SARS-CoV-2 Detection and Culture in Different Biological Specimens from Immunocompetent and Immunosuppressed COVID-19 Patients Infected with Two Different Viral Strains

• Published in: Viruses Vol. 15; no. 6; p. 1270
• Main Authors: Mendes-Correa, Maria Cássia, Salomão, Matias Chiarastelli, Ghilardi, Fábio, Tozetto-Mendoza, Tania Regina, Santos Villas-Boas, Lucy, de Paula, Anderson Vicente, Paiao, Heuder Gustavo Oliveira, da Costa, Antonio Charlys, Leal, Fábio E, Ferraz, Andrea de Barros Coscelli, Sales, Flavia C S, Claro, Ingra M, Ferreira, Noely E, Pereira, Geovana M, da Silva, Jr, Almir Ribeiro, Freire, Wilton, Espinoza, Evelyn Patricia Sánchez, Manuli, Erika R, Romano, Camila M, de Jesus, Jaqueline G, Sabino, Ester C, Witkin, Steven S
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 29-05-2023; MDPI
• Subjects: cell culture; COVID-19; COVID-19 - diagnosis; COVID-19 Testing; Genomes; Humans; Immune clearance; Immune response; Immune status; Immunocompetence; Infections; infectiousness; Influenza; Laboratories; Medical research; Medicine, Experimental; Patients; persistence; Replication; RNA, Viral - genetics; Saliva; SARS-CoV-2; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Specimen Handling; Urine; viral load dynamics; viral shedding; Virus Shedding; Viruses; Brazil; COVID-19; SARS-CoV-2; viral load dynamics; cell culture; viral shedding; persistence; infectiousness
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v15061270

Introduction-The dynamics of SARS-CoV-2 shedding and replication in humans remain incompletely understood. Methods-We analyzed SARS-CoV-2 shedding from multiple sites in individuals with an acute COVID-19 infection by weekly sampling for five weeks in 98 immunocompetent and 25 immunosuppressed individuals. Samples and culture supernatants were tested via RT-PCR for SARS-CoV-2 to determine viral clearance rates and in vitro replication. Results-A total of 2447 clinical specimens were evaluated, including 557 nasopharyngeal swabs, 527 saliva samples, 464 urine specimens, 437 anal swabs and 462 blood samples. The SARS-CoV-2 genome sequences at each site were classified as belonging to the B.1.128 (ancestral strain) or Gamma lineage. SARS-CoV-2 detection was highest in nasopharyngeal swabs regardless of the virus strain involved or the immune status of infected individuals. The duration of viral shedding varied between clinical specimens and individual patients. Prolonged shedding of potentially infectious virus varied from 10 days up to 191 days, and primarily occurred in immunosuppressed individuals. Virus was isolated in culture from 18 nasal swab or saliva samples collected 10 or more days after onset of disease. Conclusions-Our findings indicate that persistent SARS-CoV-2 shedding may occur in both competent or immunosuppressed individuals, at multiple clinical sites and in a minority of subjects is capable of in vitro replication.