2020–2021 rhinovirus genetic diversity in Saint Petersburg

Abstract

Introduction. Rhinoviruses represent one of the most common respiratory viruses and belong to the Picornoviridae family, genus Enterovirus, being divided into three types: A, B, C, which account for 169 types. Rhinoviruses predominate in autumn and spring periods, although they circulate throughout almost entire epidemic season. The rhinovirus genome is represented by a single-stranded 7.2 thousand base-long +RNA. According to the publications, the most common rhinovirus species is rhinovirus A (HRV-A), followed by rhinoviruses C (HRV-C) and finally rhinovirus B (HRV-B). The aim of our study was to define rhinovirus genetic diversity in Saint Petersburg . Materials and methods. The study was conducted at the Laboratory of Molecular Virology, Smorodintsev Research Institute of Influenza. Samples (smears from the nasopharynx and oropharynx) were delivered from the S.P. Botkin Clinical Infectious Diseases Hospital, St. Olga’s Children's City Hospital, N.F. Filatov Children's City Clinical Hospital No. 5. Outpatient samples were used as well. Samples received from December 2020 to October 2021 were analyzed. Detection of rhinoviruses was carried out by real-time PCR, typing — by Sanger sequencing, with primers developed by da Costa Souza L. et al. (2021). Results. According to total specimen testing, rhinoviruses comprise 3.2% total number of specimens tested. Of these, 71 rhinoviruses were typed, representing 17.03% total number of rhinovirus-positive specimens. The most common was HRV-A (55%), among which 21 types were found (the most common HRV-A46 is 13%, n = 5). HRV-B and HRV-C were found in equal numbers — 23% (n = 16) of each species out of total number of typed rhinoviruses. Among HRV-B, 8 types were found; the most common HRV-B06 comprised 33% (n = 5). Among HRV-C, 7 types were found (the most common types are HRV-C42, HRV-C32 and HRV-C15 — 19% each, n = 3). HRV-A was detected mainly in patients aged 18 to 65 years (57.5%, n = 23). HRV-B was detected only in adult patients (100%, n = 16). HRV-C was detected in children under 2 years of age (43.75%, n = 7) and adults aged 18–65 years (31.25%, n = 5). In some cases, HRV-A and HRV-C were associated with various respiratory tract syndromes such as acute nasopharyngitis, laryngotracheitis, obstructive bronchitis, and pneumonia. HRV-B was related to clinical manifestations of pneumonia in seven cases. Conclusion. Rhinovirus type A prevails in Saint Petersburg . Rhinoviruses can be associated with diverse respiratory tract syndromes.