Polymorphisms and mutations of ACE2 and TMPRSS2 genes are associated with COVID-19: a systematic review

Molecular dynamic simulation reveals spider antimicrobial peptide Latarcin-1 and human eosinophil cationic protein as peptide inhibitors of SARS-CoV-2 variants

COVID-19 has rapidly proliferated around 180 countries, and new cases are reported frequently. No peptide medication has been developed that can reliably block SARS-CoV-2 infection. The investigation focuses on the crucial host receptors angiotensin-converting enzyme 2 (ACE2) , which can bind receptor-binding domain (RBD) on the SARS-CoV-2 spike protein (S). To investigate the inhibitory effects of human Eosinophil Cationic Protein (hECP) and Latarcin-1 (L1)on SARS-CoV-2 infection, we have selected them as research subjects. Further, we ran extensive molecular dynamics simulations to bring the docked peptide-ACE2 complex into its equilibrium state. The outcomes were then evaluated with g_MMPBSA and interaction analysis. We have also considered the Delta and Omicron variants to examine these peptides' inhibitory effects. The experimental findings revealed an enhanced capability of L1 and hECP as SARS-CoV-2 inhibitors, occupying hot spots and numerous key residues in ACE2. These include ASP30, ASP38, GLU35 and GLU75, which significantly inhibit the binding of RBD and ACE2 and are effective against two common variants in a similar manner. In addition, this study can serve as a springboard for future research on SARS-CoV-2 inhibitors.Communicated by Ramaswamy H. Sarma.

Association of ACE2 and TMPRSS2 genes variants with disease severity and most important biomarkers in COVID-19 patients in Bosnia and Herzegovina

AIM

To assess the association of single nucleotide polymorphisms (SNPs) in the ACE2 and TMPRSS2 genes with COVID-19 severity and key biomarkers.

METHODS

The study involved 750 COVID-19 patients from Bosnia and Herzegovina, divided into three groups: mild, moderate, and severe cases. Genetic variations within the ACE2 (rs2285666) and TMPRSS2 (rs2070788) genes were examined with real-time polymerase chain reaction. Biochemical markers were determined with standard procedures.

RESULTS

There was a significant difference in the rs2070788 genotype distribution between patients with mild and moderate symptoms, but not between other groups. For the rs2285666 polymorphism, no significant difference in genotype distribution was found. In patients with mild symptoms, carriers of the GG genotype of rs2070788 had significantly higher total bilirubin levels than carriers of the AA genotype. Similarly, carriers of the TT genotype of rs2285666 had significantly higher activated partial thromboplastin time and international normalized ratio, and lower lactate dehydrogenase levels compared with the CC genotype. Among patients with severe symptoms, carriers of the GG genotype showed significantly higher potassium levels than carriers of the AA genotype, while carriers of the TT genotype showed significantly higher erythrocyte count as well as hemoglobin and hematocrit levels compared with the CC genotype.

CONCLUSION

This study highlights the role of genetic factors, particularly SNPs in the ACE2 and TMPRSS2 genes, in determining COVID-19 severity, aiding patient risk assessment and prognosis.

The weekly P25 of the age of the influenza-like illness shows a higher correlation with COVID-19 mortality than rapid tests and could predict the evolution of COVID-19 pandemics in sentinel surveillance, Piura, Perú, 2021

GOAL

To describe the dynamics of syndromic surveillance of ILI cases in seasonal and COVID-19 pandemic scenarios.

METHODOLOGY

A descriptive study of the epidemiological behavior of ILI in the seasonal and COVID-19 pandemic scenarios. Of a sample of 16,231 cases of ILI from 2013 to 2021, the features of cases from 68 weeks before and during the pandemic were selected and compared; weekly endemic channels were built; data fluctuations on the trend of ILI cases were analyzed; and estimated weekly correlations between weekly P25 age, cases confirmed by rapid tests, and mortality from COVID-19. To analyze clinical-epidemiological and mortality data, Student's t test, Mann-Whitney U, Chi2, Spearman's Ro, polynomial, and multinomial regression with a 95% confidence interval were used.

