# Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024

## TL;DR

This study tracks how SARS-CoV-2 evolved and spread in Peru from 2020 to 2024, showing how new variants like Lambda emerged and spread locally and internationally.

## Contribution

The study provides a detailed genomic epidemiology of SARS-CoV-2 in Peru, highlighting locally evolved variants and their global spread.

## Key findings

- Lima was the primary hub for viral spread within Peru, with significant movements to Ancash, Cusco, and Piura.
- Peru was a source of lineages that spread internationally to Chile, the USA, and Europe.
- Key mutations in the spike protein, such as L452Q and F490S in Lambda, were linked to immune evasion and increased transmissibility.

## Abstract

Peru recorded one of the world’s highest COVID-19 mortality rates, with nearly 4.5 million reported cases and 220,000 deaths by March 2024. Understanding the emergence and spread of SARS-CoV-2 variants in this context is key to informing effective public health responses. This study describes the genomic diversity, transmission dynamics, and geographic spread of SARS-CoV-2 in Peru from 2020 to 2024.

We analyzed nearly 50,000 high-quality public SARS-CoV-2 genome sequences collected nationwide between March 2020 and March 2024. Phylogeographic and mutational analyses were performed to identify variant lineages, trace their origins, and map viral movements within and beyond Peru.

We show that Peru’s epidemic waves were shaped by the emergence of locally evolved variants, including Lambda (C.37), Gamma (P.1.12), and Omicron (XBB.2.6 and DJ.1) sub-lineages. The city of Lima acted as the primary hub for inter-regional spread, accounting for 47.3% of inferred viral movements to other departments, notably Ancash, Cusco, and Piura. Peru was the source of various lineages that spread internationally, primarily to Chile, the USA, and Europe. Mutational analysis highlighted critical mutations in the spike protein, including L452Q and F490S in Lambda, associated with immune evasion and increased transmissibility.

This work demonstrates the capacity of genomic surveillance in Peru to detect and track emerging SARS-CoV-2 variants, providing insights into regional and global transmission dynamics in a high-transmission, middle-income country setting. Sustained, cost-effective genomic monitoring, combined with strengthened bioinformatics and laboratory capacity, is essential for pandemic preparedness in resource-limited settings.

Sobkowiak et al., present a comprehensive genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024, highlighting the emergence and spread of key variants including Lambda and Gamma P.1.12. The work provides valuable insights into regional viral transmission dynamics in a high-burden, middle-income setting, emphasizing the importance of sustained genomic surveillance.

Peru is one of the countries worst hit by COVID-19, with one of the highest death rates from the disease worldwide. We studied nearly 50,000 viral genomes (the complete set of the virus’s genetic instructions) collected across the country between March 2020 and March 2024 to understand how the virus evolved and spread between Peru’s 25 administrative regions. We demonstrate that new variants, including Lambda, first emerged in Peru and subsequently spread to other countries. The capital city of Lima was the central hub for the virus’s spread to other regions of Peru. We identified changes in the genome that may help it transmit better or evade host defences. Our findings demonstrate how genomic surveillance can help in tracking new variants and inform efforts to control future outbreaks.