Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru

Author(s)

Justo Arevalo, Santiago ; Uribe Calampa, Carmen Sofia ; Jimenez Silva, Cinthy ; Quinones Aguilar, Mauro ; Bouckaert, Remco ; Rebello Pinho, Joao Renato

• Document type: Journal article
• Source: NATURE COMMUNICATIONS; v. 14, n. 1, p. 13-pg., 2023-06-15.

Abstract

At over 0.6% of the population, Peru has one of the highest SARS-CoV-2 mortality rate in the world. Much effort to sequence genomes has been done in this country since mid-2020. However, an adequate analysis of the dynamics of the variants of concern and interest (VOCIs) is missing. We investigated the dynamics of the COVID-19 pandemic in Peru with a focus on the second wave, which had the greatest case fatality rate. The second wave in Peru was dominated by Lambda and Gamma. Analysis of the origin of Lambda shows that it most likely emerged in Peru before the second wave (June-November, 2020). After its emergence it reached Argentina and Chile from Peru where it was locally transmitted. During the second wave in Peru, we identify the coexistence of two Lambda and three Gamma sublineages. Lambda sublineages emerged in the center of Peru whereas the Gamma sublineages more likely originated in the north-east and mid-east. Importantly, it is observed that the center of Peru played a prominent role in transmitting SARS-CoV-2 to other regions within Peru. (AU)

• FAPESP's process: 15/13318-4 - Structural engineering of the active site of diguanylate cyclase (GGDEF) domains to produce new second messengers
• Grantee: Santiago Justo Arevalo
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 22/00943-1 - Structural and functional studies on the cyanide degrading enzyme CynD from Bacillus safensis PER-URP-08
• Grantee: Santiago Justo Arevalo
• Support Opportunities: Scholarships in Brazil - Post-Doctoral