INTRODUCTION

Currently, there are reports of the similarity of the clinical features in patients with COVID-19 and influenza [1]. So, for COVID-19, the most typical clinical symptoms are respiratory failure, up to development of acute respiratory distress syndrome (ARDS), alteration in the hemostatic system, the development of disseminated intravascular coagulation syndrome (DIC), cardiovascular dysfunction, cardiomyopathy, multiple organ failure [2–5]. Similar symptoms were recorded during the period of the severe H1N1 influenza pandemic of 1918 (“Spanish flu”) and, to a lesser extent, during the swine influenza A(H1N1)pdm09 pandemic [6–10]. Most of these symptoms are the result of endothelial dysfunction and alteration in the hemostatic system, which leads to dysregulation of the protective inflammatory responses [6]. The mechanism by which viruses are involved in this dysregulation of inflammatory responses is unknown. There is an assumption that one of the mechanisms, perhaps, maybe participation in these processes of viral proteins fragments that mimic a number of cellular proteins of the human hemostatic system [11]. In this regard, it was of interest to compare the repertoire of hemostatic system proteins, mimicry fragments of which were identified in proteins of SARS-CoV and SARS-СoV-2 viruses and proteins of H1N1 influenza viruses (isolated in 1918 and 2016).

The aim of the study was to compare the repertoire of proteins of the human hemostatic system and fragments that mimic these proteins in the proteins of H1N1 influenza viruses (isolated in 1918 and 2016) and coronaviruses (SARS-CoV and SARS-СoV-2). The objectives of the study included obtaining an assessment of the similarity of the repertoire of proteins of the hemostatic system, mimicry to which was found in the proteins of the studied viruses.

MATERIALS AND METHODS

Influenza viruses A/H1N1 (A/Brevig Mission/1/18), A/St. Petersburg/RII04/2016 (H1N1)pdm09, coronaviruses SARS-CoV and SARS-CoV-2 (strain Wuhan-Hu-1) were used for comparative computer analysis. The sources of the primary structures of proteins of the analyzed viruses and 41 proteins of the human hemostatic system were publicly available Internet databases, respectively, www.ncbi.nlm.nih.gov and www.nextprot.org. The search for homologous sequences in the structure of viral proteins and hemostatic proteins was carried out by comparing fragments of 12 amino acids in length, taking as related those that showed identity at ≥ 8 positions.

RESULTS

The results of comparison of fragments mimicking proteins of the human hemostatic system in proteins of influenza A(H1N1) viruses (isolated in 1918 and 2016) are presented in Table 1.

Table 1.   Fragment comparison of human hemostatic proteins homologous to proteins in influenza viruses A/H1N1 1918 and A(H1N1)pdm09 isolated in 2016; SARS-CoV and SARS-CoV-2
Full size table

Table 1.   (Contd.)

  Table 1.  (Contd.)

Table 1.   (Contd.)

  Table 1.  (Contd.)

Table 1.  (Contd.)

Table 1.  (Contd.)

Table 1.  (Contd.)

Table 1.  (Contd.)

Table 1.  (Contd.)

Table 1.  (Contd.)

Table 1.  (Contd.)

As shown in Table 1, PA polymerase subunit of influenza virus isolated in 1918 differs significantly from the same polymerase subunit of influenza A(H1N1)pdm09 isolated in 2016 in the number of fragments homologous to a number of hemostatic proteins, 7 and 3, respectively. From 7 fragments in the PA polymerase subunit of influenza A/H1N1 1918 virus, only 2 fragments are common with the PA subunit of the influenza A/St. Petersburg/RII04/2016 (H1N1)pdm09 virus—mimicking von Willebrand factor (vWF) and coagulation factor XI (FXI). In addition, the structure of PA subunit of the A/H1N1 1918 virus lacks one fragment homologous to coagulation factor III (FIII), which is present in A/St. Petersburg/RII04/2016 (H1N1)pdm09 virus PA subunit.

In structure of the PB1 polymerase subunit of influenza A/H1N1 1918 virus, compared to PB1 of A/St. Petersburg/RII04/2016 (H1N1)pdm09 virus, there is an additional fragment homologous to FV, only one fragment homologous to FIX and FXI; there are no fragments homologous to vWF and FVIII, and there are 3 new fragments homologous to tissue factor (TF) and fibrinogen (α and β chains). There are also significant differences in PB2 polymerase subunit of influenza viruses isolated in 1918 and 2016. In the PB2 subunit of the A/H1N1 1918, 5 fragments homologous to FVIII were found, while in the PB2 of A(H1N1)pdm09 virus isolated in 2016 there are only 2 homologous fragments; fewer fragments homologous to FXI and FXIII and 5 fragments missing in PB2 subunit of the A(H1N1)pdm09 virus isolated in 2016.

The HA of A/H1N1 1918 influenza virus differs in the repertoire of the hemostatic proteins from the A(H1N1)pdm09 virus isolated in 2016: 8 new homologous fragments were found, 2 fragments are common, but with different localization in the HA molecule, and there are no fragments homologous to FVIII, FIX, FX, FXI.

The NA of A/H1N1 1918 influenza virus contains 5 fragments homologous to different hemostatic proteins (Table 1), which are absent in the NA of the A(H1N1)pdm09 virus isolated in 2016; only one fragment mimicking vWF was identified (the NA of A(H1N1)pdm09 virus isolated in 2016 has 2 fragments) and there is no fragment mimicking PAI-1 (Plasminogen activator inhibitor-1).

The NP of A/H1N1 1918 influenza virus contains 6 fragments homologous to various hemostatic proteins (there are only 3 of them in the NP of A(H1N1)pdm09 virus isolated in 2016), of which only 1 fragment is common.

