The immunogenetics of COVID-19.

The worldwide coronavirus disease 2019 pandemic was sparked by the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) that first surfaced in December 2019 (COVID-19). The effects of COVID-19 differ substantially not just between patients individually but also between populations with different ancestries. In humans, the human leukocyte antigen (HLA) system coordinates immune regulation. Since HLA molecules are a major component of antigen-presenting pathway, they play an important role in determining susceptibility to infectious disease. It is likely that differential susceptibility to SARS-CoV-2 infection and/or disease course in COVID-19 in different individuals could be influenced by the variations in the HLA genes which are associated with various immune responses to SARS-CoV-2. A growing number of studies have identified a connection between HLA variation and diverse COVID-19 outcomes. Here, we review research investigating the impact of HLA on individual responses to SARS-CoV-2 infection and/or progression, also discussing the significance of MHC-related immunological patterns and its use in vaccine design.

The Genetics of Primary Biliary Cholangitis: A GWAS and Post-GWAS Update.

Primary biliary cholangitis (PBC) is a chronic, progressive cholestatic liver disease in which the small intrahepatic bile ducts are destroyed by autoimmune reactions. Among autoimmune diseases, which are polygenic complex traits caused by the combined contribution of genetic and environmental factors, PBC exhibits the strongest involvement of genetic heritability in disease development. As at December 2022, genome-wide association studies (GWASs) and associated meta-analyses identified approximately 70 PBC susceptibility gene loci in various populations, including those of European and East Asian descent. However, the molecular mechanisms through which these susceptibility loci affect the pathogenesis of PBC are not fully understood. This study provides an overview of current data regarding the genetic factors of PBC as well as post-GWAS approaches to identifying primary functional variants and effector genes in disease-susceptibility loci. Possible mechanisms of these genetic factors in the development of PBC are also discussed, focusing on four major disease pathways identified by in silico gene set analyses, namely, (1) antigen presentation by human leukocyte antigens, (2) interleukin-12-related pathways, (3) cellular responses to tumor necrosis factor, and (4) B cell activation, maturation, and differentiation pathways.

Association of ABO blood group with susceptibility to SARS-CoV-2 infection in Rupandehi district of Nepal.

Objectives: Recent studies after the outbreak of coronavirus disease 2019 have shown an association of the ABO blood group to the susceptibility of severe acute respiratory syndrome coronavirus 2 infection. Anti-A and anti-B antibodies, carbohydrate clustering, interleukin-6 levels and host transmembrane protease serine subtype 2 were suggested to cause the variable susceptibility of severe acute respiratory syndrome coronavirus 2 infection to the ABO blood groups. This study aims to find the association of the ABO blood group with severe acute respiratory syndrome coronavirus 2 infection susceptibility in Nepal. Methods: Population-based matched case-control study was conducted from October 2021 to February 2022 in Rupandehi district of Nepal. A total of 1091 reverse transcription-polymerase chain reaction confirmed coronavirus disease 2019 cases and 2182 controls were included in the study by convenient sampling method. Results: A statistically significant association of severe acute respiratory syndrome coronavirus 2 infection was observed for the blood group AB between cases and controls (11.5% vs 8.5%; odds ratio = 1.4, 95% confidence interval = 1.10-1.78). However, there was no association of severe acute respiratory syndrome coronavirus 2 infection for blood group A (26.7% vs 28.23%; odds ratio = 0.93, 95% confidence interval = 0.79-1.09), B (26.9% vs 29.84%; odds ratio = 0.86, 95% confidence interval = 0.73-1.02) and O (34.9% vs 33.41%; odds ratio = 1.07, 95% confidence interval = 0.92-1.25). Conclusion: This study reported slightly more susceptibility to severe acute respiratory syndrome coronavirus 2 infection among individuals with blood group AB.

Association of blood group with COVID-19 disease susceptibility and severity in Saudi Arabia.