RESULTS

During the COVID-19 pandemic, those most affected with ILI were: adults and the elderly; higher median age; autochthonous cases predominated; a lower proportion of other syndromes; delays in seeking care; and a higher rate of pneumonia attack than in the seasonal period (p< 0.01). Rapid tests (serological and antigenic) confirmed 52.7% as COVID-19. Two ILI pandemic waves were seasonally consistent with confirmed COVID-19 cases and district mortality with robust correlation (p<0.01) before and during the pandemic, especially the ILI weekly P25 age, which has a more robust correlation with mortality than ILI and rapid tests (p<0.01) whose endemic channels describe and could predict the evolution of the pandemic (p<0.01).

CONCLUSIONS

The pandemic changed the clinical and epidemiological behavior of ILI, and the weekly P25 of age is a more robust indicator to monitor the COVID-19 pandemic than a rapid test and could predict its evolution.

Host genetics and the profile of COVID-19 in indigenous people from the Brazilian Amazon: A pilot study with variants of the ACE1, ACE2 and TMPRSS2 genes

This pilot study aimed to investigate genetic factors that may have contributed to the milder clinical outcomes of COVID-19 in Brazilian indigenous populations. 263 Indigenous from the Araweté, Kararaô, Parakanã, Xikrin do Bacajá, Kayapó and Munduruku peoples were analyzed, 55.2% women, ages ranging from 10 to 95 years (average 49.5 ± 20.7). Variants in genes involved in the entry of SARS-CoV-2 into the host cell (ACE1 rs1799752 I/D, ACE2 rs2285666 C/T, ACE2 rs73635825 A/G and TMPRSS2 rs123297605 C/T), were genotyped in indigenous peoples from the Brazilian Amazon, treated during the SARS-CoV-2 pandemic between 2020 and 2021. The distribution of genotypes did not show any association with the presence or absence of IgG antibodies. Additionally, the influence of genetic variations on the severity of the disease was not examined extensively because a significant number of indigenous individuals experienced the disease with either mild symptoms or no symptoms. It is worth noting that the frequencies of risk alleles were found to be lower in Indigenous populations compared to both continental populations and Brazilians. Indigenous Brazilian Amazon people exhibited an ethnic-specific genetic profile that may be associated with a milder disease, which could explain the unexpected response they demonstrated to COVID-19, being less impacted than Brazilians.

Predictive Factors and ACE-2 Gene Polymorphisms in Susceptibility to Long COVID-19 Syndrome

Long COVID-19 syndrome is present in 5-10% of patients infected with SARS-CoV-2, and there is still little information on the predisposing factors that lead to its development. The purpose of the study was to evaluate the predictive factors in early symptoms, clinical features and the role of Angiotensin-Converting Enzyme-2 (ACE-2) c.513-1451G>A (rs2106806) and c.15643279T>C (rs6629110) polymorphisms in the susceptibility to developing Long COVID-19 syndrome subsequent to COVID-19 infectionA total of 29 patients who suffered COVID-19 were recruited in a descriptive longitudinal study of two groups: Long COVID-19 (n = 16) and non-Long COVID-19 (n = 13). Early symptoms and clinical features during COVID-19 were classified by a medical service. ACE-2 polymorphisms were genotyped by using a Single Nucleotide Primer Extension (SNPE). Of the early symptoms, fatigue, myalgia and headache showed a high risk of increasing Long COVID-19 susceptibility. Clinical features such as emergency care, SARS-CoV-2 reinfection, previous diseases, respiratory disease and brain fog also had a high risk of increasing Long COVID-19 susceptibility. The A allele in the rs2106806 variant was associated with an odds ratio (OR) of 4.214 (95% CI 2.521-8.853; p < 0.001), and the T allele in the rs6629110 variant was associated with an OR of 3.754 (95% CI 1.785-6.105; p = 0.002) of increasing Long COVID-19 susceptibility. This study shows the risk of ACE-2 polymorphisms, different early symptoms and clinical features during SARS-CoV-2 infection in susceptibility to Long COVID-19.

Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.

