SARS-CoV-2 was already spreading in France in late December 2019
Authors: S Brichler
E Carbonnelle
A Deslandes
J R Zahar
Y Tandjaoui-Lambotte
Yves Cohen
V Berti
Chakib Alloui
Journal: International Journal of Antimicrobial Agents (2020)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: COVID-19; Coronavirus disease 2019; France; Intensive care unit; SARS-CoV-2.
Affiliations: Université Paris 13, Sorbonne Paris Cité, France, and Service de Microbiologie Clinique et Unité de Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France., Réanimation polyvalente, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France; INSERM U1272 Hypoxie et Poumon, Bobigny, France., Université Paris 13, Sorbonne Paris Cité, France, and Service de Microbiologie Clinique et Unité de Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France; IAME, UMR 1137, Université Paris 13, Sorbonne Paris Cité, France., Université Paris 13, Sorbonne Paris Cité, France, and Service de Microbiologie Clinique et Unité de Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France; IAME, UMR 1137, Université Paris 13, Sorbonne Paris Cité, France. Electronic address: ., Réanimation polyvalente, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France; INSERM, U942, F-75010, Paris, France.

Abstract:  The COVID-19 epidemic is believed to have started in late January 2020 in France. Here we report a case of a patient hospitalised in December 2019 in an intensive care unit in a hospital in the north of Paris for haemoptysis with no aetiological diagnosis. RT-PCR was performed retrospectively on the stored respiratory sample and confirmed the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Based on this result, it appears that the COVID-19 epidemic started much earlier in France. 

Retracted: No

PubPeer comments:
 The authors have used two detection systems: the first one is the rt-qpcr developed by the charitu00e9, targetting the E gene. This is the positive reported in the fig. The Ct is 31, modest, but not very low. The second one is this kit: https: www.elitechgroup.com wp-content uploads sites 16 2020 03 GeneFinder-COVID-19-RealAmp-Plus-Kit_Full-manual_V1_IVD.pdf that targets simultaneously three viral genes plus one human gene, all of them by rt-qpcr. The interpretation depends on the precise result of the different genes (see page 7 in the manual above). With the key potential impact of the findings, the authors should do their best to assure this is not a false positive, but it all remains dubious because: 1) It is bizarre that they use one figure (the only one) in the article to merely present an amplification curve, instead of simply reporting the Ct value, and that they not say whether all three genes in the second test were positive and whether the human gene was positive. 2) They say that the sample was tested twice but they do not say whether thy performed two extractions, or only one. If only one extraction and it was contaminated, the two tests should be positive and they simply confirm the presence of RNA in the same extraction. If two different extractions, one for each test, and both are true positives, the chances that the sample could have been contaminated (and thus a false positive) are lower. But the most important caveat is that the authors do not even mention whether they have tried to sequence the amplified fragment, or whether they have tried to use any of the multiple available methods to cover the genome (e.g. Artic-like) so that even if incomplete they should have been able to recover a good fraction of the genome so that they can place it in space and time using phylogenomics. Without this information to confirm the true nature of the sequence, it all remains purely speculative. , 
 Dear all Thank you for your email and your judicious remarks. Indeed the sequencing is in progress Concerning the PCR curve we had to choose one, I join you the second one with the CT Finally, you are right, the possibility of contamination cannot be ruled out, however we have tried to take as many measures as possible to avoid this. thanks again for your feedback, we are available to answer if any other remarks kind regards ![file] ![file] ![file] , 
 Would you communicate the results of the sequencing ? Until now no such early (partial) sequence has been released (France December pneumonia, Milan December wastewater, Barcelona March wastewater) and it is very hard to make definitive conclusions without such information. , 
 Hi, I agree with the previous comments. More specifically: - the Charitu00e9 test is a pancoronavirus test, so it is quite irrelevant here, as it detects multiple coronaviruses. Strange that this passed even quick review. - this implies that just one technique is used, not two. A second technique would be an antigen or antibody test for example (maybe on an old sample from this patient?). - the positive point is that the genefinder kit contains multiple genes. However, also here, the E-gene assay detects at least SARS as well. - concerning the genefinder kit: the negative control here is just water: https: www.fda.gov media 137116 download. Were human samples (from earlier maybe) taken as negative controls for this kit? Maybe it is a false positive, maybe it is not ... - The positive controls in the genefinder kit are plasmids. Often these positive controls are important sources of contamination. So, with one extraction and one positive sample, it is still hard to exclude contamination. Did the authors at least repeat this PCR? - If the patient is willing to cooperate, a good antibody test might confirm that the patient got infected in 2019 2020. Did the authors try to contact this patient and perform a test? I know, it is not ideal. If it is negative, it does not exclude infection; If it is positive, it might have happend later. At least, it is a second technique. - Indeed, at least partial sequencing of the sample should be included, preferably with primers that do not bind to the genefinder positive controls. In general: the title is a very bold statement which requires bold evidence. However, this is not the case here. ,