BACKGROUND: Novel SARS-CoV-2 (COVID-19) virus has rapidly spread worldwide and was declared a pandemic, making identifying and prioritizing individuals most at risk a critical challenge. The literature describes an association between blood groups and the susceptibility to various viral infections and their severity. Knowing if a specific blood group has more susceptibility to COVID-19 may help improve understanding the pathogenesis and severity of the disease. We aimed to assess the association between ABO/RhD and COVID-19 susceptibility and severity, and to compare results with similar studies in Saudi Arabia. STUDY DESIGN AND METHODS: This study was conducted between March and October 2021 on 600 patients confirmed positive for COVID-19 infection. Patients' data were collected and analyzed. As a control, 8423 healthy blood donors were enrolled as a sample representative of the population for blood group distribution. RESULTS: More individuals had blood group B in the COVID-19 group in comparison with the control group (24.2% vs. 18%), The opposite was observed among individuals of group O (39.5% vs. 47.3%). The B blood group was predictive of higher risk of mortality. No significant difference in the distribution of RhD was observed between the COVID-19 and the control groups. Neither ABO nor RhD was significantly associated with the severity of COVID-19. DISCUSSION: Although there was no significant association with the disease severity, the B blood group may be associated with a higher risk for COVID-19 infection. Further studies with a larger sample size are necessary to evaluate this correlation.

Shared 6mer Peptides of Human and Omicron (21K and 21L) at SARS-CoV-2 Mutation Sites.

We investigated the short sequences involving Omicron 21K and Omicron 21L variants to reveal any possible molecular mimicry-associated autoimmunity risks and changes in those. We first identified common 6mers of the viral and human protein sequences present for both the mutant (Omicron) and nonmutant (SARS-CoV-2) versions of the same viral sequence and then predicted the binding affinities of those sequences to the HLA supertype representatives. We evaluated change in the potential autoimmunity risk, through comparative assessment of the nonmutant and mutant viral sequences and their similar human peptides with common 6mers and affinities to the same HLA allele. This change is the lost and the new, or de novo, autoimmunity risk, associated with the mutations in the Omicron 21K and Omicron 21L variants. Accordingly, e.g., the affinity of virus-similar sequences of the Ig heavy chain junction regions shifted from the HLA-B*15:01 to the HLA-A*01:01 allele at the mutant sequences. Additionally, peptides of different human proteins sharing 6mers with SARS-CoV-2 proteins at the mutation sites of interest and with affinities to the HLA-B*07:02 allele, such as the respective SARS-CoV-2 sequences, were lost. Among all, any possible molecular mimicry-associated novel risk appeared to be prominent in HLA-A*24:02 and HLA-B*27:05 serotypes upon infection with Omicron 21L. Associated disease, pathway, and tissue expression data supported possible new risks for the HLA-B*27:05 and HLA-A*01:01 serotypes, while the risks for the HLA-B*07:02 serotypes could have been lost or diminished, and those for the HLA-A*03:01 serotypes could have been retained, for the individuals infected with Omicron variants under study. These are likely to affect the complications related to cross-reactions influencing the relevant HLA serotypes upon infection with Omicron 21K and Omicron 21L.

