Italian ancestral HLA haplotype predisposing to severe COVID-19 by low spike and high IFNalpha binding affinity

Background/Objectives: Validated association between COVID-19 and the most obvious candidate genes, e.g. HLA, is still missing. A weak association with class I HLA-C*04:01 was found for infection in Sardinians and for severity in another mixed population. Auto-antibodies to interferon type I have been implicated in the severity of COVID-19 in two studies. Method(s): The binding affinity between HLA molecules and SARS-CoV-2 spike protein and IFNalpha subunits was evaluated in silico. The presence of antibodies against one or more of the 12 IFNalpha subunits was evaluated in 160 hospitalized COVID-19 patients. The 10 most frequent haplotypes in the Italian population were tested in 1.997 SARS-CoV-2 infected patients (hospitalized versus not hospitalized). Result(s): The presence of auto-antibodies against at least one IFNalpha subunit was detected in 26% of patients. The haplotype A*24:02-B*35:02-C*04:01-DRB1*11:04-DQB1*03:01 was found to predispose to severity (p = 0.0018;p = 0.07 after Bonferroni correction) in patients <50 years. The haplotype includes alleles able to bind spike with low affinity (i.e. C*04:01 and DRB1*11:04) and IFNalpha with high affinity (i.e. DRB1*11:04). Conclusion(s): One of the 10 most frequent ancestral haplotype of the Italian population predisposes to severity likely reducing both innate immunity through IFNalpha auto-antibodies induction and adaptive immunity through weaker spike protein presentation.

McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks.

Haplotype networks are graphs used to represent evolutionary relationships between a set of taxa and are characterized by intuitiveness in analyzing genealogical relationships of closely related genomes. We here propose a novel algorithm termed McAN that considers mutation spectrum history (mutations in ancestry haplotype should be contained in descendant haplotype), node size (corresponding to sample count for a given node) and sampling time when constructing haplotype network. We show that McAN is two orders of magnitude faster than state-of-the-art algorithms without losing accuracy, making it suitable for analysis of a large number of sequences. Based on our algorithm, we developed an online web server and offline tool for haplotype network construction, community lineage determination, and interactive network visualization. We demonstrate that McAN is highly suitable for analyzing and visualizing massive genomic data and is helpful to enhance the understanding of genome evolution. Availability: Source code is written in C/C++ and available at https://github.com/Theory-Lun/McAN and https://ngdc.cncb.ac.cn/biocode/tools/BT007301 under the MIT license. Web server is available at https://ngdc.cncb.ac.cn/bit/hapnet/. SARS-CoV-2 dataset are available at https://ngdc.cncb.ac.cn/ncov/. Contact: songshh@big.ac.cn (Song S), zhaowm@big.ac.cn (Zhao W), baoym@big.ac.cn (Bao Y), zhangzhang@big.ac.cn (Zhang Z), ybxue@big.ac.cn (Xue Y).

HLA-A*03:01 significantly predicts strong humoral response at six months after mRNA vaccination: Results from the observational prospective cohort study RENAISSANCE

While several studies have been conducted on HLA and Covid-19 infection, few investigated the role of HLA polymorphism on vaccination response. We previously analyzed the HLA allele and haplotype frequencies in a hundred weak responders (antibody levels <5th percentile) after mRNA anti-Covid vaccine and found some suggestions about specific alleles and one haplotype. We moved on typing individuals enrolled in the same cohort study ("RENAISSANCE") with antibody titers above the 95th percentile at six months after vaccination, in order to search for any alleles predictive of strong humoral response. Individuals with clinical history of COVID-19 or positive anti-nucleocapsid antibodies were excluded. Allelic frequencies were compared with those of weak responders and of the general population, taken from the national bone marrow donor registry, IBMDR. N = 123 evaluable individuals presented with >95th percentile antibody titers at six months after BNT162b2 vaccine. One-third of them had >2080 BAU/mL, lowest value was 1261 BAU/mL. Comparison of allelic frequencies with weak responders showed a significant different proportion of individuals carrying A*03:01, A*24:02 and DRB1*16:01 (21.5% vs. 3.6%, 7.7% vs. 14.9% and 3.2% vs. 8.1% respectively). Moreover, when looking at alleles of the ancestral haplotype A3-B35-C4-DR1, we observed frequencies of 4.47%, 0.84% and 0% in the present cohort, IBMDR and weak responders, respectively. After adjusting for age, gender and BMI, the presence of A*03:01 confirmed to be statistically significant (p<0.0001) and was predictive of high antibody titers at six months with an odds ratio of 12.5 with respect to weak antibody levels. Age was the only other significant variable, with an odds ratio of 0.96. Clinical collection data is underway to correlate Covid-19 infection rates in both cohorts, in an attempt to find a definite correlation between HLA and vaccine protection.

