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. 2021 Oct;93(10):5961-5968.
doi: 10.1002/jmv.27167. Epub 2021 Jul 16.

Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru

Eduardo Juscamayta-López  1   2 , Dennis Carhuaricra  2 , David Tarazona  1   2 , Faviola Valdivia  1 , Nancy Rojas  3 , Lenin Maturrano  2 , Ronnie Gavilán  4   5
Affiliations

Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru

Eduardo Juscamayta-López et al. J Med Virol. 2021 Oct.

Abstract

Peru has become one of the countries with the highest mortality rates from the current coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To investigate early transmission events and the genomic diversity of SARS-CoV-2 isolates circulating in Peru in the early COVID-19 pandemic, we analyzed 3472 viral genomes, of which 149 were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia and a high diversity of genetic lineages circulating in Peru. In addition, we found evidence for community-driven transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different regions of Peru.

Keywords: SARS-CoV-2; evolution; molecular epidemiology; phylogenomics; transmission; whole-genome sequencing.

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Conflict of interest statement

The authors declare that there are no conflicts of interest.

Figures

Figure 1
Figure 1
Geographic distribution of the Peruvian SARS‐CoV‐2 isolates circulating across regions of Peru. (A) Distribution of sequenced cases across Peru departments. (B) Breakdown of sequenced cases according to phylogenetic clades across Peru departments. SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2
Figure 2
Figure 2
Phylogenetic relationships of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) from Peru and other global strains. (A) Maximum‐Likelihood phylodynamic inference of 149 SARS‐CoV‐2 sequences from Peru in a global background of 3323 sequences available in the GISAID database as of 4 July 2020. Branches are colored according to the region of origin. Tip circles (red) indicate the position of the 149 Peruvian isolates. Clades that contain Peru sequences are highlighted, with names shown on the left. The node positions for the transmission events are marked by the numbers in white circles. (B) Stacked bar plot showing the fraction of genome sequences per location by clade. (C) Local transmission clusters on the ML tree showing the source of cases by departments. Bootstrap support values ≥ 70% are shown; sibling clusters are collapsed for easier visualization. The mutations identified specific to the community transmission cluster are indicated (ORF1b: H604Y; S: Y119V). The scale bar at the bottom indicates the number of nucleotide substitutions per site
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