PARAMETER ESTIMATION OF COVID-19 COMPARTMENT MODEL IN INDONESIA USING PARTICLE SWARM OPTIMIZATION

Background: The government established a vaccination program to deal with highly reactive COVID-19 cases in Indonesia. In obtaining accurate predictions of the dynamics of the compartment model of COVID-19 spread, a good parameter estimation technique was required. Purpose: This research aims to apply Particle Swarm Optimization as a parameter estimation method to obtain parameters value from the Susceptible-Vaccinated-Infected-Recovered compartment model of COVID-19 cases. Methods: This research was conducted in April-May 2020 in Indonesia with exploratory design research. The researchers used the data on COVID-19 cases in Indonesia, which was accessed at covid19.go.id. The data set contained the number of reactive cases, vaccinated cases, and recovered cases. The data set was used to estimate the parameters of the COVID-19 compartment model. The results were shown by numerical simulations that apply to the Matlab program. Results: Research shows that the parameters estimated using Particle Swarm Optimization have a fairly good value because the mean square error is relatively small compared to the data size used. Reactive cases of COVID-19 have decreased until August 21, 2021. Next, reactive cases of COVID-19 will increase until the end of 2021. It is because the virus infection rate of the vaccinated population is positive   0. If   0 occurs before the stationary point, then the reactive cases of COVID-19 will decrease mathematically. Conclusion: Particle Swarm Optimization methods can estimate parameters well based on mean square error and the graphs that can describe the behavior of COVID-19 cases in the future. (English) [ FROM AUTHOR] Latar Belakang: Baru-baru ini pemerintah menetapkan program vaksinasi untuk mengatasi tingginya kasus reaktif COVID-19 di Indonesia. Metode estimasi parameter yang baik diperlukan untuk menghasilkan prediksi yang akurat dari dinamika model kompartemen penyebaran COVID-19. Tujuan: Penelitian ini dilakukan untuk mengaplikasikan Particle Swarm Optimization untuk mendapatkan parameter dari model kompartemen Susceptible-Vaccinated-Infected-Recovered untuk kasus COVID-19. Metode: Penelitian ini dilakukan pada bulan April-Mei 2020 di Indonesia dengan desain penelitian eksperimen. Penelitian ini menggunakan data kasus COVID-19 di Indonesia melalui laman covid19.go.id. Perangkat data tersebut memuat banyaknya kasus reaktif, tervaksinasi, dan sembuh. Data tersebut digunakan untuk mengestimasi parameter dari model kompartemen COVID-19. Metode estimasi yang digunakan adalah Particle Swarm Optimization. Hasil penelitian berupa simulasi numerik yang didukung oleh program Matlab. Hasil: Penelitian menunjukkan bahwa parameter yang diestimasi memiliki nilai yang cukup baik karena mean square error cukup kecil jika dibandingkan dengan data yang digunakan. Kasus reaktif COVID-19 mengalami penurunan hingga 21 Agustus 2021. Pada waktu selanjutnya, grafik kasus reaktif COVID-19 akan mengalami kenaikan hingga akhir tahun 2021. Hal ini disebabkan oleh laju infeksi virus populasi tervaksinasi masih bernilai positif, 0  . Apabila terjadi 0   di titik stasioner, maka secara matematis, kasus reaktif COVID-19 akan mengalami penurunan. Kesimpulan: Metode Particle Swarm Optimization dapat mengestimasi parameter dengan baik berdasarkan mean square error dan grafik yang dapat mendeskripsikan perilaku kasus COVID-19 dan solusi dari fenomena yang terjadi di masa depan. (Indonesian) [ FROM AUTHOR] Copyright of Jurnal Berkala Epidemiologi is the property of Universitas Airlangga and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Epigenetic mechanisms and host factors impact ACE2 gene expression: Implications in COVID-19 susceptibility.