A Protective HLA Extended Haplotype Outweighs the Major COVID-19 Risk Factor Inherited from Neanderthals in the Sardinian Population

During the first and second waves of coronavirus-19 disease, Sardinia had one of the lowest hospitalization and related mortality rates in Europe. However, in contrast with this evidence, the Sardinia population showed a very high frequency of the Neanderthal risk locus variant rs35044562, considered to be a major risk factor for a severe SARS-CoV-2 disease course. We evaluated 358 patients who had tested positive for SARS-CoV-2 and 314 healthy Sardinian controls (Italy). Patients were divided according to WHO classification: 120 patients asymptomatic, 90 pauci-symptomatic, 108 with a moderate disease course and 40 severely ill. The allele frequencies of Neanderthal-derived genetic variants reported as being protective (rs1156361) or causative (rs35044562) for severe illness were calculated in patients and controls. The Thalassemia variant (rs11549407), the HLA haplotypes, the KIR genes, as well as KIRs and their HLA class I ligand combinations were also investigated. The rs35044562 and rs1156361 Neanderthal variants revealed a distribution in Hardy-Weinberg equilibrium (HWE) both in SARS-CoV-2 patients and the control population (X2HWE = 0.82, p = 0.37 and X2HWE = 0.13, p = 0.72, respectively). Our findings reported an increased risk for severe disease in Sardinian patients carrying the rs35044562 high-risk variant [OR 5.32 (95% CI 2.53-12.01), p<0.0001]. Conversely, the protective effect of the HLA-A*02:01~B*18:01~DRB1*03:01 three-loci extended haplotype in the Sardinian population was shown to efficiently contrast the high risk of a severe and devastating outcome of the infection predicted for carriers of the Neanderthal locus [OR 15.47 (95% CI 5.8 - 41.0), p<0.0001]. This result suggests that the balance between risk and protective immunogenetic factors plays an important role in the evolution of COVID-19. A better understanding of these mechanisms may well turn out to be the biggest advantage in the race for the development of more efficient drugs and vaccines.

Genomic characterization and phylogenetic analysis of sars-cov-2 in libya

The COVID-19 epidemic started in Libya in March 2020 and rapidly spread. To shed some light on the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) strains circulating in Libya, viruses isolated from 10 patients in this country were sequenced, characterized at the genomic level, and compared to genomes isolated in other parts of the world. As nine genomes out of 10 belonged to the SS1 cluster and one to SS4, three datasets were built. One included only African strains and the other two contained internationally representative SS1 and SS4 genomes. Genomic analysis showed that the Libyan strains have some peculiar features in addition to those reported in other world regions. Considering the countries in which the strains are genetically more similar to the Libyan strains, SARS-CoV-2 could have entered Libya from a North African country (possibly Egypt), sub-Saharan Africa (e.g., Ghana, Mali, Nigeria), the Middle East (e.g., Saudi Arabia), or Asia (India, Bangladesh).Copyright © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines.

Introduction: Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression allelic imbalance can be measured by allele-specific expression analysis (ASE) across heterozygous informative expressed single nucleotide variants (eSNVs). ASE reflects many regulatory biological phenomena that can be assessed by combining genome and transcriptome information. ASE contributes to the interindividual variability associated with the disease. We aim to estimate the transcriptome-wide impact of SARS-CoV-2 infection by analyzing eSNVs. Methods: We compared ASE profiles in the human lung cell lines Calu-3, A459, and H522 before and after infection with SARS-CoV-2 using RNA-Seq experiments. Results: We identified 34 differential ASE (DASE) sites in 13 genes (HLA-A, HLA-B, HLA-C, BRD2, EHD2, GFM2, GSPT1, HAVCR1, MAT2A, NQO2, SUPT6H, TNFRSF11A, UMPS), all of which are enriched in protein binding functions and play a role in COVID-19. Most DASE sites were assigned to the MHC class I locus and were predominantly upregulated upon infection. DASE sites in the MHC class I locus also occur in iPSC-derived airway epithelium basal cells infected with SARS-CoV-2. Using an RNA-Seq haplotype reconstruction approach, we found DASE sites and adjacent eSNVs in phase (i.e., predicted on the same DNA strand), demonstrating differential haplotype expression upon infection. We found a bias towards the expression of the HLA alleles with a higher binding affinity to SARS-CoV-2 epitopes. Discussion: Independent of gene expression compensation, SARS-CoV-2 infection of human lung cell lines induces transcriptional allelic switching at the MHC loci. This suggests a response mechanism to SARS-CoV-2 infection that swaps HLA alleles with poor epitope binding affinity, an expectation supported by publicly available proteome data.

