Viral pathogens in autopsy material from patients with fatal pneumonia in Khabarovsk in 2023

Introduction. In recent years, the proportion of viral pathogens in the etiology of community-acquired pneumonia has increased. Identification of the causative agent in postmortem (autopsy) material may provide a more accurate etiological cause of fatal pneumonias.
Aim. To analyze the species diversity of viral pathogens isolated from patients with fatal outcomes of community-acquired pneumonia, compared with the results of virological examination of respiratory samples from individuals with favorable disease outcomes.
Materials and Methods. The analysis included protocols of virological examination of autopsy material (lung tissue) from 140 individuals who died from pneumonia in Khabarovsk in 2023. The comparison group consisted of data from virological examinations of patients with clinical manifestations of community-acquired pneumonia and favorable outcomes, in which 1136 DNA and RNA viral agents were identified. The search targeted detecting DNA/RNA of 11 respiratory viral pathogens and four viruses causing opportunistic diseases. The study was performed using polymerase chain reaction with reagents produced by domestic manufacturers.
Results. DNA and RNA of respiratory viruses (10 types) were detected in autopsy material with a frequency of 46.43%. DNA of viruses causing opportunistic diseases (four types) was detected with a frequency of 27.14%. Clinical samples from patients with a favorable outcome more frequently contained rhinoviruses (25.6%), adenoviruses (13.03%), respiratory syncytial viruses (12.4%), and parainfluenza type 3 viruses (11.09%). In the spectrum of viruses isolated from clinical samples, rhinoviruses predominated (25.6%), followed by adenoviruses (13.03%), respiratory syncytial viruses (12.4%), and parainfluenza type 3 viruses (11.09%). SARS-CoV-2 viruses accounted for 6.6% of cases, and influenza A(H1N1) viruses for 1.1% of cases. Seasonal patterns in virus detection in fatal pneumonias were identified.
Conclusion. In cases of pneumonia with virologically confirmed etiology, fatal outcomes were determined in nearly half of cases by SARS-CoV-2 and influenza A(H1N1) viruses.

1. Kharitonov M.A., Salukhov V.V., Kryukov E.V., Patsenko M.B., Rudakov Yu.V., Bogomolov А.B., Ivanov V.V., Minakov A.A. [Viral pneumonia: a new look at an old problem (review)]. Meditsinskiy sovet = Medical Council 2021; (16):60–77 (in Russian). https://doi.org/10.21518/2079-701X-2021-16-60-77

2. Yakovenko, O. N. Kravchenko N.A. [Features of the epidemiology of community-acquired pneumonia]. Sibirskiy meditsinskiy zhurnal (Irkutsk) = Siberian Medical Journal (Irkutsk) 2014; 2:8–11 (in Russian).

3. Kruglyakova L.V., Naryshkina S.V., Odireev A.N. [Modern aspects of community-acquired pneumonia]. Bûlleten' fiziologii i patologii dyhaniâ = Bulletin Physiology and Pathology of Respiration 2019; (71):120–134 (in Russian). https://doi.org/10.12737/article_5c89acc410e1f3.79881136

4. Orlova E.D., Babachenko I.V., Tian N.S., Kozyrev E.A., Alekseeva L.A. [Clinical and laboratory features of viral lower respiratory tract infections in children]. Jurnal infektologii = Journal Infectology 2023; 15(2):84–92 (in Russian). https://doi.org/10.22625/2072-6732-2023-15-2-84-92

5. Febbo J., Revels J., Ketai L. Viral Pneumonias. Radiol. Clin. North. Am. 2022; 60(3):383–397. https://doi.org/10.1016/j.rcl.2022.01.010

6. Reimann H.A. An acute infection of the respiratory tract with atypical pneumonia: a disease entity probably caused by a filtrable virus. JAMA 1984; 111(26):2377–2384.

