This Hospital Assistance Publique – Hôpitaux de Paris (AP-HP) in Val-de-Marne manages one of the four national platforms for monitoring and sequencing the SARS-CoV-2 genome in order to identify the development variants.

“Technically we were ready to face a pandemic”, assures the head of the Biology-Pathology Pole Jean-Michel Pawlotsky and walks through his department with a confident step. His team, scattered in a labyrinth of rooms, has been studying the genome of viruses such as HIV and hepatitis since 2011.

With the advent of Covid-19 and its variants, the task took on a whole new dimension at the end of 2020. At the request of Public Health France and the ANRS Emerging Infection Diseases, linked to Inserm, the Créteil center received almost 3 million euros to hire ten technicians and adapt its technology to the study of SARS-Cov-2.

The sequencing of the “new generation”, which is divided into several phases, makes it possible to identify the virus by analyzing its genome, explains the virologist and head of the platform Christophe Rodriguez.

“Within ten years there has been a leap in technology: the sequencing and technology of messenger RNA vaccines have saved us valuable time for this epidemic,” Professor Pawlotsky is in abundance.

Every week, Henri-Mondor receives several thousand positive tests, collected by 200 laboratories in north-eastern France, using refrigerated trucks packed in airtight envelopes.

The platform was ramped up in the summer of 500 genome sequencing per week in early 2021 and now reaches 2,500 per week, partly thanks to the automation of the process.

In an air-conditioned room, two masked technicians carefully handle tubes of various sizes and colors. Under a hood, they carefully transfer the contaminated swabs into containers the size of the extractor, where the RNA is isolated by removing all cell debris.

After the extraction, the millions of long strands of RNA are cut into fragments in order to decipher a needle in the form of DNA on her lab coat under the watchful eye of laboratory assistant Vanessa Demontant.

A reader with a relatively ordinary appearance, but the latest version of which costs almost a million euros, finally makes it possible to compare the genome sequences with the reference sequence in order to identify the mutations.

The whole process takes 3 to 4 days and the results are fed into national and international databases, which, according to Professor Rodriguez, is a real one “Universal Covid Dictionary”.

The “Flash Studies” by Henri-Mondor also make it possible every week to draw a local cartography of variants with dominants and micro-emergences.

First Alpha, the English variant that arrived in France at the end of 2020, then Beta (South African) and Gamma (Brazil), which never got the advantage. Last March, the hospital also discovered its own variant, a minority called “Henri-Mondor”.

Read: Créteil: The Mondor variant weighs 2% of the Covid-19 contamination in France

After a wave in winter, Alpha was successively replaced by the Indian Delta, which is still largely in the majority at over 99% and is currently experiencing its second eruption.

It is this variant that is still preoccupying Professor Pawlotsky’s team, more so than Omicron, which is still very little present. “The question is whether Delta will give him his place or wait for his fall to get the upper hand,” he explains.

“The dominant variant is exhausted, and if it is not, another one takes over”. It all depends on their characteristics, but also on the chances of the epidemic. “What is certain is that the virus is there forever. You have to learn to live with it ”.

by Clara LALANNE