Journal Pre-proof

SARS-COV-2 was already spreading in France in late December
2019
A Deslandes , V Berti , Y Tandjaoui-Lambotte MD ,
Chakib Alloui MD , E Carbonnelle MD, PhD , JR Zahar MD, PhD ,
S Brichler MD, PhD , Yves Cohen MD, PhD
PII:
DOI:
Reference:

S0924-8579(20)30164-3
https://doi.org/10.1016/j.ijantimicag.2020.106006
ANTAGE 106006

To appear in:

International Journal of Antimicrobial Agents

Please cite this article as: A Deslandes , V Berti , Y Tandjaoui-Lambotte MD , Chakib Alloui MD ,
E Carbonnelle MD, PhD , JR Zahar MD, PhD , S Brichler MD, PhD , Yves Cohen MD, PhD , SARSCOV-2 was already spreading in France in late December 2019, International Journal of Antimicrobial
Agents (2020), doi: https://doi.org/10.1016/j.ijantimicag.2020.106006

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition
of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of
record. This version will undergo additional copyediting, typesetting and review before it is published
in its final form, but we are providing this version to give early visibility of the article. Please note that,
during the production process, errors may be discovered which could affect the content, and all legal
disclaimers that apply to the journal pertain.
© 2020 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

 Highlights




Covid-19 was already spreading in France in late December 2019, a month before the official
first cases in the country
Early community spreading changes our knowledge of covid-19 epidemic
This new case changes our understanding of the epidemic and modeling studies should
adjust to this new data

 SARS-COV-2 was already spreading in France in late December 2019
A Deslandes1, V Berti1, Y Tandjaoui-Lambotte2, 3MD, Chakib Alloui1 MD, E Carbonnelle1, 4 MD, PhD, JR
Zahar1,4 MD, PhD , S Brichler1 MD, PhD, Yves Cohen2,5 MD, PhD.

1- Université Paris 13, Sorbonne Paris Cité, France; Service de Microbiologie Clinique et Unité de
Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP,
Bobigny, France.
2-Réanimation polyvalente, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France
3- INSERM U1272 Hypoxie et Poumon, Bobigny
4-IAME, UMR 1137, Université Paris 13, Sorbonne Paris Cité, France;
5- INSERM, U942, F-75010, Paris, France
Corresponding author:
Pr Jean Ralph Zahar
Unité de Contrôle et de Prévention du risque infectieux
GH Paris Seine Saint-Denis
Email : jrzahar@gmail.com

Key words: COVID-19, Intensive Care Unit,

 Abstract
The COVID-19 epidemic is believed to have started in late January 2020 in France. We report here a
case of a patient hospitalized in December 2019 in our intensive care, of our hospital in the north of
Paris, for hemoptysis with no etiological diagnosis and for which RT-PCR was performed
retrospectively on the stored respiratory sample which confirmed the diagnosis of COVID-19
infection. Based on this result, it appears that the COVID-19 epidemic started much earlier.