BACKGROUND: The ACE2 protein acts as a gateway for SARS-CoV-2 in the host cell, playing an essential role in susceptibility to infection by this virus. Genetics and epigenetic mechanisms related to the ACE2 gene are associated with changes in its expression and, therefore, linked to increased susceptibility to infection. Although some variables such as sex, age, and obesity have been described as risk factors for COVID-19, the molecular causes involved in the disease susceptibility are still unknown. AIM: To evaluate the ACE2 gene expression profiles and their association with epigenetic mechanisms and demographic or clinical variables. METHODS: In 500 adult volunteers, the mRNA expression levels of the ACE2 gene in nasopharyngeal swab samples and its methylation status in peripheral blood samples were quantified by RT-qPCR and qMSP, respectively. The existence of significant differences in the ACE2 gene expression and its determinants were evaluated in different study groups according to several demographic or clinical variables such as sex, age, body mass index (BMI), smoking, SARS-CoV-2 infection, and presence of underlying diseases such as type II diabetes mellitus (DM2), asthma and arterial hypertension (AHT). RESULTS: Our results show that ACE2 gene overexpression, directly involved in susceptibility to SARS-CoV-2 infection, depends on multiple host factors such as male sex, age over 30 years, smoking, the presence of obesity, and DM2. Likewise, it was determined that the ACE2 gene expression is regulated by changes in the DNA methylation patterns in its promoter region. CONCLUSIONS: The ACE2 gene expression is highly variable, and this variability is related to habits such as smoking and demographic or clinical variables, which details the impact of environmental and host factors on our epigenome and, therefore, in susceptibility to SARS-CoV-2 infection.

Association of ABO blood group with susceptibility, severity and breakthrough COVID-19 infections in Indian Population

Since the COVID-19 eruption in December 2019, the investigation has been focused on its treatment and preventing the disease spread. Currently, there is no biomarker available that can predict the predisposition and severity of COVID-19 infection. In the present study, we have used the cross-sectional survey study data to decipher the association between the ABO blood group and susceptibility, severity and breakthrough COVID-19 infections. Further, we have also investigated the association between antibody class and the risk of contracting COVID-19 infection. Our results indicated that individuals with blood group B had higher susceptibility to acquire COVID-19 infection. In contrast, blood group A was found to be associated with a low risk of acquiring severe COVID-19. In addition, we did not find any correlation between ABO blood group and breakthrough COVID-19 infections. Further, we examined the association of antibodies;anti-A (blood groups B and O) and anti-B (blood groups A and O) with COVID-19 infection. The analysis of antibody classes showed that anti-A antibody associated with a high predisposition to acquire COVID-19 infection. The present study indicates that blood group B and anti-A antibodies are associated with proneness to COVID-19 infection and severity. © ScienceIN.

A Novel Soluble ACE2 Protein Provides Lung and Kidney Protection in Mice Susceptible to Lethal SARS-CoV-2 Infection.

BACKGROUND: Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) uses full-length angiotensin converting enzyme 2 (ACE2) as a main receptor to enter target cells. The goal of this study was to demonstrate the preclinical efficacy of a novel soluble ACE2 protein with increased duration of action and binding capacity in a lethal mouse model of COVID-19. METHODS: A human soluble ACE2 variant fused with an albumin binding domain (ABD) was linked via a dimerization motif hinge-like 4-cysteine dodecapeptide (DDC) to improve binding capacity to SARS-CoV-2. This novel soluble ACE2 protein (ACE2-1-618-DDC-ABD) was then administered intranasally and intraperitoneally to mice before intranasal inoculation of SARS-CoV-2 and then for two additional days post viral inoculation. RESULTS: Untreated animals became severely ill, and all had to be humanely euthanized by day 6 or 7 and had pulmonary alveolar hemorrhage with mononuclear infiltrates. In contrast, all but one mouse infected with a lethal dose of SARS-CoV-2 that received ACE2-1-618-DDC-ABD survived. In the animals inoculated with SARS-CoV-2 that were untreated, viral titers were high in the lungs and brain, but viral titers were absent in the kidneys. Some untreated animals, however, had variable degrees of kidney proximal tubular injury as shown by attenuation of the proximal tubular brush border and increased NGAL and TUNEL staining. Viral titers in the lung and brain were reduced or nondetectable in mice that received ACE2-1-618-DDC-ABD, and the animals developed only moderate disease as assessed by a near-normal clinical score, minimal weight loss, and improved lung and kidney injury. CONCLUSIONS: This study demonstrates the preclinical efficacy of a novel soluble ACE2 protein, termed ACE2-1-618-DDC-ABD, in a lethal mouse model of SARS-CoV-2 infection that develops severe lung injury and variable degrees of moderate kidney proximal tubular injury.

