Persistent SARS-CoV-2 infection with repeated clinical recurrence in a patient with common variable immunodeficiency

doi:10.1016/j.cmi.2021.10.021

. 2022 Feb;28(2):308-310.

doi: 10.1016/j.cmi.2021.10.021. Epub 2021 Nov 10.

Persistent SARS-CoV-2 infection with repeated clinical recurrence in a patient with common variable immunodeficiency

Marta Dafne Cabañero-Navalon¹, Victor Garcia-Bustos², Paula Ruiz-Rodriguez³, Iñaki Comas⁴, Mireia Coscollá³, Llúcia Martinez-Priego⁵, José Todolí¹, Pedro Moral Moral¹

Affiliations

¹ Department of Internal Medicine and Infectious Diseases, Hospital Universitari i Politècnic La Fe, Valencia, Spain.
² Department of Internal Medicine and Infectious Diseases, Hospital Universitari i Politècnic La Fe, Valencia, Spain. Electronic address: victorgarciabustos@gmail.com.
³ Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain.
⁴ Biomedical Institute of Valencia IBV-CSIC, Valencia, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain.
⁵ Servicio de Secuenciación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad valenciana (FISABIO), Valencia, Spain.

PMID: 34774757
PMCID: PMC8579735
DOI: 10.1016/j.cmi.2021.10.021

Persistent SARS-CoV-2 infection with repeated clinical recurrence in a patient with common variable immunodeficiency

Marta Dafne Cabañero-Navalon et al. Clin Microbiol Infect. 2022 Feb.

. 2022 Feb;28(2):308-310.

doi: 10.1016/j.cmi.2021.10.021. Epub 2021 Nov 10.

Authors

Marta Dafne Cabañero-Navalon¹, Victor Garcia-Bustos², Paula Ruiz-Rodriguez³, Iñaki Comas⁴, Mireia Coscollá³, Llúcia Martinez-Priego⁵, José Todolí¹, Pedro Moral Moral¹

Affiliations

¹ Department of Internal Medicine and Infectious Diseases, Hospital Universitari i Politècnic La Fe, Valencia, Spain.
² Department of Internal Medicine and Infectious Diseases, Hospital Universitari i Politècnic La Fe, Valencia, Spain. Electronic address: victorgarciabustos@gmail.com.
³ Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain.
⁴ Biomedical Institute of Valencia IBV-CSIC, Valencia, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain.
⁵ Servicio de Secuenciación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad valenciana (FISABIO), Valencia, Spain.

PMID: 34774757
PMCID: PMC8579735
DOI: 10.1016/j.cmi.2021.10.021

No abstract available

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Figures

**Fig. 1**
Whole-genome viral sequencing of subsequent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patient's isolates during hospital admissions. (a) Maximum-likelihood phylogeny of 191 SARS-CoV-2 genomes rooted with reference sequence from Wuhan. Bootstrap values ranging from 70 to 100 are represented in nodes as circles whose size is proportional to the value. Branches are coloured by identified PANGO lineages. Branches leading to the three sequences of interest are coloured red and marked with a red star. The scale bar indicates the number of nucleotide substitutions per site. (b) Intra-host variation along three sampling times and its corresponding Cycle threshold (Ct) values detected for N gene. Non-synonymous changes are plotted in panels on the left and synonymous changes on the right. Upper panel shows non-fixed single nucleotide polymorphisms (SNPs) in the first sample, middle panel shows non-fixed SNPs in the second sample, and lower panel shows non-fixed and fixed SNPs in the third sample.

**Fig. 2**
Amino acid replacements in the sequenced samples and timeline of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection course in our patient. (a) Amino acid replacements found in at least one of three analysed samples indicated on a graphical representation of the SARS-CoV-2 genome. Amino acid replacements in black indicate those fixed in at least one of the samples, in grey those that only appeared transitorily but did not get fixed. Underlined amino acid replacements are the ones shared by all three sampling points. (b) Timeline of patient's clinical evolution, hospital admissions, virological studies and treatments. BAL, bronchoalveolar lavage.