A cell-based assay for rapid assessment of ACE2 catalytic function

Angiotensin-converting enzyme II (ACE2) is a monocarboxypeptidase expressed throughout multiple tissues and its catalysis of bioactive peptides regulates the renin-angiotensin system mediating blood pressure homeostasis. ACE2 is implicated in a variety of diseases, including obesity, diabetes, and cardiovascular diseases, and is the obligate entry receptor for SARS-CoV-2 infection. Disease-associated genetic variants of ACE2 are increasingly being identified but are poorly characterized. To aid this problem, we introduce a fluorometric cell-based assay for evaluating surface-expressed ACE2 catalytic activity that preserves the native glycosylation of the host environment and is amenable to high-throughput analysis of ACE2 variants in multi-well plates. We demonstrate sensitivity to detecting catalysis of the key ACE2 substrates, Angiotensin II, Apelin-13, and des-Arg9-bradykinin, and impact of a catalytically-deficient ACE2 variant. Normalizing catalytic measures to surface ACE2 expression accounts for variability in ACE2 variant transfection, surface delivery or stability. This assay provides a convenient and powerful approach for investigating the catalytic characteristics of ACE2 variants involved in cardiovascular peptide cascades and homeostasis of multiple organs.

Association between genetic polymorphism, severity, and treatment response among COVID-19 infected Egyptian patients

Background: The world has been suffering from the Coronavirus Disease-2019 (COVID-19) pandemic since the end of 2019. The COVID-19-infected patients differ in the severity of the infection and the treatment response. Several studies have been conducted to explore the factors that affect the severity of COVID-19 infection. One of these factors is the polymorphism of the angiotensin converting enzyme 2 (ACE-2) and the type 2 transmembrane serine protease (TMPRSS2) genes since these two proteins have a role in the entry of the virus into the cell. Also, the ACE-1 regulates the ACE-2 expression, so it is speculated to influence the COVID-19 severity. Objective: This study investigates the relationship between the ACE-1, ACE-2, and TMPRSS2 genes single nucleotide polymorphism (SNPs) and the COVID-19 disease severity, treatment response, need for hospitalization, and ICU admission in Egyptian patients. Patients and Methods: The current study is an observational prospective, cohort study, in which 109 total COVID-19 patients and 20 healthy volunteers were enrolled. Of those 109 patients, 51 patients were infected with the non-severe disease and were treated in an outpatient setting, and 58 suffered from severe disease and required hospitalization and were admitted to the ICU. All 109 COVID-19 patients received the treatment according to the Egyptian treatment protocol. Results: Genotypes and allele frequencies among severe and non-severe patients were determined for ACE-1 rs4343, TMPRSS2 rs12329760, and ACE-2 rs908004. The GG genotype and the wild allele of the ACE-2 rs908004 and the mutant allele of the ACE-1 rs4343 were significantly more predominant in severe patients. In contrast, no significant association existed between the TMPRSS2 rs12329760 genotypes or alleles and the disease severity. Conclusion: The results of this study show that the ACE-1 and ACE-2 SNPs can be used as severity predictors for COVID-19 infection since also they have an effect on length of hospitalization.

Newly arrived migrants did not represent an additional COVID-19 burden for Italy: data from the italian information flow

BACKGROUND

During the COVID-19 pandemic, migrants arriving in host countries irregularly have not infrequently been perceived as increasing the COVID-19 burden. Italy is a transit and destination country for migrants who cross the Central Mediterranean route and, during the pandemic, all migrants who landed on Italian shores were COVID-19 tested and quarantined. Our study aimed to investigate the impact of the SARS-CoV-2 infection among migrants who landed on the Italian coasts by analyzing both incidence and health outcomes.

METHODS

A retrospective observational study has been designed. The population of interest was represented by 70,512 migrants (91% male, 99% <60 years old) who landed in Italy between January 2021 and 2022. SARS-CoV-2 incidence rate per 1,000 (with 95%CI) in migrants and the resident population in Italy of the corresponding age group was computed. The incidence rate ratio (IRR) was used to compare the incidence rates in migrants and the resident population.

RESULTS

2,861 migrants out of those landed in Italy during the observation period tested positive, with an incidence rate of 40.6 (39.1-42.1) cases per 1,000. During the same period, 177.6 (177.5-177.8) cases per 1,000 were reported in the resident population, with an IRR of 0.23 (0.22-0.24). 89.7% of cases were male and 54.6% belonged to the 20-29 age group. 99% of cases reported no symptoms, no relevant comorbidities were reported and no cases were hospitalized.

CONCLUSIONS

Our study found a low rate of SARS-CoV-2 infection in migrants reaching Italy by sea with an incidence rate that is roughly a quarter of that of the resident population. Thus, irregular migrants who arrived in Italy during the observation period did not increase the COVID-19 burden. Further studies are needed to investigate possible reasons for the low incidence observed in this population.