The Novel Coronavirus SARS-CoV-2 Vulnerability Association with ABO/Rh Blood Types.

BACKGROUND & OBJECTIVE: Coronavirus disease 2019 (COVID-19) is the most recent emerging viral disease. Defining the epidemiological aspects and factors influencing the susceptibility of the patients to COVID-19 has been an ongoing struggle. In the present study, we have investigated the connection between ABO histo-blood group phenotypes and the COVID-19. METHODS: This study was conducted on 397 patients with confirmed diagnoses of COVID-19 admitted to our center. Also, 500 individuals were selected to form the controls, all of whom had been disclosed to the same medical center in June 2019, before the onset of the outbreak. RESULTS: Our results demonstrated ABO histo-blood phenotypes are correlated with patients' susceptibility to the infection. A higher rate of infection was observed among patients with the AB histo-blood group, while patients with the O histo-blood group have shown a lower rate of infection. The Rh blood group phenotype was not statistically significant in determining a patient's vulnerability. CONCLUSION: Similar to several previous studies about other viral diseases' association with ABO histo-blood groups, we have concluded that an individual's ABO histo-blood group phenotype and his/her susceptibility to COVID-19 are indeed connected. So far, only one research has been conducted about this association. Interestingly, while we observed a decreased vulnerability to the disease among patients with an O histo-blood group, we have reached discordant results regarding the increased susceptibility among individuals with an AB histo-blood group, unlike A histo-blood group in the previous study.

Inconsistent trends regarding the association between ABO blood groups and susceptibility to SARS-CoV-2 infections

ABO antigens, produced from the ABO gene, are known to impact host interactions with various viruses. One characteristic is the host's susceptibility to viral infections. Host interaction with viral particles is altered by the blood type-determined combination of ABO antigens on the cellular surface. SARS-CoV-2 is a novel strain of the coronavirus family known to have structural similarities with SARS-CoV. Considering ABO antigens' association with SARS-CoV, studies have examined their relationship with SARS-CoV-2 as well. We reviewed current perspectives on the relationship between host susceptibility to SARS-CoV-2 infections and ABO antigens by examining cohort studies observing proportional differences between patients of varying blood types. While many studies indicated a higher risk of type A patients and a lower risk for type O patients, trends tended to vary per population. Consequently, we investigated the differences in study design between cohort studies that produced the variation in trends. Additionally, we examined genome-wide association studies that indicate a genetic association between the variables. We present the need for a standardized calculation method determining the significance of each blood group in its relationship with SARS-CoV-2 susceptibility per cohort.

Metabolic Snapshot of Plasma Samples Reveals New Pathways Implicated in SARS-CoV-2 Pathogenesis.

Despite the scientific and human efforts to understand COVID-19, there are questions still unanswered. Variations in the metabolic reaction to SARS-CoV-2 infection could explain the striking differences in the susceptibility to infection and the risk of severe disease. Here, we used untargeted metabolomics to examine novel metabolic pathways related to SARS-CoV-2 susceptibility and COVID-19 clinical severity using capillary electrophoresis coupled to a time-of-flight mass spectrometer (CE-TOF-MS) in plasma samples. We included 27 patients with confirmed COVID-19 and 29 healthcare workers heavily exposed to SARS-CoV-2 but with low susceptibility to infection ("nonsusceptible"). We found a total of 42 metabolites of SARS-CoV-2 susceptibility or COVID-19 clinical severity. We report the discovery of new plasma biomarkers for COVID-19 that provide mechanistic explanations for the clinical consequences of SARS-CoV-2, including mitochondrial and liver dysfunction as a consequence of hypoxemia (citrulline, citric acid, and 3-aminoisobutyric acid (BAIBA)), energy production and amino acid catabolism (phenylalanine and histidine), and endothelial dysfunction and thrombosis (citrulline, asymmetric dimethylarginine (ADMA), and 2-aminobutyric acid (2-AB)), and we found interconnections between these pathways. In summary, in this first report several metabolic pathways implicated in SARS-CoV-2 susceptibility and COVID-19 clinical progression were found by CE-MS based metabolomics that could be developed as biomarkers of COVID-19.