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References

1. Choudhary M.C., Crain C.R., Qiu X., Hanage W., Li J.Z. SARS-CoV-2 sequence characteristics of COVID-19 persistence and reinfection. Clin Infect Dis. 2021 - PMC - PubMed
1. Kemp S.A., Collier D.A., Datir R.P., Ferreira I.A.T.M., Gayed S., Jahun A., et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature. 2021;592:277–282. - PMC - PubMed
1. Sepulcri C., Dentone C., Mikulska M., Bruzzone B., Lai A., Fenoglio D., et al. The longest persistence of viable SARS-CoV-2 with recurrence of viremia and relapsing symptomatic COVID-19 in an immunocompromised patient—a case study. Open Forum Infect Dis. 2021;8 - PMC - PubMed
1. Choi B., Choudhary M.C., Regan J., Sparks J.A., Padera R.F., Qiu X., et al. Persistence and evolution of SARS-CoV-2 in an immunocompromised host. N Engl J Med. 2020;383:2291–2293. - PMC - PubMed
1. Hueso T., Pouderoux C., Péré H., Beaumont A.L., Raillon L.A., Ader F., et al. Convalescent plasma therapy for B-cell-depleted patients with protracted COVID-19. Blood. 2020;136:2290–2295. - PMC - PubMed

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[1] Choudhary M.C., Crain C.R., Qiu X., Hanage W., Li J.Z. SARS-CoV-2 sequence characteristics of COVID-19 persistence and reinfection. Clin Infect Dis. 2021 - PMC - PubMed

[2] Choudhary M.C., Crain C.R., Qiu X., Hanage W., Li J.Z. SARS-CoV-2 sequence characteristics of COVID-19 persistence and reinfection. Clin Infect Dis. 2021 - PMC - PubMed

[3] Kemp S.A., Collier D.A., Datir R.P., Ferreira I.A.T.M., Gayed S., Jahun A., et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature. 2021;592:277–282. - PMC - PubMed

[4] Kemp S.A., Collier D.A., Datir R.P., Ferreira I.A.T.M., Gayed S., Jahun A., et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature. 2021;592:277–282. - PMC - PubMed

[5] Sepulcri C., Dentone C., Mikulska M., Bruzzone B., Lai A., Fenoglio D., et al. The longest persistence of viable SARS-CoV-2 with recurrence of viremia and relapsing symptomatic COVID-19 in an immunocompromised patient—a case study. Open Forum Infect Dis. 2021;8 - PMC - PubMed

[6] Sepulcri C., Dentone C., Mikulska M., Bruzzone B., Lai A., Fenoglio D., et al. The longest persistence of viable SARS-CoV-2 with recurrence of viremia and relapsing symptomatic COVID-19 in an immunocompromised patient—a case study. Open Forum Infect Dis. 2021;8 - PMC - PubMed

[7] Choi B., Choudhary M.C., Regan J., Sparks J.A., Padera R.F., Qiu X., et al. Persistence and evolution of SARS-CoV-2 in an immunocompromised host. N Engl J Med. 2020;383:2291–2293. - PMC - PubMed

[8] Choi B., Choudhary M.C., Regan J., Sparks J.A., Padera R.F., Qiu X., et al. Persistence and evolution of SARS-CoV-2 in an immunocompromised host. N Engl J Med. 2020;383:2291–2293. - PMC - PubMed

[9] Hueso T., Pouderoux C., Péré H., Beaumont A.L., Raillon L.A., Ader F., et al. Convalescent plasma therapy for B-cell-depleted patients with protracted COVID-19. Blood. 2020;136:2290–2295. - PMC - PubMed

[10] Hueso T., Pouderoux C., Péré H., Beaumont A.L., Raillon L.A., Ader F., et al. Convalescent plasma therapy for B-cell-depleted patients with protracted COVID-19. Blood. 2020;136:2290–2295. - PMC - PubMed

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Persistent SARS-CoV-2 infection with repeated clinical recurrence in a patient with common variable immunodeficiency

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Persistent SARS-CoV-2 infection with repeated clinical recurrence in a patient with common variable immunodeficiency

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