A nationwide indicator to smooth and normalize heterogeneous SARS-CoV-2 RNA data in wastewater.

Since many infected people experience no or few symptoms, the SARS-CoV-2 epidemic is frequently monitored through massive virus testing of the population, an approach that may be biased and may be difficult to sustain in low-income countries. Since SARS-CoV-2 RNA can be detected in stool samples, quantifying SARS-CoV-2 genome by RT-qPCR in wastewater treatment plants (WWTPs) has been carried out as a complementary tool to monitor virus circulation among human populations. However, measuring SARS-CoV-2 viral load in WWTPs can be affected by many experimental and environmental factors. To circumvent these limits, we propose here a novel indicator, the wastewater indicator (WWI), that partly reduces and corrects the noise associated with the SARS-CoV-2 genome quantification in wastewater (average noise reduction of 19%). All data processing results in an average correlation gain of 18% with the incidence rate. The WWI can take into account the censorship linked to the limit of quantification (LOQ), allows the automatic detection of outliers to be integrated into the smoothing algorithm, estimates the average measurement error committed on the samples and proposes a solution for inter-laboratory normalization in the absence of inter-laboratory assays (ILA). This method has been successfully applied in the context of Obépine, a French national network that has been quantifying SARS-CoV-2 genome in a representative sample of French WWTPs since March 5th 2020. By August 26th, 2021, 168 WWTPs were monitored in the French metropolitan and overseas territories of France. We detail the process of elaboration of this indicator, show that it is strongly correlated to the incidence rate and that the optimal time lag between these two signals is only a few days, making our indicator an efficient complement to the incidence rate. This alternative approach may be especially important to evaluate SARS-CoV-2 dynamics in human populations when the testing rate is low.

[Biochemical and statistical lessons from the evolution of the SARS-CoV-2 virus: paths for novel antiviral warfare]. / Leçons biochimiques et statistiques de l'évolution du virus SARS-CoV-2 : nouveaux chemins pour combattre les virus.

In the fight against the spread of COVID-19 the emphasis is on vaccination or on reactivating existing drugs used for other purposes. The tight links that necessarily exist between the virus as it multiplies and the metabolism of its host are systematically ignored. Here we show that the metabolism of all cells is coordinated by the availability of a core building block of the cell's genome, cytidine triphosphate (CTP). This metabolite is also the key to the synthesis of the viral envelope and to the translation of its genome into proteins. This unique role explains why evolution has led to the early emergence in animals of an antiviral immunity enzyme, viperin, that synthesizes a toxic analogue of CTP. The constraints arising from this dependency guide the evolution of the virus. With this in mind, we explored the real-time experiment taking place before our eyes using probabilistic modelling approaches to the molecular evolution of the virus. We have thus followed, almost on a daily basis, the evolution of the composition of the viral genome to link it to the progeny produced over time, particularly in the form of blooms that sparked a firework of viral mutations. Some of those certainly increase the propagation of the virus. This led us to make out the critical role in this evolution of several proteins of the virus, such as its nucleocapsid N, and more generally to begin to understand how the virus ties up the host metabolism to its own benefit. A way for the virus to escape CTP-dependent control in cells would be to infect cells that are not expected to grow, such as neurons. This may account for unexpected body sites of viral development in the present epidemic.

Dans la lutte contre la propagation de la COVID-19 l'accent est mis sur la vaccination, d'une part, et sur le redéploiement de traitements utilisés pour d'autres usages, d'autre part. Les liens qui existent nécessairement entre la multiplication du virus et le métabolisme de l'hôte sont systématiquement ignorés. Ici nous montrons que le métabolisme de toutes les cellules est coordonné par l'accessibilité d'un composant central du génome cellulaire, le triphosphate de cytidine (CTP). Ce métabolite est aussi la clé de la synthèse de l'enveloppe virale et de la traduction de son génome en protéines. Ce rôle unique explique pourquoi l'évolution a fait apparaître très tôt chez les animaux une activité enzymatique de l'immunité antivirale, la vipérine, destinée à synthétiser un analogue toxique du CTP. Les contraintes nées de cette dépendance orientent l'évolution du virus. Avec cette servitude à l'esprit, nous avons exploré l'expérience en vraie grandeur qui se déroule sous nos yeux au moyen d'approches de modélisation probabiliste de l'évolution moléculaire du virus. Nous avons ainsi suivi, presque au jour le jour, le devenir de la composition du génome viral pour la relier à la descendance produite au cours du temps, en particulier sous la forme d'efflorescences où apparaît un véritable feu d'artifice de mutations virales. Certaines d'entre elles augmentent certainement la propagation du virus. Cela nous conduit à proposer un rôle important dans cette évolution à certaines protéines du virus, comme celle de la nucléocapside N et plus généralement de commencer à comprendre comment le virus asservit à son bénéfice le métabolisme de l'hôte. L'un des moyens possibles pour le virus d'échapper au contrôle par le CTP serait d'infecter des cellules qui ne se multiplient pas, comme les neurones. Cela pourrait expliquer les sites de développement viral inattendus qu'on observe dans l'épidémie actuelle.