Cytokines are a group of small proteins, including IFNs, interleukins (ILs), chemokines, colony-stimulating factors and tumor necrosis factor-alpha (TNF-α) that are released by specific cells to regulate intercellular signaling (Figure 4). In this section, the elements of inflammation in coronavirus, RSV and influenza infection will be discussed (Table 2).

3.1.1 IFNs

IFNs are a subgroup of cytokines that have a fundamental role in the immune response against both viral and microbial pathogens.47 Three major types of IFNs (IFN-I, IFN -II and IFN -III) are characterized based on their receptor specificity.

3.1.1.1 Relevance to coronavirus

IFN gamma (IFNG) is the only member of IFN-II, which is located on chromosome 12. The ability of IFNG to interfere with viral infections through inducing the production of free radicals and other proinflammatory cytokines have made it an intriguing factor to study in determining genetic variants involving both susceptibility and vulnerability to viral infections.

The immunopathological events related to the IFN-mediated pathway have a critical role in the immune response against SARS-CoV infection.48 In China, a case-control study genotyped the IFNG +874 A/T polymorphism (rs2430561) in 476 SARS patients and 449 healthy controls; the IFNG c.874A allele was significantly overrepresented in patients compared to the controls. Particularly, the IFNG c.874A allele shows a significant association with susceptibility to SARS-CoV infection.49 This polymorphism has been previously reported to be associated with other infectious diseases such as parvovirus, tuberculosis, and hepatitis B virus infection.50, 51 The T allele of IFNG c.874A>T variant prepares a site for binding transcription factor nuclear factor kappa B (NF-κB).52 It is suggested that the c.874A allele results in the downexpression of IFNG, which could impair antiviral responses.

In studies related to Covid-19, a recent investigation uncovered two LOF homozygote variants (p.Trp73Cys, p.Ser422Arg) and one LOF heterozygote variant (p.Pro335del) in the IFNAR1 gene, as well as one LOF heterozygote variant (p.Glu140fs) in the IFNAR2 gene in patients with life-threatening Covid-19.24 IFNAR1 and IFNAR2 subunits comprise the IFN receptor that binds to the type I IFNs including IFN-α and IFN-β.

3.1.1.2 Relevance to RSV

Members of the IFN type I family are involved in RSV-related infection, as the rs10757212 SNP in IFNA5 is associated with RSV-related bronchiolitis.53 Moreover, IFNA13 rs643070 and IFNAR2 rs7279064 were associated with RSV-related bronchiolitis in term-born children and IFNG rs1861493 was associated with RSV-related bronchiolitis in premature birth.54

Another type of genetic variation associated with RSV-related bronchiolitis severity and susceptibility is attributed to the polymorphism in the CA microsatellite (rs3138557) in the first intron of IFNG. The number of repeats varies from 11 to 17, and the highest level of IFNG is produced when the number of repeats equals 12 (CA12). Children with the CA12+/CA12+ or CA12+/CA12− genotypes demonstrated a significantly lower RSV bronchiolitis respiratory score compared to those carrying the CA12−/CA12− genotype. Furthermore, the CA12 repeat frequency was lower in RSV-infected children compared to controls; patients in whom CA repeats did not reach 12 had high respiratory scores and severe disease.55

3.1.1.3 Relevance to influenza virus

Several lines of evidence indicate that IFN-III contributes greatly in defense against pathogens that infect respiratory tracts such as influenza A and B virus, which predominantly affect the elderly population. Association of IFNL3 SNP rs8099917 with influenza virus is controversial as this SNP was associated with influenza virus infection in one Iranian study56 while no association was observed in another report.57

3.1.2 ILs

ILs are regulatory cytokines involved in the activation and differentiation of immune cells. They could show both pro- and anti-inflammatory functions.

3.1.2.1 Relevance to coronavirus

IL18 and IL1A are constitutively expressed in the lungs.58 Investigation of 281 SNPs in the Taiwanese patients with SARS-CoV-1 infection revealed that detectable nasopharyngeal shedding of the virus is associated with the T allele of rs1946518 in the promoter of the IL18 gene and the T allele of rs1800587 in the IL1A gene.59 It is postulated that these polymorphisms could affect IL gene expression, thereby participating in the clearance of viral infection.

IL12A is another inflammatory cytokine that is naturally produced by macrophages, neutrophils and DCs. A study on cases with SARS-CoV infection and two control groups including healthy individuals without contact history with SARS-CoV-infected patients and 141 healthy individuals with close contacts discovered a significant association between susceptibility to SARS-CoV infection and c.1664 CT/TT genotypes (rs1331950321) in the IL12RB1 gene.60 This variant is a missense SNP (p.P534L) in the extracellular coding sequence of IL12RB1 protein.