S Protein, ACE2 and Host Cell Proteases in SARS-CoV-2 Cell Entry and Infectivity; Is Soluble ACE2 a Two Blade Sword? A Narrative Review

Since the spread of the deadly virus SARS-CoV-2 in late 2019, researchers have restlessly sought to unravel how the virus enters the host cells. Some proteins on each side of the interaction between the virus and the host cells are involved as the major contributors to this process: (1) the nano-machine spike protein on behalf of the virus, (2) angiotensin converting enzyme II, the mono-carboxypeptidase and the key component of renin angiotensin system on behalf of the host cell, (3) some host proteases and proteins exploited by SARS-CoV-2. In this review, the complex process of SARS-CoV-2 entrance into the host cells with the contribution of the involved host proteins as well as the sequential conformational changes in the spike protein tending to increase the probability of complexification of the latter with angiotensin converting enzyme II, the receptor of the virus on the host cells, are discussed. Moreover, the release of the catalytic ectodomain of angiotensin converting enzyme II as its soluble form in the extracellular space and its positive or negative impact on the infectivity of the virus are considered.

Association of hypernatremia with outcomes of COVID-19 patients: A protocol for systematic review and meta-analysis

BACKGROUND

This systematic review and meta-analysis aimed to assess the association of hypernatremia with the outcomes of COVID-19 patients.

METHODS

We performed a systematic literature search on PubMed, Google Scholar, and Science Direct until October 2021 and found a total of 131 papers. With meticulous screening finally, 17 papers met the inclusion criteria. COVID-19 patients with sodium levels greater than the reference level were the study population and the outcome of interest was the poor outcome; such as mortality, mechanical ventilation, intensive care unit (ICU) admission, and prolonged hospital stay. The pooled estimate was calculated as the odds ratio (OR).

RESULTS

There were 19,032 patients with hypernatremia in the 17 studies included. An overall random effect meta-analysis showed that hypernatremia was associated with mortality (OR: 3.18 [1.61, 6.28], P < .0001, I2 = 91.99%), prolong hospitalization (OR: 1.97 [1.37, 2.83], P < .001, I2 = 0.00%) and Ventilation (OR: 5.40 [1.89, 15.42], P < .001, I2 = 77.35%), ICU admission (OR: 3.99 [0.89, 17.78], P = .07, I2 = 86.79%). Meta-regression analysis showed the association of age with the ICU outcome of hypernatremia patients. Whereas, other parameters like male, hypertension, chronic kidney disease, and diabetes mellitus did not significantly influence the odds ratio.

CONCLUSION

Hypernatremia was markedly associated with poor outcomes in patients with COVID-19. Hence, a blood ionogram is warranted and special attention must be given to hypernatremia COVID-19 patients.

The COVID-19 Pandemic and Explaining Outcomes in Africa: Could Genomic Variation Add to the Debate?

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, emanated from the Wuhan Province in China and rapidly spread across the globe causing extensive morbidity and mortality rate, and affecting the global economy and livelihoods. Contrary to early predictions of "body bags" across Africa, the African COVID-19 pandemic was marked by apparent low case numbers and an overall mortality rate when compared with the other geographical regions. Factors used to describe this unexpected pattern included a younger population, a swifter and more effective national health policy, limited testing capacities, and the possibility of inadequate reporting of the cases, among others. However, despite genomics contributing to interindividual variations in many diseases across the world, there are inadequate genomic and multiomics data on COVID-19 in Africa that prevent richer transdisciplinary discussions on the contribution of genomics to the spread of COVID-19 pandemic. To invite future debates on comparative studies of COVID-19 genomics and the pandemic spread around the world regions, this expert review evaluates the reported frequency distribution of genetic variants in candidate genes that are likely to affect COVID-19 infection dynamics/disease outcomes. We propose here that genomic variation should be considered among the many factors determining the COVID-19 infection and its outcomes in African populations and across the world.

