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Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma.
Borges, Vítor; Isidro, Joana; Cunha, Mário; Cochicho, Daniela; Martins, Luís; Banha, Luís; Figueiredo, Margarida; Rebelo, Leonor; Trindade, Maria Céu; Duarte, Sílvia; Vieira, Luís; Alves, Maria João; Costa, Inês; Guiomar, Raquel; Santos, Madalena; Cortê-Real, Rita; Dias, André; Póvoas, Diana; Cabo, João; Figueiredo, Carlos; Manata, Maria José; Maltez, Fernando; Gomes da Silva, Maria; Gomes, João Paulo.
  • Borges V; Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal.
  • Isidro J; Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal.
  • Cunha M; Clinical Pathology-Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal.
  • Cochicho D; Clinical Pathology-Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal.
  • Martins L; Clinical Pathology-Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal.
  • Banha L; Clinical Pathology-Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal.
  • Figueiredo M; Clinical Pathology-Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal.
  • Rebelo L; Clinical Pathology-Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal.
  • Trindade MC; Serviço de Hematologia, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal.
  • Duarte S; Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal.
  • Vieira L; Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal.
  • Alves MJ; Centre for Vectors and Infectious Diseases Research, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal.
  • Costa I; National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
  • Guiomar R; National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
  • Santos M; Laboratório de Biologia Molecular, Serviço de Patologia Clínica do CHULC, Lisbon, Portugal.
  • Cortê-Real R; Laboratório de Biologia Molecular, Serviço de Patologia Clínica do CHULC, Lisbon, Portugal.
  • Dias A; Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal.
  • Póvoas D; Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal.
  • Cabo J; Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal.
  • Figueiredo C; Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal.
  • Manata MJ; Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal.
  • Maltez F; Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal.
  • Gomes da Silva M; Serviço de Hematologia, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal.
  • Gomes JP; Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal.
mSphere ; 6(4): e0024421, 2021 08 25.
Article in English | MEDLINE | ID: covidwho-1329039
ABSTRACT
Recent studies have shown that persistent SARS-CoV-2 infections in immunocompromised patients can trigger the accumulation of an unusual high number of mutations with potential relevance at both biological and epidemiological levels. Here, we report a case of an immunocompromised patient (non-Hodgkin lymphoma patient under immunosuppressive therapy) with a persistent SARS-CoV-2 infection (marked by intermittent positivity) over at least 6 months. Viral genome sequencing was performed at days 1, 164, and 171 to evaluate SARS-CoV-2 evolution. Among the 15 single-nucleotide polymorphisms (SNPs) (11 leading to amino acid alterations) and 3 deletions accumulated during this long-term infection, four amino acid changes (V3G, S50L, N87S, and A222V) and two deletions (18-30del and 141-144del) occurred in the virus Spike protein. Although no convalescent plasma therapy was administered, some of the detected mutations have been independently reported in other chronically infected individuals, which supports a scenario of convergent adaptive evolution. This study shows that it is of the utmost relevance to monitor the SARS-CoV-2 evolution in immunocompromised individuals, not only to identify novel potentially adaptive mutations, but also to mitigate the risk of introducing "hyper-evolved" variants in the community. IMPORTANCE Tracking the within-patient evolution of SARS-CoV-2 is key to understanding how this pandemic virus shapes its genome toward immune evasion and survival. In the present study, by monitoring a long-term COVID-19 immunocompromised patient, we observed the concurrent emergence of mutations potentially associated with immune evasion and/or enhanced transmission, mostly targeting the SARS-CoV-2 key host-interacting protein and antigen. These findings show that the frequent oscillation in the immune status in immunocompromised individuals can trigger an accelerated virus evolution, thus consolidating this study model as an accelerated pathway to better understand SARS-CoV-2 adaptive traits and anticipate the emergence of variants of concern.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Lymphoma, Non-Hodgkin / Immunocompromised Host / Immune Evasion / SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study Topics: Long Covid / Variants Limits: Animals / Female / Humans / Middle aged Language: English Journal: MSphere Year: 2021 Document Type: Article Affiliation country: MSphere.00244-21

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Lymphoma, Non-Hodgkin / Immunocompromised Host / Immune Evasion / SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study Topics: Long Covid / Variants Limits: Animals / Female / Humans / Middle aged Language: English Journal: MSphere Year: 2021 Document Type: Article Affiliation country: MSphere.00244-21