 Introduction
After its onset in December 2019 in China, the new coronavirus (SARS-COV-2) spreads widely in
several countries, causing COVID-19 illness.1 World Health Organization (WHO) declared COVID-19 a
pandemic on March 11, 2020.3 France reported the first cases of SARS-COV-2 related infection on
January 24, 2020.5 Both cases had a history of travel to Wuhan.6 To the best of our knowledge, these
2 cases are believed to be the first confirmed cases in France. COVID-19 most commonly present
with influenza-like illness (ILI).7 While China was facing COVID-19 outbreak, European countries were
struggling with seasonal influenza.8 Clinical symptomatology between COVID-19 and ILIis similar,we
therefore decided retrospectively to look for SARS-COV2 in respiratory samples collected in the
intensive care units (ICUs) of our hospital near Paris.
Methods - Retrospective analysis
Selected records
We reviewed medical record of ICUs patients admitted for ILI between December 2, 2019 and
January 16, 2020, with a negative RT-PCR performed at admission. Every respiratory sample
collected in our hospital are frozen at -80°C in ThermoScientific -86°C freezer and stored for four
years in case of a need for further analysis. Samples taken from patients with both ILI symptoms
(fever higher than 38.5°C, cough, rhinitis, sore throat or myalgia) and ground glass opacity according
to their medical record underwent SARS-COV-2 RT-PCR. A description of sample selection is available
in Figure 1.
Testing for COVID-19
SARS-COV-2 RT-PCR was performed on the 14 selected biobanks between April 6 and 9, 2020. RT-PCR
was performed strictly according to the Charité protocol11 targeting the E gene, coding for envelope
protein, pangenomic of SARS-COV-1 and SARS-COV-2, on a QuantStudio7 (Thermofisher) device.
Positive result (Figure 2) was confirmed with the Gene finder® COVID19 Plus RealAmp kit (IFMR-45)
according to the manufacturer’s recommandations. This test targets 3 viral genes (RdRp, E and N
coding respectively for the viral RNA-dependant RNA polymerase, envelope and nucleocapsid
protein), and the cellular RNAse P gene, in order to confirm the quality of the respiratory sample.
Results:
During the study period, 14 (24%) patients out of 58 admitted for ILI were included in our analysis
(Table 1).One sample was positive taken from a 42 years old manborn in Algeria, who lived in France
for many years, and worked as a fishmonger. His last trip was in Algeria during August 2019. One of
his child presented with ILI prior to the onset of his symptoms. His medical history consisted in
asthma, type II diabetes mellitus. He presented to the emergency ward on December 27 2019 with
hemoptysis, cough, headache and fever, evolving for 4 days. Initial examination was unremarkable
and the performed CT scan revealed bilateral ground glass opacity in inferior lobes (Figure 3).
at admission he had a lymphopenia, an elevated C-Reactive Protein and fibrinogen while Pro
Calcitonin was in normal range value. No pathogen was identified on sputum sample collected in the
emergency ward. The patient was admitted to the ICU with antibiotic therapy, and evolution was
favorable until discharge on December 29,2019

 Discussion
We report an observation of a patient infected with COVID-19 one month before the first reported
cases in our country. On admission, the patient presented clinical signs and radiological patterns
frequently seen previously in the Chinese12 and Italian13 cohorts. Identifying the first infected patient
is of great epidemiological interest as it changes dramatically our knowledge regarding SARS-COV-2
and its spreading in the country. Moreover, the absence of a link with China and the lack of recent
travel suggest that the disease was already spreading among the French population at the end of
December, 2019.
Further studies are required to evaluate SARS-COV-2’s actual onset on French territory, the actual
extent of SARS-COV-2 contamination in the population during late 2019 and January 2020, and
explore the potential unnoticed deaths that could have happen at the time. COVID-19 is considered
to be responsible for 86334 cases and 12210 deaths as of April 10, 20204 in France, but our findings
suggest that these numbers could be underestimating the actual burden of COVID-19. Two recent
studies suggested that around 18 to 23% infected with SARS-COV-2 were asymptomatic16 and that
around 55% of infected were caused by unidentified infected persons.17 Our results strongly support
these two assumptions, suggesting that many asymptomatic patients were not diagnosed during
January 2020 and contributed to the spread of this epidemic.
Furthermore, since these results change our understanding of the dynamic of the epidemic, it also
means that several models used to predict the evolution and outcomes of the SARS-COV-2
propagation might be based on biased data and would need to be adjusted to the actual profile of
the epidemic.18
Our study presents several limitations. Firstly, due to the retrospective nature of the analyses carried
out, medical records were not exhaustive and some relevant information might have been missing.
Secondly, we are not able to rule out false negative results due to the sensitivity of RT-PCR19 and a
technique of storage that possibly damage the quality of the samples.20 To avoid any false positive
result we have taken all the usual precautions and we also confirmed it by two different, techniques
and staff. Thirdly we restricted our analyses to only a few samples and we chose to limit the selected
records to ICU patients with compatible symptoms and CT, even though most patients actually have
mild symptoms. Fourthly, we restricted our analyses to patients with a negative multiplex PCR at the
time even though cross contamination has been described in literature.9 Finally, we conducted a
monocentric study in the Northern Paris area, which faced a particularly high burden in this
epidemic.21 These limitations could explain why we were only able to identify one person infected
with SARS-COV-2, in our population.

