map, currency by region, where are we?

[Mise à jour le vendredi 20 novembre à 09h47] R0 (or actual R) designates the rate of reproduction of a virus. It concerns average number of new cases caused by an infected person in a population without immunity. It takes into account several indicators (positive tests, hospitalizations or emergency room visits). The two to keep an eye on in particular are hospitalizations and emergencies. As of November 19, three weeks after the start of childbirth, according to data from Public Health France, it is less than 1 in all regions French. To understand, a rate greater than 1 means that an infected person contaminates on average more than another and therefore that the epidemic is progressing. Conversely, when it falls below 1, it falls. Which is R0 ? The effective R ? How is it calculated? What is its national rate? And in every region of France? Menu and explanations.

Being able to quantify the transmission capacity of a virus during an epidemic is essential to implement measures at the right time to stop it (especially when there is no treatment or vaccine as in the case of Covid-19). This capacity called “transmissibility” is measured by the R virus reproduction number, also called “reproduction rate”, ie the average number of secondary cases caused by a single infected person during his contagious period. We must therefore distinguish:

• the number of reproductions of the virus during the epidemic crisis: the “R effective” (the one given by the French health authorities since June)
• of the initial breeding number at the beginning of the outbreak that was called “R0”.

“The goal of control efforts is to reduce R below the limit value of 1 and as close to 0 as possible, thus bringing an outbreak under control.“explained Anne Cori in an article in the American Journal of Epidemiology in 2013. In the case of the coronavirus which is a virus very contagious, this R0 was before delivery at 3 or more. For the same virus, R0 can vary from one population to another depending on population density, susceptibility, and other factors.

To confront : the R0 of influenza in France has been reduced to less than 1 thanks to the vaccination policy that immunizes part of the population. The OR for measles it is 16. The The SARS OR in 2003 was 3 and it was reduced to 0.5 which made it possible to stop the epidemic.

The R0 (initial virus reproduction rate) is calculated from a population that is fully susceptible to infection (i.e. that has not yet been vaccinated or immunized against an infectious agent). It is the product of three factors: R0 = ßcD.

• ß = risk of contracting the virus during contact (hence the respect of a social distance of at least 1 meter recommended at the moment),
• c = the number of contacts in a unit of time : if we reduce the number of contacts by half, we reduce R0 Half.
• D = the number of days an infected person is contagious (up to 14 days for coronavirus).

There are therefore several methods to estimate the actual R. In France, it is the Cori’s method (named Anne Cori, researcher at Imperial College London, specializing in infectious diseases) who was selected by Santé Publique France in its weekly epidemiological points. This R can be calculated from several indicators.

• the Reff calculated from the number of confirmed cases in France (virological data, SI-DEP)
• the Reff calculated from the data of the emergency visits (OSCOUR®)
• from 24 September, the actual R calculated from hospitalization data for COVID-19 cases (SI-VIC data)

→ The actual R is an indicator of the dynamics of virus transmission approximately 1 to 2 weeks earlier (including the time between contamination and testing and the fact that the calculation is made over a period of 7 days).

Calculation of R is important for assessing the epidemiological situation in a department or region. Since the start of the Covid-19 epidemic in France, the Ministry of Health has kept repeating that the goal is for the virus’ reproduction rate to drop below 1. The “1” is therefore the supervisory point. An R greater than 1 means that the virus is starting to circulate again and therefore that the epidemic is progressing. An R of 1.4 corresponds to a doubling time of cases of approximately 2 weeks.

• 1
• R> 1.5: warning threshold

Reproduction rates calculated from emergency room visits and hospitalizations are those to be followed as a priority in the coming weeks.

Since the end of June, we have observed a marked increase in the reproduction rate. Estimates of the number of weekly reproductions are based on the number of positive PCR tests for SARS-COV-2, on emergency room visits for suspected COVID-19 and hospitalizations. November 19, three weeks after the start of the confinement in France, the R rate is less than 1 in metropolitan France in the three data sources: from SI-DEP virological data (0.65), from visits to the emergency room (0.87) and hospitalization data (0.89): “These three reproduction rates are decreasing compared to the previous week’s estimates “ states Public Health France in its epidemiological bulletin of November 19. Reproduction rates calculated from emergency room visits and hospitalizations are those monitored as a priority by the government.

Actual Reproduction Number Curve (R-effective) based on positive PCR tests for SARS-COV-2, emergency room visits suspected of COVID-19, and hospitalizations for COVID-19 in metropolitan France from March 15 to November 14, 2020.

As a reminder : March 15, 2020, shortly before the confinement of France and the peak of the outbreak, the actual R0 had been estimated at 2.8. Then he went to 0.8 the May 11, 2020, at the beginning of the decline and had dropped to 0.73 according to the June 11 Public Health France report. It was at 1.14 on November 4th, a week after the start of the second block.

According to the French public health epidemiological bulletin of 19 “no region, both in metropolitan France and abroad, shows a staff estimate significantly higher than 1 in week 46 (9-15 November”.

→ Reproduction rate estimates from virological PCR (SI-DEP) data are less than 1 for all regions metropolitan.

→ Even those carried out by emergency room visits and hospitalization data are less than 1 in almost all metropolitan regions, except in the Grand-Est region where the estimates are greater than 1 “but not significantly” specifies the agency and in Bourgogne-Franche-Comté, where the estimate from the hospitalization data is greater than 1, “but not significantly”.

Number of effective (R-effective) reproductions from SARS-CoV-2 positive PCR tests, COVID-19 suspected emergency visits and COVID-19 hospitalizations by region, metropolitan and ultra-marine France, on rolling 7 days (from 08 to 14 November 2020 for SI-DEP and OSCOUR®, from 09 to 15 November for SI-VIC)

Reproduction rate is only an indicator and, like all indicators, it should not be considered alone. Indeed, this number of virus reproductions varies over time and space. Three other indicators are being monitored by the French government to observe the evolution of the coronavirus epidemic in France from decline. “As soon as a threshold (vigilance and / or alert) is exceeded, a thorough risk analysis is initiated in order to identify the causes of the signal and trigger an alarm if this proves necessary” the Ministry of Health explained in a press release on 8 July.

→ The incidence of the epidemic, i.e. the number of people infected within a week per 100,000 inhabitants: estimated based on the number of positive RT-PCR tests (tests performed in the nose). If the figure is between 10 and 50: alarm threshold. If it is greater than 50: vigilance threshold. On November 19, the incidence rate of the virus in France is at 248.39.

→ The ICU bed occupancy rate by COVID patients compared to the initial ICU capacity

Hospital tensions on intensive care beds corresponding to the average occupancy rate of intensive care beds by patients with COVID-19, relative to the initial capacity of intensive care beds, by region: if the rate increases between 40 and 60% threshold of supervision. If it exceeds 60%, this is the warning threshold.

→ The number of positive virological tests for Covid-19 per 100,000 inhabitants per week

Since July, all French people, whether or not they have symptoms suggestive of Covid-19, whether they have a prescription or not, can go for testing. The positivity rate of the RT-PCR tests corresponding to the positivity rate of virological samples (tests carried out in the nose) carried out in each department is an indicator: if the rate is between 5 and 10%: alert threshold. If it is greater than 10%: warning threshold.

Source: COVID-19: epidemiological point of November 19, 2020. Public Health France.