Population genetic characteristics of Aedes aegypti in 2019 and 2020 under the distinct circumstances of dengue outbreak and the COVID-19 pandemic in Yunnan Province, China.

Introduction: Since Aedes aegypti invaded Yunnan Province in 2002, its total population has continued to expand. Shi et al. used microsatellite and mitochondrial molecular markers to study the Ae. aegypti populations in Yunnan Province in 2015 and 2016, found that it showed high genetic diversity and genetic structure. However, there are few studies on the population genetic characteristics of Ae. aegypti in Yunnan Province under different levels of human intervention. This study mainly used two common types of molecular markers to analyze the genetic characteristics of Ae. aegypti, revealing the influence of different input, prevention and control pressures on the genetic diversity and structure of this species. Understanding the genetic characteristics of Ae. aegypti populations and clarifying the diversity, spread status, and source of invasion are essential for the prevention, control and elimination of this disease vector. Methods: We analyzed the genetic diversity and genetic structure of 22 populations sampled in Yunnan Province in 2019 and 17 populations sampled in 2020 through nine microsatellite loci and COI and ND4 fragments of mitochondrial DNA. In 2019, a total of 22 natural populations were obtained, each containing 30 samples, a total of 660 samples. In 2020, a total of 17 natural populations were obtained. Similarly, each population had 30 samples, and a total of 510 samples were obtained. Results: Analysis of Ae. aegypti populations in 2019 and 2020 based on microsatellite markers revealed 67 and 72 alleles, respectively. The average allelic richness of the populations in 2019 was 3.659, while that in 2020 was 3.965. The HWE analysis of the 22 populations sampled in 2019 revealed significant departure only in the QSH-2 population. The 17 populations sampled in 2020 were all in HWE. The average polymorphic information content (PIC) values were 0.546 and 0.545, respectively, showing high polymorphism. The average observed heterozygosity of the 2019 and 2020 populations was 0.538 and 0.514, respectively, and the expected average heterozygosity was 0.517 and 0.519, showing high genetic diversity in all mosquito populations. By analyzing the COI and ND4 fragments in the mitochondrial DNA of Ae. aegypti, the populations sampled in 2019 had a total of 10 COI haplotypes and 17 ND4 haplotypes. A total of 20 COI haplotypes were found in the populations sampled in 2020, and a total of 24 ND4 haplotypes were obtained. STRUCTURE, UPGMA and DAPC cluster analyses and a network diagram constructed based on COI and ND4 fragments showed that the populations of Ae. aegypti in Yunnan Province sampled in 2019 and 2020 could be divided into two clusters. At the beginning of 2020, due to the impact of COVID-19, the flow of goods between the port areas of Yunnan Province and neighboring countries was reduced, and the sterilization was more effective when goods enter the customs, leading to different immigration pressures on Ae. aegypti population in Yunnan Province between 2019 and 2020, the source populations of the 2019 and 2020 populations changed. Mantel test is generally used to detect the correlation between genetic distance and geographical distance, the analysis indicated that population geographic distance and genetic distance had a moderately significant correlation in 2019 and 2020 (2019: p < 0.05 R2 = 0.4807, 2020: p < 0.05 R2 = 0.4233). Conclusion: Ae. aegypti in Yunnan Province maintains a high degree of genetic diversity. Human interference is one reason for the changes in the genetic characteristics of this disease vector.