Declarations
Funding: No
Competing Interests: None

Ethical Approval: Not required

 References

1. Zhu, N. et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. New
England Journal of Medicine 382, 727–733 (2020).
2. Li, Q. et al. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–
Infected Pneumonia. New England Journal of Medicine 382, 1199–1207 (2020).
3. WHO Director-General’s opening remarks at the media briefing on COVID-19 - 11
March 2020. https://www.who.int/dg/speeches/detail/who-director-general-s-openingremarks-at-the-media-briefing-on-covid-19---11-march-2020.
4. Situation update worldwide, as of 12 April 2020. European Centre for Disease Prevention
and Control https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases.
5. Lescure, F.-X. et al. Clinical and virological data of the first cases of COVID-19 in
Europe: a case series. The Lancet Infectious Diseases 0, (2020).
6. Stoecklin, S. B. et al. First cases of coronavirus disease 2019 (COVID-19) in France:
surveillance, investigations and control measures, January 2020. Eurosurveillance 25,
2000094 (2020).
7. Guan, W. et al. Clinical Characteristics of Coronavirus Disease 2019 in China. New
England Journal of Medicine (2020) doi:10.1056/NEJMoa2002032.
8. Communicable-disease-threats-report-4-apr-2020.pdf.
9. Wu, X. et al. Early Release - Co-infection with SARS-CoV-2 and Influenza A Virus in
Patient with Pneumonia, China - Volume 26, Number 6—June 2020 - Emerging
Infectious Diseases journal - CDC. doi:10.3201/eid2606.200299.
10. Acute Respiratory Distress Syndrome: The Berlin Definition. JAMA 307, 2526–2533
(2012).
11. Corman, V. M. et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RTPCR. Eurosurveillance 25, 2000045 (2020).
12. Shi, H. et al. Radiological findings from 81 patients with COVID-19 pneumonia in
Wuhan, China: a descriptive study. The Lancet Infectious Diseases 20, 425–434 (2020).

 13. Caruso, D. et al. Chest CT Features of COVID-19 in Rome, Italy. Radiology 201237
(2020) doi:10.1148/radiol.2020201237.
14. Huang, C. et al. Clinical features of patients infected with 2019 novel coronavirus in
Wuhan, China. The Lancet 395, 497–506 (2020).
15. Shi, F., Yu, Q., Huang, W. & Tan, C. 2019 Novel Coronavirus (COVID-19) Pneumonia
with Hemoptysis as the Initial Symptom: CT and Clinical Features. Korean Journal of
Radiology 21, (2020).
16. Mizumoto, K., Kagaya, K., Zarebski, A. & Chowell, G. Estimating the asymptomatic
proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond
Princess cruise ship, Yokohama, Japan, 2020. Eurosurveillance 25, 2000180 (2020).
17. Tuite, A. R., Ng, V., Rees, E. & Fisman, D. Estimation of COVID-19 outbreak size in
Italy. The Lancet Infectious Diseases 0, (2020).
18. Wynants, L. et al. Prediction models for diagnosis and prognosis of covid-19 infection:
systematic review and critical appraisal. BMJ 369, m1328 (2020).
19. Wang, W. et al. Detection of SARS-CoV-2 in Different Types of Clinical Specimens.
JAMA (2020) doi:10.1001/jama.2020.3786.
20. Röder, B., Frühwirth, K., Vogl, C., Wagner, M. & Rossmanith, P. Impact of Long-Term
Storage on Stability of Standard DNA for Nucleic Acid-Based Methods. J Clin Microbiol
48, 4260–4262 (2010).
21. Géodes - Santé publique France - Indicateurs : cartes, données et graphiques.
https://geodes.santepubliquefrance.fr/#view=map2&c=indicator.

 Figure 1. Selection process for testing.
SARS-COV-2 : severe acute respiratory syndrome coronavirus-2

 Figure 2. Result of Charite Protocol RT-PCR assay.
Patient’s curb in yellow, Positive and negative test sample in purple)

 Figure 3. Chest computed tomography performed at baseline.
Bilateral ground glass opacities appear in inferior lobes