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. 2023 Jul 22;15(7):1608.
doi: 10.3390/v15071608.

Rhinovirus Genotypes Circulating in Bulgaria, 2018-2021

Irina Georgieva  1 , Asya Stoyanova  1 , Svetla Angelova  2 , Neli Korsun  1 , Savina Stoitsova  1 , Lubomira Nikolaeva-Glomb  1
Affiliations

Rhinovirus Genotypes Circulating in Bulgaria, 2018-2021

Irina Georgieva et al. Viruses. .

Abstract

Rhinoviruses (RV) are one of the most common causative agents of respiratory infections, with significant socioeconomic impact. RV infections are not notifiable in Bulgaria, and little is known about the different RV genotypes circulating in the country. This study aims to investigate the diversity of RV genotypes that were circulating in Bulgaria in the period 2018-2021 in samples from ILI/ARI patients. Genotype assignment was based on sequencing and phylogenetic analysis of the 5' untranslated region and the VP4-VP2 region. Out of a total of 1385 nasopharyngeal swabs tested, 166 were RV-positive (RV detection rate: 11.99% (166/1385)). Those with a cycle threshold <25 were selected for genotyping (n = 63). RV isolates were successfully genotyped and classified into 34 genotypes within Rhinovirus A (RV-A), Rhinovirus B (RV-B) and Rhinovirus C (RV-C) species. Presumptive recombination events between the 5'UTR and VP4-VP2 regions were detected in three of the isolates. RV-A and RV-C were the prevalent RV species, with significantly more frequent detections of RV-A in the years before the COVID-19 pandemic compared to the post-pandemic period, when RV-C prevailed. The present study is the first to determine RV genotypes in Bulgaria and the circulation of RV-C has been described for the first time in the country.

Keywords: genotype; rhinovirus; sequencing.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Phylogenetic tree based on the 5′UTR region of RV, constructed by the maximum-likelihood method with 1000 bootstrap iterations. Tree branches are proportional to genetic distance and all bootstrap values greater than 70 are shown at the branches. Reference sequences are represented by GenBank accession numbers and strains. Isolates from clinical samples are indicated by a sample ID number, the collection year and genotype. Strains most similar to RV-A reference strains are shown in red, strains most similar to RV-B reference strains are shown in green and strains most similar to RV-C reference strains are shown in blue. The strains in clusters 1 and 2 are indicated by circles. Enterovirus D68 was used as an outgroup. Enterovirus D68, identified in this study, is shown in purple.
Figure 2
Figure 2
Phylogenetic tree based on the 5′UTR region of RV-C, constructed by the neighbor-joining method with 500 bootstrap iterations. Bootstrap values greater than 70 are shown at the branches. Reference sequences are represented by GenBank accession numbers and strains. Isolates from clinical samples are shown in blue and indicated by a sample ID number, the collection year and strains. Enterovirus D68 was used as an outgroup.
Figure 3
Figure 3
Phylogenetic tree based on the VP4/VP2 region of RV, constructed by the maximum-likelihood method with 1000 bootstrap iterations. Tree branches are proportional to genetic distance, and all bootstrap values greater than 90 are shown at the branches. Reference sequences are represented by GenBank accession numbers and strains. Isolates from clinical samples are indicated by a sample ID number, collection year and strain. Strains most similar to RV-A reference strains are shown in red, strains most similar to RV-B reference strains are shown in green, and strains most similar to RV-C reference strains are shown in blue. The strains in mixed clusters 1 and 2 from the previous analysis are indicated by circles. Enterovirus D68 was used as an outgroup.
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