Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity.

Adult; COVID-19/diagnosis/epidemiology/transmission/virology; Epidemiological Monitoring; Female; Genome, Viral/genetics; Humans; Male; Phylogeny; Phylogeography; RNA, Viral/genetics/isolation & purification; Rwanda/epidemiology; SARS-CoV-2/genetics/isolation & purification/pathogenicity; Travel-Related Illness; Whole Genome Sequencing

Abstract :

[en] COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.

Disciplines :

Microbiology

Author, co-author :

Butera, Yvan

Mukantwari, Enatha

Artesi, Maria ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Génétique humaine

Umuringa, Jeanne D Arc

O'Toole, Áine Niamh

Hill, Verity

Rooke, Stefan

Hong, Samuel Leandro

Dellicour, Simon

Majyambere, Onesphore

More authors (26 more)

^✱ These authors have contributed equally to this work.

Language :

English

Title :

Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity.

Publication date :

2021

Journal title :

Nature Communications

eISSN :

2041-1723

Publisher :

Nature Publishing Group, United Kingdom

Volume :

Issue :

Pages :

5705

Peer reviewed :

Peer Reviewed verified by ORBi

Commentary :

Available on ORBi :

since 22 October 2021

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