COVID-19 Re-Infection by a Phylogenetically Distinct SARS-CoV-2 Variant, First Confirmed Event in South America.

11 Pages Posted: 8 Sep 2020

See all articles by Belen Prado-Vivar

Belen Prado-Vivar

USFQ

Monica Becerra-Wong

Universidad San Francisco de Quito (USFQ)

Juan Jose Guadalupe

Universidad San Francisco de Quito (USFQ)

Sully Marquez

Universidad San Francisco de Quito (USFQ)

Bernardo Gutierrez

Universidad San Francisco de Quito (USFQ)

Patricio Rojas-Silva

Universidad San Francisco de Quito (USFQ)

Michelle Grunauer

Universidad San Francisco de Quito (USFQ)

Gabriel Trueba

Universidad San Francisco de Quito (USFQ)

Veronica Barragan

Universidad San Francisco de Quito (USFQ)

Paul Cardenas

Universidad San Francisco de Quito (USFQ)

Date Written: September 3, 2020

Abstract

The permanence of rt-PCR positivity after a long time in COVID-19 patients has prompted the question of whether SARS-CoV-2 could cause a persistent infection or patients can become re-infected by this virus. Both possibilities could have critical implications for the management and control of COVID-19. Here we present the first confirmed case of SARS-CoV-2 reinfection in Ecuador and South America.

Materials and methods: Our diagnostic laboratory detected a potential re-infection in one patient who was SARS-COv2 rt-PCR positive twice (in May and July 2020). The first laboratory-confirmed infection presented with mild symptoms and full recovery, reaffirmed by a negative RT-PCR test result obtained two weeks after symptom onset. More severe COVID-19-like symptoms presented again four weeks after the first event, and a third RT-PCR test was performed which resulted positive. The total RNA extraction (from the samples collected on both occasions) was sequenced in an Oxford Nanopore MinION using a tilling PCR protocol developed by the ARTIC-Network, and the reads were analyzed using the artic-medaka consensus generation tool. Anti SARS-CoV-2 IgM and IgG antibodies were investigated.

Results: different SARS-CoV-2 variants were identified in each infection event. For the first infection, the genome was assigned to the B1.p9 GISAID clade while the variant associated with the second episode was assigned to the A.1.1 GISAID clade. High levels of both SARS-CoV-2 specific IgM and IgG were observed during the second event.

Discussion: a patient with two COVID-19 events presented two different SARS-CoV-2 variants on each event, confirming reinfection. This phenomenon is still considered rare.

Note: Funding: This work was funded by Universidad San Francisco de Quito and CADDE project (www.caddecentre.org/). P.C. is funded by NIH FIC D43TW010540 Global Health Equity Scholars.

Conflict of Interest: The authors do not report conflicts of interest.

Keywords: SARS-CoV-2, COVID-19, reinfection, whole-genome sequencing

Suggested Citation

Prado-Vivar, Belen and Becerra-Wong, Monica and Guadalupe, Juan Jose and Marquez, Sully and Gutierrez, Bernardo and Rojas-Silva, Patricio and Grunauer, Michelle and Trueba, Gabriel and Barragan, Veronica and Cardenas, Paul, COVID-19 Re-Infection by a Phylogenetically Distinct SARS-CoV-2 Variant, First Confirmed Event in South America. (September 3, 2020). Available at SSRN: https://ssrn.com/abstract=3686174 or http://dx.doi.org/10.2139/ssrn.3686174

Belen Prado-Vivar

USFQ ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Monica Becerra-Wong

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Juan Jose Guadalupe

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Sully Marquez

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Bernardo Gutierrez

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Patricio Rojas-Silva

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Michelle Grunauer

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Gabriel Trueba

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Veronica Barragan

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Paul Cardenas (Contact Author)

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

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