The spike protein of SARS-CoV-2 is the surface protein that provides attachment and entry to the host cell. So, any mutation in the spike protein will likely alter virulence and pathogenicity. Most alterations are expected to reduce virulence or be deleterious. So, this mutational hotspot protein affects alterations in transmissibility, infectivity, and immunogenicity. As SARS-CoV-2 mutations accumulate, it is critical to investigate how they affect the severity and progression of the COVID-19 illness, such as asymptomatic, hospitalization, ICU admissions, and mortality rate [22, 23]. Age, gender, and host genetics are important factors that are related to clinical outcome and mortality in COVID-19 [24, 25]. However, viral mutations also have implications for the severity and mortality [26]. Spike protein mutations are related to transmissibility and host cell tropism [27], but they also affect the neutralization of antibodies and the pathogenicity of COVID-19 [24, 28]. This study analyzed, the association of SARS-CoV-2 spike protein mutations between the asymptomatic and ICU/deceased COVID-19 patients at a time when there were an accumulating number of mutations and virus variants. It was found that four mutations, P26S, D253G, K417N, and D614G, were statistically significant and had a high odd ratio in ICU/ diseased patients (Fig. 3). The P26S mutation, which is mostly found in the Gamma variant, is essential for resistance to (N-terminal domain) NTD-targeting antibodies [29]. The D253G mutation decreases neutralization mediated by antibodies [30]. The K417N mutation is located in the receptor binding domain and alters the antigenic profile of the spike gene as well as affect the immune response [31]. This study is in line with several researches in which the G614 mutation of the SARS-CoV-2 viral spike is associated with higher infectivity and a greater fatality rate [32, 33]. Escape and resistance to the neutralizing antibody could explain the higher prevalence of the four mutations in the ICU or deceased patient. All of the mutations with higher odds ratios associated with ICU/deceased cases reduced protein stability (Fig. 3) (Supplemental S3).
Point mutations in the viral spike protein were also studied using powerful meta data that combined six prediction tools to predict mutation pathogenicity; however, they identified nine distinct deleterious mutations that did not correspond to those with a higher incidence in ICU/death cases. This may be due to the limited ability to relate the predicted deleterious mutation with the actual clinical genome sequencing [34].
This study analyzed the prevalence of total infection among SARS-CoV-2 variants and foun that the Omicron variant caused a higher percentage of both COVID-19 and asymptomatic infection since the outbreak's inception. This may be due to the higher infectivity and transmission efficiency of the Omicron variant (Fig. 3A, C) [13]. Accordingly, the total number of asymptomatic cases of the omicron variant increased in comparison with the other variants. The cause of asymptomatic infection in the Omicron variant is dubious, but it might be related to less immune activation, alternative viral tropisms, different anatomical localizations, booster vaccination, or a combination of all these factors [8, 35, 36]. The percentage of asymptomatic and ICU/deceased cases within a single variant, on the other hand, is quite different; the Beta variant revealed a higher percentage of asymptomatic infection than ICU/deceased for the same variant (Fig. 3B). but because the percentage of beta variant infection is comparatively much smaller than the other variants (Fig. 3C) [37], beta variant asymptomatic cases come in third rank after Omicron and delta variant (Fig. 3A).
The Delta variant showed the highest percentage of total ICU/deceased cases in this pandemic (Fig. 1A). However, it shows a low odd ratio compared to the asymptomatic cases for the same variant (Fig. 4D). The P681R mutation is highly conserved in this lineage, which may increase the fusogenicity and pathogenicity by increasing the furin cleavage site of spike proteins [38]. Some research has stated that the delta variant is more transmissible than the alpha variant due to the P681R mutation [12]. This is clearly indicated in this study, in which the percentages of infection were 8.39% and 1.22% for the delta and alpha variants, respectively (Fig. 4C). Death and admission to an intensive care unit, on the other hand, were more likely during the alpha phase than during the delta phase [39], which is consistent with our findings. Accordingly,
The Delta variant was the only one with both a high proportion of ICU/deceased and a high incidence of infection [40], and as a result, its percentage of ICU/deceased was greater than that of the Alpha variant among other SARS-CoV-2 variants (Fig. 4A).
This study declares that since the COVID-19 began, the Gamma variant has had the fourth highest rate of overall ICU and mortality (6.44%) (Fig. 4C). But when comparing the proportion of ICU/deceased to asymptomatic instances within a single variant, the Gamma variant exhibited the greatest ICU/deceased to asymptomatic percentage, suggesting that it is the most pathogenic variant (Fig. 4B) [41]. For ICU and deceased cases, the Gamma, Mu, and Lambda variants statistically demonstrated a significant odd ratio value (Fig. 4D). These results are consistent with a Colombian study [42]. However, the Gamma, Mu, and Lambda variants did not generate a notably high overall mortality percentage due to their relatively low infectivity rates [43, 44].
This study has some limitations, one of which is the small number of cases in both the asymptomatic and ICU/deceased groups that were included in the local laboratory work. Surprisingly, the frequency of mutations was low, and the number of SARS-CoV-2 variants was the same in both groups. This limitation was overcome by mining the mutations and variants among asymptomatic and ICU/deceased groups on a global scale. Another limitation of this study is that the patient status filter was used in the GISAID database to find spike protein mutations and SARS-COV-2 variants in the asymptomatic and ICU/deceased groups, but there could be a large number of SARS-COV-2 sequences without knowing the patient status, so these data are missing in this type of study.