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Article

Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration

1
i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
2
Ipatimup—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
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ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
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CHUSJ—Centro Hospitalar Universitário S. João, 4200-319 Porto, Portugal
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FMUP—Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
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IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
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EPIUnit—Instituto de Saúde Pública, Universidade do Porto, 4050-091 Porto, Portugal
*
Author to whom correspondence should be addressed.
Authors contributed equally to this work.
Academic Editor: Hanna M. Oksanen
Microorganisms 2021, 9(2), 300; https://doi.org/10.3390/microorganisms9020300
Received: 18 January 2021 / Revised: 27 January 2021 / Accepted: 28 January 2021 / Published: 2 February 2021
(This article belongs to the Special Issue From Host-Pathogen Interaction to Host-Directed Therapies)
A few molecularly proven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases of symptomatic reinfection are currently known worldwide, with a resolved first infection followed by a second infection after a 48 to 142-day intervening period. We report a multiple-component study of a clinically severe and prolonged viral shedding coronavirus disease 2019 (COVID-19) case in a 17-year-old Portuguese female. She had two hospitalizations, a total of 19 RT-PCR tests, mostly positive, and criteria for releasing from home isolation at the end of 97 days. The viral genome was sequenced in seven serial samples and in the diagnostic sample from her infected mother. A human genome-wide array (>900 K) was screened on the seven samples, and in vitro culture was conducted on isolates from three late samples. The patient had co-infection by two SARS-CoV-2 lineages, which were affiliated in distinct clades and diverging by six variants. The 20A lineage was absolute at the diagnosis (shared with the patient’s mother), but nine days later, the 20B lineage had 3% frequency, and two months later, the 20B lineage had 100% frequency. The 900 K profiles confirmed the identity of the patient in the serial samples, and they allowed us to infer that she had polygenic risk scores for hospitalization and severe respiratory disease within the normal distributions for a Portuguese population cohort. The early-on dynamic co-infection may have contributed to the severity of COVID-19 in this otherwise healthy young patient, and to her prolonged SARS-CoV-2 shedding profile. View Full-Text
Keywords: COVID-19 and SARS-CoV-2; viral shedding; co-infection; viral whole-genome sequencing; polygenic risk score COVID-19 and SARS-CoV-2; viral shedding; co-infection; viral whole-genome sequencing; polygenic risk score
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MDPI and ACS Style

Pedro, N.; Silva, C.N.; Magalhães, A.C.; Cavadas, B.; Rocha, A.M.; Moreira, A.C.; Gomes, M.S.; Silva, D.; Sobrinho-Simões, J.; Ramos, A.; Cardoso, M.J.; Filipe, R.; Palma, P.; Ceia, F.; Silva, S.; Guimarães, J.T.; Sarmento, A.; Fernandes, V.; Pereira, L.; Tavares, M. Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration. Microorganisms 2021, 9, 300. https://doi.org/10.3390/microorganisms9020300

AMA Style

Pedro N, Silva CN, Magalhães AC, Cavadas B, Rocha AM, Moreira AC, Gomes MS, Silva D, Sobrinho-Simões J, Ramos A, Cardoso MJ, Filipe R, Palma P, Ceia F, Silva S, Guimarães JT, Sarmento A, Fernandes V, Pereira L, Tavares M. Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration. Microorganisms. 2021; 9(2):300. https://doi.org/10.3390/microorganisms9020300

Chicago/Turabian Style

Pedro, Nicole, Cláudio N. Silva, Ana C. Magalhães, Bruno Cavadas, Ana M. Rocha, Ana C. Moreira, Maria S. Gomes, Diogo Silva, Joana Sobrinho-Simões, Angélica Ramos, Maria J. Cardoso, Rita Filipe, Pedro Palma, Filipa Ceia, Susana Silva, João T. Guimarães, António Sarmento, Verónica Fernandes, Luisa Pereira, and Margarida Tavares. 2021. "Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration" Microorganisms 9, no. 2: 300. https://doi.org/10.3390/microorganisms9020300

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