SARS-CoV-2 coinfection in immunocompromised host leads to the generation of recombinant strain. (June 2023)

• Record Type: Journal Article
• Authors: Zannoli, Silvia; Brandolini, Martina; Marino, Maria Michela; Denicolò, Agnese; Mancini, Andrea; Taddei, Francesca; Arfilli, Valentina; Manera, Martina; Gatti, Giulia; Battisti, Arianna; Grumiro, Laura; Scalcione, Agata; Dirani, Giorgio; Sambri, Vittorio
• Is Part Of: International journal of infectious diseases. Volume 131(2023)
• Page Start: 65
• Page End: 70
• Publication Date: 2023-06
• Subjects: SARS-CoV-2 variants -- Whole genome sequencing -- Recombinant XS -- Plaque assay -- Co-infection; Communicable diseases -- Periodicals; Communicable Diseases -- Periodicals; Communicable diseases; Periodicals; Electronic journals; 616.9
• DOI: 10.1016/j.ijid.2023.03.014
• Languages: English
• ISSNs: 1201-9712

Abstract

Highlights: Homologous recombination due to coinfection is a driving force of viral evolution. A specimen suggestive of coinfection was analyzed with sequencing and plaque assay. Sequencing on primary sample is consistent with double viral population. Plaque assay showed a recombinant strain deriving from Delta and Omicron. Monitoring co-infections, particularly in patients who are immunocompromised, is needed. Abstract: Objectives: Recombination related to coinfection is a huge driving force in determining the virus genetic variability, particularly in conditions of partial immune control, leading to prolonged infection. Here, we characterized a distinctive mutational pattern, highly suggestive of Delta-Omicron double infection, in a lymphoma patient. Methods: The specimen was characterized through a combined approach, analyzing the results of deep sequencing in primary sample, viral culture, and plaque assay. Results: Bioinformatic analysis on the sequences deriving from the primary sample supports the hypothesis of a double viral population within the host. Plaque assay on viral culture led to the isolation of a recombinant strain deriving from Delta and Omicron lineages, named XS, which virtually replaced its parent lineages within a single viral propagation. Conclusion: It is impossible to establish whether the recombination event happened within the host or in vitro ; however, it is important to monitor co-infections, especially in the exceptional intrahost environment of patients who are immunocompromised, as strong driving forces of viral evolution.