In the structure of M1, M2 and N proteins of SARS-CoV-2, NEF proteins of the A/H1N1 1918 influenza virus, there are significantly fewer fragments homologous to hemostasis proteins (1–2 fragments) than in the corresponding proteins of the A(H1N1)pdm09 virus isolated in 2016 (2–7 fragments).

So, when comparing fragments homologous to human hemostatic proteins in the proteins of the 1918 and 2016 influenza viruses, the following can be noted: the repertoire of proteins to which mimicry has been identified is much wider in the proteins of the A/H1N1 1918 influenza virus, especially many fragments that mimic plasminogen, fibrinogen α and β chains, α-macroglobulin, tissue factor, antiplasmin, thrombomodulin, kallikrein, annexin, tPA (tissue plasminogen activator). Fragments that mimic these proteins are practically absent in the proteins of the A(H1N1)pdm09 virus isolated in 2016.

Comparison of the fragments homologous to cellular hemostatic proteins in coronavirus proteins is presented in Table 1. In the SARS-CoV-2 replicase structure, there are fewer fragments homologous to vWF than in the SARS-CoV replicase (4 and 9, respectively); there are no fragments homologous to PAI-1, FV, FVII, FXI, fibrinogen α, β, γ chains, α-antiplasmin; new fragments homologous to plasminogen (2 fragments), kallikrein, tissue factor inhibitor were identified.

The SARS-CoV-2 S protein differs significantly from S protein of SARS-CoV. Almost 25 fragments mimicking various hemostatic proteins were found in its structure. A new fragment homologous to FV was found in the E protein. The M protein of SARS-CoV-2 contains 6 fragments to different hemostatic proteins that are absent in the M protein of SARS-CoV. In the N protein of SARS-CoV-2, 9 new fragments were found to different hemostatic proteins, which are absent in the N protein of SARS-CoV. It should be noted that only the N protein of SARS-CoV-2 contained a fragment that mimics insulin-like growth factor (IGF). The NS proteins of SARS-CoV-2 and SARS-CoV do not contain fragments homologous to cellular hemostatic proteins.

The results of comparison of the repertoire of cellular hemostatic proteins, the mimicry of which was found in the proteins of the influenza A/H1N1 1918 virus and A(H1N1)pdm09 virus isolated in 2016 and SARS-CoV and SARS-CoV-2 coronaviruses are shown in Table 2.

Table 2. Comparison of repertoire of human hemostatic proteins, mimicry to which was detected in proteins of influenza A/H1N1 viruses and SARS-associated coronaviruses
Full size table

As shown in Table 2, viral proteins of SARS-CoV-2 have homologous fragments to 39 analyzed proteins; SARS-CoV has homologous fragments to 23 hemostatic proteins; fragments with molecular mimicry to 24 cellular hemostatic proteins were found in the viral proteins of the A/H1N1 1918 influenza virus, and only 11 in the proteins of A(H1N1)pdm09 influenza virus isolated in 2016.

Thus, a comparative analysis of the repertoire of cellular proteins of the hemostatic system and fragments that mimic these proteins in the structure of the proteins of viruses A/H1N1 1918, A(H1N1)pdm09 isolated in 2016, SARS-CoV and SARS-CoV-2 revealed a significant difference between SARS-CoV-2 and other analyzed viruses. In the protein structure of the SARS-CoV-2, mimicry was found to almost all analyzed hemostatic proteins (39 out of 41), and such a significant increase in mimicry was mainly due to the mimicry of additional proteins involved in the processes of thrombosis. In addition, it should be noted that only SARS-CoV-2 has a fragment that mimics insulin-like growth factor. Based on these data, it can be assumed that increased mimicry of proteins involved in the processes of thrombosis is associated with a more severe clinical manifestation of the disease caused by this virus [12–14]. Comparison with the influenza viruses A/H1N1 1918, A(H1N1)pdm09 isolated in 2016 and SARS-CoV revealed that the most similar to SARS-CoV-2 in terms of repertoire of hemostatic proteins, mimicry to which was found in the proteins of these viruses, are influenza virus A/H1N1 1918, and SARS-CoV.

By now, it has become obvious that the hemostatic system is part of the host defense system, which limits the spread of various pathogens, including viruses, by regulating the inflammatory response and the immune response [6, 15, 16]. What role can mimicry of cellular proteins play in these processes? It is likely that fragments of viral proteins homologous to fragments of hemostatic proteins disorganize the hemostatic system, being released during proteolysis of viral proteins, using either cellular or viral proteases. The mechanism of release of active peptides by cleavage of the precursor protein is widely known in biochemistry, since regulatory peptides that are involved in the regulation of many processes are synthesized by such a mechanism. Another mechanism of dysregulation of hemostatic processes by fragments homologous to cellular proteins may be the induction by these fragments of autoimmune antibodies synthesis that can block cellular proteins containing these fragments. The possibility of such autoimmune antibodies production was demonstrated in the study of side effects such as narcolepsy after vaccination with influenza vaccine Pandemrix (GlaxoSmithKline). It turned out that the structure of the NP antigen in the vaccine contains a fragment of the amino acid sequence homologous to hypocretin (orexin) receptor 2, and autoimmune antibodies to this fragment block this receptor [17–20].

CONCLUSION

Comparative bioinformative analysis of the repertoire of hemostatic proteins and proteins of influenza viruses (1918, 2009 and 2016 isolation) and coronaviruses (SARS-CoV and SARS-CoV-2) showed a sharp difference between the SARS-CoV-2 virus and the analyzed viruses, mainly due to the mimicry of additional proteins involved in the processes of thrombosis. The data obtained can serve as a basis for further experimental studies on the role of homologous fragments in the regulation of host hemostasis by viruses.