hubei, an outbreak of apparently viral pneumonia of unknown etiology occurred.
In a new coronavirus, known as 2019-nCoV, discovered as the pneumonia-responsible agent on 9 January 2020, the Chinese health agencies (CHA) and the World Health Organización (WHO) announced the discovery (see the Institut Pasteur fact sheet “Coronavirus Wuhan“).
The whole coronavirus genome sequence was shared by the Chinese Authorities in samples taken in the early patients during the weekend of 11-12 January. “To establish accurate diagnostic tests and identify treatment options, sequencing of pathogens is important,” states Sylvie van der Werf, Director of the Pasteur Institute National Reference Center (CNR).
Saturday, 24 January 2020. Virus identification in France confirmed
Samples of three suspected cases (two patients in Paris, one at Bordeaux) were collected at the Pasteur Institut on Friday 24th January late in the morning. “We found the novel coronavirus with the samples taken from these patients,” says Sylvie Behillil, Deputy CNR Director at Pasteur Institute.
From 24 January 2020. Thursday. Pasteur Institute viral genome sequenced
The scientists initiated the sample-based sequencing process that same Friday night. The CNR has prepared the sequencing data, ready for P2 M to start work on Monday afternoon. The sequencing process was completed by Tuesday evening and data analysis was conducted in two of the first three French confirmed cases to obtain the sequence of the whole genome. “This demonstrates the efficacy of the CNR viral sequencing analysis method,” Vincent Enouf continues.
The coronavirus sequence is finally completed!
Thursday, 30 Jan 2020. Thursday. The Pasteur Institute gets and shares the whole virus chain.
The P2 M Platform is actually at an extremely high level; the average sequence time taken is from 3 days (for emergency) to up to 10 days. The P2 M platform (see insert below). In that scenario, the whole process took just three days:’ We analyzed data from Tuesday night to Wednesday, then on Wednesday we checked with counter analysis,’ says Vincent Enouf. “In just three days, the entire sequence was tested.”
What can we do? What can we know about it? The two complete sequences of the virus isolated in two of the first French cases were sent to the database GISAID (the Global Initiative on the Sharing All Influenza Data)1 initially designed to exchange a sequence and track genetic evolution of influenza “Influenza in all our samples: one member of the pair must have infected one another since the virus is the same” To order that the scientist group can work together and progress in a quicker way, a special “coronavirus” tab was developed.
With 20 more samples of the latest coronavirus genome worldwide available and when we compare them with our sample, we can see that they are all very close; the analyzed virus does not show much variability, indicating that the 2019-nCoV virus did not need to change to accommodate and spread, “Vincent Enouf continues.
One of the WHO’s coronaviral reference laboratories 2019-nCoV is the Centre National de Reference (CNR) for Respiratory Viruses at the Pasteur Institute in Paris.
In the past week, a total of 8 CNR workers and 2 P2 M sequenced workers will continue to monitor the disease outbreak in France. This week, the virus has been addressed.
P2M, a new, reciprocal microbiology platform also open to external CNRs
P2M can also be used for sampling by external CNRs. In 2019, four CNRs were working outside the Pasteur Institute. Bacteria, bacteria, parasites, and fungi are sequenced on the server.
P2M now provides a highly efficient service thanks to the experience gained over the past five years (since 2015), as shown by a first pass success rate (i.e. high-quality sequence that includes comprehensive genome-wide information) of over 95% in 2019. The processing of sequence takes three days (for emergencies) to a maximum of ten days.
In 2019, about 25,000 pathogens were sequenced by P2M. The sequencing of the genome raises the threshold for the identification of the outbreak. The early detection of outbreaks by scientists of the Institut Pasteur (clustered cases caused by a single pathogen in the short term) helps epidemiologists to work at once to identify the source of an outbreak and allows the public health response to be coordinated by the authorities.
The coronavirus sequence is finally completed! Comment down your takeaway!