IL6 is transiently produced in response to infectious agents. Two variants—c.-572C/G (rs1800797) and c.-174G/C (rs1800795)—have been confirmed to affect both the transcription and secretion levels of IL6.61 Interestingly, the c.-174 G/C variant of the IL6 gene is significantly associated with the severity of pneumonia.62 It was demonstrated that carriers of the C allele show a higher IL6 expression and 2.42-fold higher risk for septic shock.63, 64 Moreover, susceptibility to acute lung injury is associated with an IL6 gene haplotype that spans −1363 to +4835 from the transcription start site.65, 66 It is suggested that IL6 polymorphisms are involved in the progression of coronavirus infection, and suppression of the IL6 signaling cascade is suggested as a promising therapeutic strategy against severe SARS-CoV-2 infection.62

IL4 plays a fundamental role in shaping the immune reaction to pathogens through inducing both T-cell and B-cell differentiation and its dysregulation could interfere with the balance between Th1 and Th2 responses.67 A meta-analysis of studies on respiratory infectious diseases including RSV, influenza virus, SARS-CoV and pneumonia has revealed that the T allele of rs2070874 polymorphism from the IL4 gene is significantly associated with the risk of respiratory infections.68

3.1.2.2 Relevance to RSV

Some SNPs in IL genes are believed to be involved in bronchiolitis caused by RSV. In this regard, the IL1RN SNPs rs315952 and IL27 rs181206 are associated with RSV-related bronchiolitis in premature birth,54 and the IL1RL1 SNP rs1921622 is associated with RSV bronchiolitis severity.69

Investigation of IL4, IL5 and IL13 genes in Korean children revealed various SNPs in various regions of these genes, among which the SNPs c.589T (rs2243250), c.-33T (rs2070874), c.8375G (rs2243289) and c.8412A form a haplotype and each was significantly associated with severe RSV infection. However, after statistical correction, the results related to each SNP were marginal.70

It is noteworthy that association studies demonstrated different results in different populations; that is, a specific SNP might be significantly associated with a specific disease in one population, but not in another. This is the case for the IL4 promoter variant rs2243250, which was reported as an RSV-associated variant in Korea70 while there was no such association observed in Canadian71 or German cohorts.72 A similar story holds true for the IL4R SNP rs1801275 that was associated with severe RSV in the study of Hoebee et al.,73 while there was no significant association reported by Marr et al.71 Similarly, IL13 SNP 1112C/T (rs1800925) was associated with severe RSV in the study of Puthothu et al.72 in contrary to the report of Choi et al.70 The two IL13 SNPs rs20541 and rs1881457 were investigated for possible association with severe RSV. However, there was no significant association observed.72

Other SNPs in ILs that were associated with RSV infection include the IL18 SNPs 133G/C (rs36072174), and IL6 SNP -174G/C rs1800795, for which the GG and GC genotypes were associated with shorter hospital stay.75 The IL10 SNP rs1800872 C allele was also associated with a higher risk of RSV-related wheeze reported by parents at the corrected age of 1.76 Association of genetic diversity in other IL including IL19 rs2243191 and rs2243188, IL20 rs2981573, IL4R rs1805015 and IL7 rs2583762 SNPs, with post-lower respiratory tract infection (LRTI) recurrent wheeze caused by RSV has also been reported.77

It is noteworthy that RSV has a gender-specific pattern of infection, as it is more predominant in boys. Investigation of possible genetic factors underlying gender specificity revealed that IL9 SNP rs2069885 confers disparate effects in boys and girls. The major allele of this SNP in boys was associated with higher susceptibility to severe forms of the disease, but reduced susceptibility in girls. On the other hand, haplotype analysis demonstrated that the TT haplotype was associated with the highest risk of bronchiolitis requiring hospitalization in girls. This haplotype includes the IL9 SNPs rs1799962 and rs2069885.78

3.1.2.3 Relevance to influenza virus

Variations in IL1A and IL1B genes are associated with susceptibility to pandemic A/H1N1 influenza virus. Allele T in IL1A rs17561 and allele C in IL1B rs1143627 are possibly associated with a higher risk of A(H1N1)pdm09 infection.79

In the Iranian population, the AA genotype of IL1B rs16944 is associated with higher protection against influenza B infection.57 However, another study stated that the decreased risk of infection is associated with the GG genotype of IL1B rs16944.56 For IL17A SNP rs2275913, the lack of allele A is associated with a higher predisposition to Influenza virus.57

The rs1554286 SNP in IL10 is significantly associated with the epiglottitis caused by invasive H. influenzae serotype B infection in immunized children. This SNP is in strong LD with two other polymorphisms within the promoter and the recessive genotype of this SNP is associated with epiglottitis.80

The IL10 −1082A (rs1800870) and −592C (rs1800872) alleles were overrepresented in influenza patients and associated with a higher risk of being affected with severe infection. In the case of inflammatory conditions, the IL10 rs1800870 A allele is associated with lower levels of cytokine production, whereas the IL10 rs1800870 G allele leads to higher levels of cytokine production. Individuals with the IL10 rs1800870 AA genotype are more susceptible to severe influenza virus infection.81 Moreover, the GG and TG genotypes of the IL10 rs1800872 SNP were associated with severe influenza A/H3N2 disease in the Iranian population56 while in another study, no association was observed between this IL10 SNP and severe influenza disease.57

3.1.3 Chemokines

Chemokines are small proteins that belong to the category of cell signaling molecules and induce chemotaxis in nearby cells.82 Concerning their central roles in inflammatory responses, many chemokines and chemokine receptors have been introduced as potential therapeutic targets for several inflammatory diseases.83

3.1.3.1 Relevance to coronavirus

C-C motif chemokine ligand 5 (CCL5), also known as RANTES, has a fundamental role in the recruitment and migration of T cells toward inflammation sites during acute infections.

