Detection of influenza virus and pathogens of acute respiratory viral infections in population of Kazakhstan during 2018-2019 epidemic season

Abstract

Influenza and other acute respiratory viral infections are the most common contemporary infectious diseases resulting in prominent harm to human health and great economic damage. At least five groups of viruses including more than 300 subtypes are currently referred to ARVI pathogens. Such infectious agents are characterized by variability resulting in their altered antigenic characteristics, increased contagiousness, "evasion from immune response and resistance to antivirals. Relevance of influenza and other ARVIs is also accounted for by rapid development of bacteria-associated respiratory diseases. Continuous variability of influenza viruses and emergence of new ARVI pathogens pose a serious threat. In recent years, a simultaneous circulation of subtype A (H1N1) and A (H3N2) influenza viruses with a predominance of a pandemic strain as well as type B viruses have been observed. Among the causative agents of non-influenza ARVIs, respiratory syncytial virus, rhino- and adenoviruses, and I/III parainfluenza viruses are recorded most often. Here we present the data of virology and serological examination of clinical samples collected during the 2018 – 2019 epidemic season in the Republic of Kazakhstan. For this, 2794 clinical samples (2530 nasopharyngeal swabs and 264 blood serums) were collected from patients diagnosed with ARVI, ARI, bronchitis, and pneumonia. Analysis of nasopharyngeal swabs for detection of influenza by RT-PCR demonstrated that mixed etiology influenza viruses with predominance of A/H1N1pdm virus circulated in Kazakhstan. The genetic fingerprints of influenza virus were found in 511 swabs (20.20% of total examined samples). Influenza A virus RNA was detected in 508 biological samples: A/H1N1 – in 289, A/H3N2 – in 209, and unidentified virus subtype in 10 samples. Type B influenza virus was detected in 3 samples. Study of 264 serum samples by HAI assay and ELISA showed emergence of antibodies against influenza A/H1N1, A/H3N2, and B viruses in residents from various regions of Kazakhstan that indirectly confirmed co-circulation of these viruses. 42 influenza virus strains were isolated in chicken embryos, from which 28 were assigned to A/H1N1pdm virus, 13 to A/H3N2 virus, and one isolate was identified as influenza B virus. Laboratory diagnostics of clinical samples for ARVIs established that among identified non-influenza agents respiratory syncytial virus dominated, while rhinoviruses and adenoviruses were less common. Metapneumoviruses, bocaviruses, coronaviruses, and type I parainfluenza viruses were detected in few cases. Comparison of study data with those obtained after examining circulation of influenza viruses during the 2017 – 2018 epidemic season showed that in 2018 – 2019 in Kazakhstan similar to the previous epidemic season, influenza A and B viruses continued to circulate, with prevalence of A/H1N1pdm virus. Identification of non-influenza viruses causing respiratory infections in 2018 – 2019 showed predominance of respiratory syncytial virus, which correlated with data on the 2017 – 2018 epidemic season.

Spread of Pathogens Causing Respiratory Viral Diseases Before and During CoVID-19 Pandemic in Kazakhstan

“…For over five years, hIv type B was found in only 14 samples (0.30%). Despite the fact, that the influenza virus was circulating in Kazakhstan in 2018 [15], no positive samples for influenza type B were found in our tested samples. Among 1,131 samples (24.00%) were positive for type A influenza, 575 samples (12.20%) belonged to A/H1N1 subtype, 312 samples (6.62%) were that of A/H3N2.…”

“…When studying the etiological structure of ARVI of non-influenza etiology in Kazakhstan between 2016 and 2019, the predominance of hRSv (15.25%) and hRv (4.34%) was established, hPiv and hAdv were detected much less frequently (about 1%). hMpv, hBov, and hCov were revealed in isolated cases [14,15]. The prevalence of hRSv and hRv in the pre-pandemic period was also recorded in different countries of Europe [41,42], Asia [35,37,39,43,44], and Africa [36,45].…”

“…The range of influenza virus epidemic strains is continually changing. In recent years, a rapid spread of influenza viruses of subtypes A/H1N1, A/ H3N2, and type B is being observed in Kazakhstan as well as throughout the world [14,15]. In addition, the extraordinary complexity of the epidemic situation is associated with the emergence of reassortant viruses.…”

Genome Sequence of Influenza B Epidemic Strain B/Almaty/8/2018

“…During a seasonal influenza epidemic in Almaty, Kazakhstan, the strain B/Almaty/8/2018 was isolated from an oropharyngeal swab sample from an elderly patient with clinical symptoms of respiratory disease ( 4 ). This virus was isolated by inoculating samples into 10-day-old embryonated chicken eggs, with 48 h of incubation at 35°C ( 5 ).…”

Coding-Complete Genome Sequence of Swine Influenza Virus Isolate A/Swine/Karaganda/04/2020 (H1N1) from Kazakhstan

“…Influenza A viruses (IAV) belong to the genus Alphainfluenzavirus in the family Orthomyxoviridae and cause one of the most important respiratory diseases in pigs as well as humans ( 1 – 3 ). An important role in the emergence of pandemic strains can be played by genetic reassortment between human and avian influenza viruses in pigs, since swine are equally susceptible to both human and avian influenza viruses ( 4 ).…”