Correlates with Vaccine Protective Capacity and COVID-19 Disease Symptoms Identified by Serum Proteomics in Vaccinated Individuals

In the last two years, the coronavirus disease 19 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a scientific and social challenge worldwide. Vaccines have been the most effective intervention for reducing virus transmission and disease severity. However, genetic virus variants are still circulating among vaccinated individuals with different disease symptomatology. Understanding the protective- or disease-associated mechanisms in vaccinated individuals is relevant to advances in vaccine development and implementation. To address this objective, serum-protein profiles were characterized by quantitative proteomics and data-analysis algorithms in four cohorts of uninfected and SARS-CoV-2-infected vaccinated individuals with asymptomatic, non-severe, and severe disease symptomatology. The results show that immunoglobulins were the most overrepresented proteins in infected cohorts when compared to PCR-negative individuals. The immunoglobulin profile varied between different infected cohorts and correlated with protective- or disease-associated capacity. Overrepresented immunoglobulins in PCR-positive individuals correlated with protective response against SARS-CoV-2, other viruses, and thrombosis in asymptomatic cases. In non-severe cases, correlates of protection against SARS-CoV-2 and HBV together with risk of myasthenia gravis and allergy and autoantibodies were observed. Patients with severe symptoms presented risk for allergy, chronic idiopathic thrombocytopenic purpura, and autoantibodies. The analysis of underrepresented immunoglobulins in PCR-positive compared to PCR-negative individuals identified vaccine-induced protective epitopes in various coronavirus proteins, including the spike receptor-binding domain RBD. Non-immunoglobulin proteins were associated with COVID-19 symptoms and biological processes. These results evidence host-associated differences in response to vaccination and the possibility of improving vaccine efficacy against SARS-CoV-2.

Association of the Transmembrane Serine Protease-2 (TMPRSS2) Polymorphisms with COVID-19

SARS-CoV-2 uses the ACE2 receptor and the cellular protease TMPRSS2 for entry into target cells. The present study aimed to establish if the TMPRSS2 polymorphisms are associated with COVID-19 disease. The study included 609 patients with COVID-19 confirmed by RT-PCR test and 291 individuals negative for the SARS-CoV-2 infection confirmed by RT-PCR test and without antibodies anti-SARS-CoV-2. Four TMPRSS2 polymorphisms (rs12329760, rs2298659, rs456298, and rs462574) were determined using the 5′exonuclease TaqMan assays. Under different inheritance models, the rs2298659 (p_codominant2 = 0.018, p_recessive = 0.006, p_additive = 0.019), rs456298 (p_codominant1 = 0.014, p_codominant2 = 0.004; p_dominant = 0.009, p_recessive = 0.004, p_additive = 0.0009), and rs462574 (p_codominant1 = 0.017, p_codominant2 = 0.004, p_dominant = 0.041, p_recessive = 0.002, p_additive = 0.003) polymorphisms were associated with high risk of developing COVID-19. Two risks (ATGC and GAAC) and two protectives (GAGC and GAGT) haplotypes were detected. High levels of lactic acid dehydrogenase (LDH) were observed in patients with the rs462574AA and rs456298TT genotypes (p = 0.005 and p = 0.020, respectively), whereas, high heart rate was present in patients with the rs462574AA genotype (p = 0.028). Our data suggest that the rs2298659, rs456298, and rs462574 polymorphisms independently and as haplotypes are associated with the risk of COVID-19. The rs456298 and rs462574 genotypes are related to high levels of LDH and heart rate.

The Prevalence and Impact of Coinfection and Superinfection on the Severity and Outcome of COVID-19 Infection: An Updated Literature Review

Patients with viral illness are at higher risk of secondary infections—whether bacterial, viral, or parasitic—that usually lead to a worse prognosis. In the setting of Corona Virus Disease 2019 (COVID-19), the Severe Acute Respiratory Syndrome Coronavirus-type 2 (SARS-CoV-2) infection may be preceded by a prior microbial infection or has a concurrent or superinfection. Previous reports documented a significantly higher risk of microbial coinfection in SARS-CoV-2-positive patients. Initial results from the United States (U.S.) and Europe found a significantly higher risk of mortality and severe illness among hospitalized patients with SARS-CoV-2 and bacterial coinfection. However, later studies found contradictory results concerning the impact of coinfection on the outcomes of COVID-19. Thus, we conducted the present literature review to provide updated evidence regarding the prevalence of coinfection and superinfection amongst patients with SARS-CoV-2, possible mechanisms underlying the higher risk of coinfection and superinfection in SARS-CoV-2 patients, and the impact of coinfection and superinfection on the outcomes of patients with COVID-19.