Nursing Aotearoa New Zealand and the establishment of the National Close Contact Service: A critical discussion

The COVID-19 pandemic has resulted in inestimable morbidity and mortality across the globe. The healthcare and political leadership of the pandemic within Aotearoa New Zealand has been internationally recognised. The pivotal role of nurses and nursing practice in the establishment of National Close Contact Service (NCCS) has been fundamental in protecting the health of our nation. Using exemplars, and the themes of shared human vulnerability and professional authority, this critical discussion draws on theoretical and philosophical nursing perspectives to demonstrate the authors' involvement in the establishment of the NCCS.

ABO blood group and COVID-19: a review on behalf of the ISBT COVID-19 Working Group.

Growing evidence suggests that ABO blood group may play a role in the immunopathogenesis of SARS-CoV-2 infection, with group O individuals less likely to test positive and group A conferring a higher susceptibility to infection and propensity to severe disease. The level of evidence supporting an association between ABO type and SARS-CoV-2/COVID-19 ranges from small observational studies, to genome-wide-association-analyses and country-level meta-regression analyses. ABO blood group antigens are oligosaccharides expressed on red cells and other tissues (notably endothelium). There are several hypotheses to explain the differences in SARS-CoV-2 infection by ABO type. For example, anti-A and/or anti-B antibodies (e.g. present in group O individuals) could bind to corresponding antigens on the viral envelope and contribute to viral neutralization, thereby preventing target cell infection. The SARS-CoV-2 virus and SARS-CoV spike (S) proteins may be bound by anti-A isoagglutinins (e.g. present in group O and group B individuals), which may block interactions between virus and angiotensin-converting-enzyme-2-receptor, thereby preventing entry into lung epithelial cells. ABO type-associated variations in angiotensin-converting enzyme-1 activity and levels of von Willebrand factor (VWF) and factor VIII could also influence adverse outcomes, notably in group A individuals who express high VWF levels. In conclusion, group O may be associated with a lower risk of SARS-CoV-2 infection and group A may be associated with a higher risk of SARS-CoV-2 infection along with severe disease. However, prospective and mechanistic studies are needed to verify several of the proposed associations. Based on the strength of available studies, there are insufficient data for guiding policy in this regard.

Relationship Between the ABO Blood Group and the Coronavirus Disease 2019 (COVID-19) Susceptibility.

To explore any relationship between the ABO blood group and the coronavirus disease 2019 (COVID-19) susceptibility, we compared ABO blood group distributions in 2173 COVID-19 patients with local control populations, and found that blood group A was associated with an increased risk of infection, whereas group O was associated with a decreased risk.

Association of ABO and Rh blood groups with obstetric outcomes in SARS-CoV-2 infected pregnancies: A prospective study with a multivariate analysis.

