Journal Article Research Support, Non-U.S. Gov't Epublish 8 citations
PubMed: 38932250 DOI: 10.3390/v16060958
Epidemiological and Genetic Characteristics of Respiratory Viral Coinfections with Different Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
Viruses 16(6)
Authors: Ivelina Trifonova, Neli Korsun, Iveta Madzharova, Ivailo Alexiev, Ivan Ivanov, Viktoria Levterova, Lyubomira Grigorova, Ivan Stoikov, Dean Donchev, Iva Christova
Affiliations
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria.
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria.
Abstract
This study aimed to determine the incidence and etiological, seasonal, and genetic characteristics of respiratory viral coinfections involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between October 2020 and January 2024, nasopharyngeal samples were collected from 2277 SARS-CoV-2-positive patients. Two multiplex approaches were used to detect and sequence SARS-CoV-2, influenza A/B viruses, and other seasonal respiratory viruses: multiplex real-time polymerase chain reaction (PCR) and multiplex next-generation sequencing. Coinfections of SARS-CoV-2 with other respiratory viruses were detected in 164 (7.2%) patients. The most common co-infecting virus was respiratory syncytial virus (RSV) (38 cases, 1.7%), followed by bocavirus (BoV) (1.2%) and rhinovirus (RV) (1.1%). Patients ≤ 16 years of age had the highest rate (15%) of mixed infections. Whole-genome sequencing produced 19 complete genomes of seasonal respiratory viral co-pathogens, which were subjected to phylogenetic and amino acid analyses. The detected influenza viruses were classified into the genetic groups 6B.1A.5a.2a and 6B.1A.5a.2a.1 for A(H1N1)pdm09, 3C.2a1b.2a.2a.1 and 3C.2a.2b for A(H3N2), and V1A.3a.2 for the B/Victoria lineage. The RSV-B sequences belonged to the genetic group GB5.0.5a, with HAdV-C belonging to type 1, BoV to genotype VP1, and PIV3 to lineage 1a(i). Multiple amino acid substitutions were identified, including at the antibody-binding sites. This study provides insights into respiratory viral coinfections involving SARS-CoV-2 and reinforces the importance of genetic characterization of co-pathogens in the development of therapeutic and preventive strategies.
MeSH
Coronavirus, Respiratory Syncytial Viruses, Sars-Cov-2, Polymerase Chain Reaction, Amino Acids, Virology, Coinfection, Genome, Severe Acute Respiratory Syndrome, Influenza, Human, Viruses, Severe Acute Respiratory Syndrome-Related Coronavirus, Orthomyxoviridae, Infections