Law et al.84 reported that nonstructural protein 1 (NSP1) of SARS coronavirus can strongly induce CCL5 expression in human lung epithelial cells. Regarding the SARS-CoV epidemic in China, it was found that the G allele of CCL5 c.-28C/G polymorphism (rs2280788) was significantly associated with more severe symptoms and admission to ICU or deaths.85 This SNP could be involved in regulating CCL5 expression by modifying the binding site of the NF-κB transcription factor.86

CCL2 is involved in the chemoattraction of monocytes and polarization of T-helper cells. CCL2 is one of the upregulated chemokines in monocytes and lung epithelial cells during the early stage of SARS-CoV infection.87 It has been revealed that the higher plasma levels of CCL2 in patients with SARS-CoV-1 infection is significantly correlated with severe symptoms.88 A functional SNP (rs1024611G/A) is located in CCL2 promoter that affects the expression level. The G allele triggers higher expression of CCL2 and is associated with more infiltration of leukocytes into tissues compared to the A allele.89 It has been suggested that the rs1024611 variant could be involved in interindividual differences of host vulnerability to SARS-CoV infection.90

A genome-wide association study on patients with severe Covid-19 (defined as respiratory failure) and control participants from Italy and Spain has been recently conducted.91 This investigation has uncovered two association signals on chromosome 3p21.31 and 9q34.2 which cover a cluster of six genes (SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6 and XCR1) and the ABO blood group, respectively. Accordingly, the rs11385942 insertion–deletion GA or G variant at 3p21.31 locus is associated with Covid-19-induced respiratory failure with genome-wide significance. Interestingly, the locus contains genes encoding chemokine receptors, including CCR9 and CXCR6. The risk allele GA is associated with lower expression of CXCR6 and higher expression of SLC6A20, and LZTFL1 in human lung cells. CXCR6 regulates the location of lung-resident memory CD8+ T cells during the immune reaction to airway pathogens. It should be noted that further studies will be needed to reveal the functional consequences of detected associations.

3.1.3.2 Relevance to RSV

The CCL5 SNP rs2107538 is associated with RSV and RSV subtype A-associated bronchiolitis.33 Polymorphisms located within the promoter (−408G/A rs2107538; −28G/C rs2280788) and the first intron (In1.1T/C rs2280789) of CCL5 are in strong LD and it was demonstrated that a common combined genotype of these polymorphisms is associated with severe RSV infection.92

In the category of chemokines, the CX3CR1 SNP rs3732378 (p.T280M; c.935C/T) variant was associated with RSV-related bronchiolitis, which is due to an interruption in the affinity of CX3CR1 to its ligand fractalkine. Carriers of the 280M allele were more prevalent among patients and individuals with genotypes containing this allele were more likely to be hospitalized due to RSV-related bronchiolitis.93

CCR5 is the receptor of CCL5 and CCL3 that recruit various immune cells such as monocytes, T cells and basophils, and so on. Regarding RSV infection, the −2459G (rs1799987) and −2554T (rs2734648) variants of CCR5 are associated with severe RSV-related bronchiolitis.94 The effect of rs2734648 is not functionally clear, and the impact of rs1799987 is debating as it leads to both increased and decreased expression of CCR5.75

Chemokine (C-X-C motif) ligand 9 (CXCL9)/induced by gamma IFN is a small cytokine of CXC chemokine and participates in several cellular and immune-related processes.95 There is a significant association between CXCL9 rs2276886 and post-RSV LRTI recurrent wheeze.77

3.1.4 TNF

TNF is vital for the innate immune response against pathogens and is a key mediator of inflammatory response. Dysregulation of this cytokine could lead to tissue injuries through the inflammation cascade and therefore, its gene regulation is a considerable factor in the pathobiology of inflammation.96

3.1.4.1 Relevance to coronavirus

A case-control study in China including 75 SARS patients, 41 healthcare workers, and 92 healthy controls revealed that the CT genotype compared to the TT genotype at the c.-204 locus of TNF gene (rs1799964) could be a protective factor for SARS-CoV infection.97

3.1.4.2 Relevance to RSV

TNF receptor superfamily member 1B (TNFRSF1B) is a TNF-binding receptor that mediates the effects of TNF in autoimmunity, inflammation and tumorigenesis.98 In patients affected with RSV, TNFRSF1B rs1061622 was associated with post-RSV LRTI recurrent wheeze.77

3.1.4.3 Relevance to influenza virus

The TNF SNP c.-308G rs1800629 was overrepresented in patients affected with influenza and was associated with disease severity.81