OBJECTIVE: To evaluate the influence of ABO and Rh blood groups on morbidity among SARS-CoV-2 infected pregnancies. DESIGN: Prospective observational study. SETTING: 78 centers of the Spanish Obstetric Emergency Group. POPULATION: Pregnant women with SARS-CoV-2 tested with polymerase-chain-reaction between 26-February and 5-November 2020. A cohort of 1278 SARS-CoV-2(+) pregnant women was analyzed and a concurrent comparison group of 1453 SARS-COV-2(-) patients was established. METHODS: Data were collected from medical charts. SARS-COV-2(+) was compared with SARS-COV-2(-) for differences in distribution of blood groups. We performed multivariate analysis, controlling for maternal age and ethnicity, to evaluate association of ABO and Rh blood groups with maternal and perinatal outcomes in SARS-CoV-2(+) patients with adjusted odds ratios (aOR) and 95% confidence intervals (CI). MAIN OUTCOMES MEASURES: Medical morbidity: Symptomatic COVID-19 and medical complications. Obstetric outcomes: caesarean delivery, preterm deliveries, preterm premature rupture of membranes (PPROM), hemorrhagic events, pre-eclampsia, maternal and neonatal mortality, stillbirth. RESULTS: Differences were noted between blood types and Rh for age and ethnicity comparing SARS-CoV-2(+) and SARS-CoV-2(-) groups (p < 0.05). Among the SARS-CoV-2(+) cohort, the odds of symptomatic COVID-19 and obstetric hemorrhagic event were higher in Rh+ vs Rh- mothers (aOR 1.48, 95% CI 1.02-2.14, p = 0.037, and aOR 8.72, 95% CI 1.20-63.57, p = 0.033, respectively), and PPROM were higher among blood type A vs non-A mothers (aOR 2.06, 95% CI 1.01-4.18, p = 0.046). CONCLUSIONS: In SARS-CoV-2(+) pregnant women, Rh- status was associated with a lower risk of symptomatic COVID-19, while Rh+ and blood group A were associated with obstetric hemorrhage and PPROM, respectively.

Peptides of H. sapiens and P. falciparum that are predicted to bind strongly to HLA-A*24:02 and homologous to a SARS-CoV-2 peptide.

AIM: This study is looking for a common pathogenicity between SARS-CoV-2 and Plasmodium species, in individuals with certain HLA serotypes. METHODS: 1. Tblastx searches of SARS-CoV-2 are performed by limiting searches to five Plasmodium species that infect humans. 2. Aligned sequences in the respective organisms' proteomes are searched with blastp. 3. Binding predictions of the identified SARS-CoV-2 peptide to HLA supertype representatives are performed. 4. Blastp searches of predicted epitopes that bind strongly to the identified HLA allele are performed by limiting searches to H. sapiens and Plasmodium species, separately. 5. Peptides with minimum 60% identity to the predicted epitopes are found in results. 6. Peptides among those, which bind strongly to the same HLA allele, are predicted. 7. Step-4 is repeated by limiting searches to H. sapiens, followed by the remaining steps until step-7, for peptides sourced by Plasmodium species after step-6. RESULTS: SARS-CoV-2 peptide with single letter amino acid code CFLGYFCTCYFGLFC has the highest identity to P. vivax. Its YFCTCYFGLF part is predicted to bind strongly to HLA-A*24:02. Peptides in the human proteome both homologous to YFCTCYFGLF and with a strong binding affinity to HLA-A*24:02 are YYCARRFGLF, YYCHCPFGVF, and YYCQQYFFLF. Such peptides in the Plasmodium species' proteomes are FFYTFYFELF, YFVACLFILF, and YFPTITFHLF. The first one belonging to P. falciparum has a homologous peptide (YFYLFSLELF) in the human proteome, which also has a strong binding affinity to the same HLA allele. CONCLUSION: Immune responses to the identified-peptides with similar sequences and strong binding affinities to HLA-A*24:02 can be related to autoimmune response risk in individuals with HLA-A*24:02 serotypes, upon getting infected with SARS-CoV-2 or P. falciparum.

Risk and Protective Factors in the COVID-19 Pandemic: A Rapid Evidence Map.

