SARS-CoV-2 shedding, infectivity, and evolution in an immunocompromised adult patient

Mendes-Correa, Maria Cassia; Ghilardi, Fábio de Rose; Salomão, Matias Chiarastelli; Villas-Boas, Lucy Santos; Paula, Anderson Vicente de; Paiao, Heuder Gustavo Oliveira; Costa, Antonio Charlys da; Tozetto-Mendoza, Tânia Regina; Freire, Wilton; Sales, Flavia Cristina Silva; Claro, Ingra Morales; Sabino, Ester Cerdeira; Faria, Nuno Rodrigues; Witkin, Steven Sol

doi:10.1590/S1678-9946202466028

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CASE REPORT • Rev. Inst. Med. trop. S. Paulo 66 • 2024 • https://doi.org/10.1590/S1678-9946202466028 copy

SARS-CoV-2 shedding, infectivity, and evolution in an immunocompromised adult patient

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT

This study aimed to provide further insight into the evolutionary dynamics of SARS-CoV-2 by analyzing the case of a 40-year-old man who had previously undergone autologous hematopoietic stem cell transplantation due to a diffuse large B-cell lymphoma. He developed a persistent SARS-CoV-2 infection lasting at least 218 days and did not manifest a humoral immune response to the virus during this follow-up period. Whole-genome sequencing and viral cultures confirmed a persistent infection with a replication-positive virus that had undergone genetic variation for at least 196 days after symptom onset.

KEYWORDS
SARS-CoV-2; Cell culture; Evolution; Immunodeficiency; Shedding

Date of sample collection	Clinical specimen	PCR SARS-CoV-2 (Ct) of the clinical specimen		GS	CPE after the 1st passage in culture	PCR SARS-CoV-2 (Ct) after the 2^nd passage in culture		Final result of viral isolation (number of culture passages)

		Gene E	Gene S			Gene E	Gene S
September 9	NFS	24.8	25.2	T1	Positive	29.6	26.5	Positive (2)
November 25	NFS	21.1	21.1	T2	Positive	26	28	Positive (2)
December 25	NFS	32.6	30		Negative	ND	ND	Negative (2)
January 15	NFS	31.5	31.7		Positive	35,93	ND	Positive (2)
January 21	NFS	16.6 35.3	16.9 35.5	T5	Positive	19.9 ND	ND ND	Positive (2)
January 21	Serum	16.6 35.3	16.9 35.5	T5	Positive	19.9 ND	ND ND	Positive (2)
January 28	NFS	14.9	15.2		Positive	12.5	11.6	Positive (2)
	Saliva	30.0	30		Positive	33	32	Positive (2)
	Serum	32.7	ND		Negative	ND	ND	Negative (2)
February 4	NFS	18.5	17.5		Positive	22	21	Positive (2)
	Saliva	20.8	21.0		Positive	25	24	Positive (2)
	Serum	32.7	32.8		Negative	ND	ND	Negative (2)
February 11	NFS	16,5	16.9		Positive	16	15	Positive (2)
	Saliva	31.2	31.3		Positive	34,9	33	Positive (2)
	Anal Swab	34.8	ND		Negative	ND	ND	Negative (2)
	Serum	37.2	38.7		Negative	ND	ND	Negative (2)
February 18	NFS	21.0	22.1		Positive	23	21.9	Positive (3)
	Saliva	37.0	ND		Negative	ND	ND	Negative (2)
	Urine	34.9	ND		Negative	ND	ND	Negative (2)
February 25	NFS Saliva Urine	15.7	15.6	T10	Positive	19	18	Positive (3)
	Saliva	31.0	30.7		Positive	ND	ND	Negative (2)
	Urine	34.7	ND		Positive	ND	ND	Negative (2)
March 18	NFS	23.8	23.6	T11	Negative	ND	ND	Negative (2)
April 9	NFS	35.1	36.4		Negative	ND	ND	Negative (2)

Instituto de Medicina Tropical de São Paulo Av. Dr. Enéas de Carvalho Aguiar, 470, 05403-000 - São Paulo - SP - Brazil, Tel. +55 11 3061-7005 - São Paulo - SP - Brazil
E-mail: revimtsp@usp.br

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[1] Correspondence to: Maria Cassia Mendes-Correa Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo (LIM-52), Av. Dr. Enéas Carvalho de Aguiar, 470, CEP 05403-000, São Paulo, SP, Brazil E-mail: cassiamc@uol.com.br