Cet article est une Preprint
Les preprints sont des rapports de recherche préliminaires qui n'ont pas été certifiés par l’évaluation par les pairs. Ils ne devraient pas être considérés comme guidant la pratique clinique ou les comportements liés à la santé et ne devraient pas être rapportés dans les médias comme des informations établies.
Les preprints publiées en ligne permettent aux auteurs de recevoir des commentaires rapidement, et toute la communauté scientifique peut évaluer indépendamment le travail et répondre en conséquence. Ces commentaires sont publiés avec les preprints que quiconque peut lire et servir d’évaluation post-publication.
Spread of Gamma (P.1) sub-lineages carrying Spike mutations close to the furin cleavage site and deletions in the N-terminal domain drives ongoing transmission of SARS-CoV-2 in Amazonas, Brazil (preprint)
medrxiv; 2021.
Preprint
Dans Anglais
| medRxiv | ID: ppzbmed-10.1101.2021.09.12.21263453
ABSTRACT
Summary The Amazonas was one of the most heavily affected Brazilian states by the COVID-19 epidemic. Despite a large number of infected people, particularly during the second wave associated with the spread of the Variant of Concern (VOC) Gamma (lineage P.1), SARS-CoV-2 continues to circulate in the Amazonas. To understand how SARS-CoV-2 persisted in a human population with a high immunity barrier, we generated 1,188 SARS-CoV-2 whole-genome sequences from individuals diagnosed in the Amazonas state from 1st January to 6th July 2021, of which 38 were vaccine breakthrough infections. Our study reveals a sharp increase in the relative prevalence of Gamma plus (P.1+) variants, designated as Pango Lineages P.1.3 to P.1.6, harboring two types of additional Spike changes deletions in the N-terminal (NTD) domain (particularly Δ 144 or Δ 141-144) associated with resistance to anti-NTD neutralizing antibodies or mutations at the S1/S2 junction (N679K or P681H) that probably enhance the binding affinity to the furin cleavage site, as suggested by our molecular dynamics simulations. As lineages P.1.4 (SN679K) and P.1.6 (SP681H) expanded (Re > 1) from March to July 2021, the lineage P.1 declined (Re < 1) and the median Ct value of SARS-CoV-2 positive cases in Amazonas significantly decreases. Still, we found no overrepresentation of P.1+ variants among breakthrough cases of fully vaccinated patients (71%) in comparison to unvaccinated individuals (93%). This evidence supports that the ongoing endemic transmission of SARS-CoV-2 in the Amazonas is driven by the spread of new local Gamma/P.1 sub-lineages that are more transmissible, although not more efficient to evade vaccine-elicited immunity than the parental VOC. Finally, as SARS-CoV-2 continues to spread in human populations with a declining density of susceptible hosts, the risk of selecting new variants with higher infectivity are expected to increase.
Texte intégral:
Disponible
Collection:
Preprints
Base de données:
medRxiv
langue:
Anglais
Année:
2021
Type de document:
Preprint
Documents relatifs à ce sujet
MEDLINE
...
LILACS
LIS