Background: Given the worldwide spread of the 2019 Novel Coronavirus (COVID-19), there is an urgent need to identify risk and protective factors and expose areas of insufficient understanding. Emerging tools, such as the Rapid Evidence Map (rEM), are being developed to systematically characterize large collections of scientific literature. We sought to generate an rEM of risk and protective factors to comprehensively inform areas that impact COVID-19 outcomes for different sub-populations in order to better protect the public. Methods: We developed a protocol that includes a study goal, study questions, a PECO statement, and a process for screening literature by combining semi-automated machine learning with the expertise of our review team. We applied this protocol to reports within the COVID-19 Open Research Dataset (CORD-19) that were published in early 2020. SWIFT-Active Screener was used to prioritize records according to pre-defined inclusion criteria. Relevant studies were categorized by risk and protective status; susceptibility category (Behavioral, Physiological, Demographic, and Environmental); and affected sub-populations. Using tagged studies, we created an rEM for COVID-19 susceptibility that reveals: (1) current lines of evidence; (2) knowledge gaps; and (3) areas that may benefit from systematic review. Results: We imported 4,330 titles and abstracts from CORD-19. After screening 3,521 of these to achieve 99% estimated recall, 217 relevant studies were identified. Most included studies concerned the impact of underlying comorbidities (Physiological); age and gender (Demographic); and social factors (Environmental) on COVID-19 outcomes. Among the relevant studies, older males with comorbidities were commonly reported to have the poorest outcomes. We noted a paucity of COVID-19 studies among children and susceptible sub-groups, including pregnant women, racial minorities, refugees/migrants, and healthcare workers, with few studies examining protective factors. Conclusion: Using rEM analysis, we synthesized the recent body of evidence related to COVID-19 risk and protective factors. The results provide a comprehensive tool for rapidly elucidating COVID-19 susceptibility patterns and identifying resource-rich/resource-poor areas of research that may benefit from future investigation as the pandemic evolves.

COVID-19: The Effect of Host Genetic Variations on Host-Virus Interactions.

Spurred into action by the COVID-19 pandemic, the global scientific community has, in a short of period of time, made astonishing progress in understanding and combating COVID-19. Given the known human protein machinery for (a) SARS-CoV-2 entry, (b) the host innate immune response, and (c) virus-host interactions (protein-protein and RNA-protein), the potential effects of human genetic variation in this machinery, which may contribute to clinical differences in SARS-CoV-2 pathogenesis and help determine individual risk for COVID-19 infection, are explored. The Genome Aggregation Database (gnomAD) was used to show that several rare germline exome variants of proteins in these pathways occur in the human population, suggesting that carriers of these rare variants (especially for proteins of innate immunity pathways) are at risk for severe symptoms (like the severe symptoms in patients who are known to be rare variant carriers), whereas carriers of other variants could have a protective advantage against infection. The occurrence of genetic variation is thus expected to motivate the experimental probing of natural variants to understand the mechanistic differences in SARS-CoV-2 pathogenesis from one individual to another.

ABO / Rh-D Blood types and susceptibility to Corona Virus Disease-19 in Peshawar, Pakistan.

OBJECTIVES: To determine the association between ABO/Rh-D blood types and susceptibility to SARS-CoV-2 infection in Pakistan. METHODS: In this cross-sectional study, 1935 confirmed cases of COVID-19 were included using consecutive sampling. Age and gender-matched sample of 1935 blood donors was used as a comparison group. Chi-square test and binary logistic regression were used for inferential statistics. RESULTS: Significantly higher proportion of blood type-B was observed in COVID-19 group (35.9% vs 31.9%, p=0.009). Blood type-AB was found more frequently (14.2% vs 11.8%, p=0.03) in the comparison group. The Rh-D Positive blood types were 93.3% in COVID-19 group and 94.9% in comparison group (p=0.03). The odds of blood type-B, AB and Rh-D positive to test positive for SARS-CoV-2 were 1.195 (95% CI 1.04 - 1.36, p=0.009), 0.80 (95% CI 0.66 - 0.97, p=0.03) and 0.75 (95% CI 0.57- 0.98, p = 0.03), respectively. Blood types A and O did not have significant association with SARS-CoV-2 PCR result (p = 0.22 and 0.88, respectively). CONCLUSIONS: There is significant association between blood types B & AB and susceptibility to COVID-19. There is no association between blood types A and O with COVID-19. Rh- D positive blood types are less susceptible to COVID-19.