7. Minakov A.A., Vakhlevskii V.V., Voloshin N.I., Kharitonov M.A., Salukhov V.V., Tyrenko V.V., Rudakov Y.V., Vakhlevskaya E.N., Alekhina E.V. [Modern view on the etiology and immunological aspects of pneumonia]. Meditsinskiy sovet = Medical Council 2023; (4):141–153 (in Russian). https://doi.org/10.21518/ms2023-056

8. Pagliano P., Sellitto C., Conti V., Ascione T., Esposito S. Characteristics of viral pneumonia in the COVID-19 era: an update. Infection 2021; 29:1–10. https://doi.org/10.1007/s15010-021-01603-y

9. Lapteva I.M. [Features of diagnosis and treatment of primary viral, secondary bacterial and viral-bacterial pneumonia in influenza]. Retsept = Recipe 2009; 68(6):74–79 (in Russian).

10. Cilla G., Oñate E., Perez-Yarza E.G., Montes M., Vicente D., Perez-Trallero E. Viruses in community-acquired pneumonia in children aged less than 3 years old: High rate of viral coinfection. J. Med. Virol. 2008; 80(10):1843–1849. https://doi.org/10.1002/jmv.21271

11. do Carmo Debur M., Raboni S.M., Flizikowski F.B., Chong D.C., Persicote A.P., Nogueira M.B., Rosele L.V., de Almeida S.M., de Noronha L. Immunohistochemical assessment of respiratory viruses in necropsy samples from lethal non-pandemic seasonal respiratory infections. J. Clin. Pathol. 2010; 63(10):930–934. https://doi.org/10.1136/jcp.2010.077867

12. Egorov A. [The problem of bacterial complications in respiratory viral infections]. MIR Journal 2018; 5(1):1–11 (in Russian). https://doi.org/10.18527/2500-2236-2018-5-1-1-11

13. Charlson E.S., Bittinger K., Haas A.R., Fitzgerald A.S., Frank I., Yadav A., Bushman F.D., Collman R.G. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am. J. Respir. Crit. Care Med. 2011; 184(8):957–963. https://doi.org/10.1164/rccm.201104-0655OC.14

14. Yang X., Steukers L., Forier K., Xiong R., Braeckmans K., Van Reeth K., Nauwynck H. A beneficiary role for neuraminidase in influenza virus penetration the respiratory mucus. PLoS One 2014; 9(10):e110026. https://doi.org/10.1371/journal.pone.0110026

15. Bosch AA, Biesbroek G, Trzcinski K, Sanders EA, Bogaert D. Viral and bacterial interactions in the upper respiratory tract. PLoS Pathog. 2013; 9(1):e1003057. https://doi.org/10.1371/journal.ppat.1003057

16. Avadhanula V., Rodriguez C.A., Devincenzo J.P., Wang Y., Webby R.J., Ulett G.C., Adderson E.E. Respiratory viruses augment the adhesion of bacterial pathogens to respiratory epithelium in a viral species- and cell type-dependent manner. J. Virol. 2006; 80(4):1629–1636. https://doi.org/10.1128/JVI.80.4.1629-1636.2006

17. Li N., Ren A., Wang X., Fan X., Zhao Y., Gao G.F., Cleary P., Wang B. Influenza viral neuraminidase primes bacterial coinfection through TGF-beta-mediated expression of host cell receptors. Proc. Natl. Acad. Sci. USA 2015; 112(1):238–243. https://doi.org/10.1073/pnas.1414422112

18. Carson J.L., Collier A.M., Hu S.S. Acquired ciliary defects in nasal epithelium of children with acute viral upper respiratory infections. N. Engl. J. Med. 1985; 312(8):463–468. https://doi.org/10.1056/NEJM198502213120802

19. Pittet L.A., Hall-Stoodley L., Rutkowski M.R., Harmsen A.G. Influenza virus infection decreases tracheal mucociliary velocity and clearance of Streptococcus pneumoniae. Am. J. Respir. Cell Mol. Biol. 2010; 42(4):450–460. https://doi.org/10.1165/rcmb.2007-0417OC

20. Sun K., Metzger D.W. Inhibition of pulmonary antibacterial defense by interferon-gamma during recovery from influenza infection. Nat. Med. 2008; 14(5):558–564. https://doi.org/10.1038/nm1765

21. Astry C.L., Jakab G.J. Influenza virus-induced immune complexes suppress alveolar macrophage phagocytosis. J. Virol. 1984; 50(2):287–292. https://doi.org/10.1128/JVI.50.2.287-292.1984