The Gift of Ancient Times:a Breakthrough in The Tracing ofModern Human Genes br

The2022Nobel Prize in Physiology or Medicine was awarded to Swedish biologist Svante Paabo forhis decisive contribution to paleoanthropogenomics and human origins.There are various theories about theorigin of human beings,and the current mainstream view is:out of the African doctrine.In other words,ancienthumans had about three times of migrations.The first time wasHomo erectus,the second was Neanderthals andDenisovans,and the third was the ancestors of modern humans.All migrated from Africa to Eurasia.Whilepioneering a new discipline,paleoanthropogenomics,Svante Paabo has been refining the"Out of Africa Theory".With the help of various biological techniques,he delved into the origin of human beings from the perspective ofgenomics and found that some genetic imprints from ancient humans were retained in our bodies.For example,the STAT2gene and TLR gene associated with immunity,the EPAS1gene that contributes to hypoxic respirationand the six genes of chromosome3are highly positively correlated with the incidence of COVID-19.Thisresearch means that we can go back to the root of certain diseases,rather than limiting our eyes to the genesthemselves,and exploring where a gene comes from will be a new way of studying diseases.We summarized hisinnovations in related biotechnology in the process of research,his exploration of ancient humans based onmitochondrial and nuclear genes and related results,and introduced some genes derived from ancient humans andtheir related information

The Risk of COVID-19 in People Having a Particular Set of Gene

These risk factors of advancing age, male gender and co-existing health conditions like cancer, cardiovascular diseases, diabetes and obesity do not fully explain why some people have no or mild symptoms whereas others have severe symptoms. Genomewide association study (GWAS) identify a 3p21.31 gene cluster as a genetic susceptibility locus in patients with COVID-19 with respiratory failure. They also found a higher risk among persons with blood group A and protective effect for blood group O than among patients with other blood groups. The particular haplotype in a region of chromosome 3 is contributed to modern humans by neandertals. Another Neanderthal haplotype on chromosome 12 is associated with a 22% reduction in relative risk of becoming severely ill with COVID-19. The ApoE e4e4 homozygous genotype was found to increase the risk of severe COVID-19. Change in angiotensin converting enzyme (ACE) 2 gene was also found to be associated with increased risk of COVID-19, cardiovascular and pulmonary conditions. Copyright © 2021, Kathmandu University. All rights reserved.

Genetic polymorphisms of IL6 gene -174G > C and -597G > A are associated with the risk of COVID-19 severity.

Coronavirus disease-2019 (COVID-19) is pro-inflammatory disorder characterized by acute respiratory distress syndrome. Interleukin-6, a cytokine secreted by macrophages, which mediates an inflammatory response, is frequently increased and associated with the severity in COVID-19 patients. The differential expression of IL6 cytokine in COVID-19 patients may be associated with the presence of single nucleotide polymorphisms (SNPs) in regulatory region of cytokine genes. The aim of this study is to investigate the role of two promoter polymorphisms of the IL6 gene (-597G > A and -174G > C) with the severity of COVID-19. The study included 242 patients, out of which 97 patients with severe symptoms and 145 patients with mild symptoms of COVID-19. Genotyping of two selected SNPs, rs1800795 (-174G > C) and rs1800797 (-597G > A) of promoter region of IL6 gene, was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). In our study, individuals with GC genotypes of IL6 (-174G > C) polymorphism showed significantly higher risk of severity [adjusted odds (OR) 3.86, p <.001] but we did not observe any association of COVID-19 severity with rs1800797 (-597G > A) polymorphism. The COVID-19 severity was significantly higher in individuals having 'C' allele of IL6 (-174G > C) polymorphism (p = .014). Linkage disequilibrium between rs1800795 (-174G > C) and rs1800797 (-597G > A) showed that individuals having AC* haplotype significantly association with COVID-19 severity (p = .034). Our results suggest that 'C' allele of rs1800795 (-174G > C) polymorphism of IL6 may be the risk allele for severity of COVID-19 in North Indian population.

Haplotypic variants of COVID-19 related genes are associated with blood pressure and metabolites levels.

The genetic association of COVID-19 with its complications has not been fully understood. This study aimed to identify variants and haplotypes of candidate genes implicated in COVID-19 related traits by combining the literature review and pathway analysis. In order to explore such genes, the protein-protein interactions and relevant pathways of COVID-19-associated genes were assessed. A number of variants on candidate genes were identified from genome-wide association studies (GWASs) which were associated with COVID-19 related traits (p˂10-6 ). Haplotypic blocks were assessed using haplotypic structures among the 1000 Genomes Project (r2 ≥0.8, D'≥0.8). Further functional analyses were performed on the selected variants. The results demonstrated that a group of variants in ACE and AGT genes were significantly correlated with COVID-19 related traits. Three haplotypes were identified to be involved in the blood metabolites levels and the development of blood pressure. Functional analyses revealed that most GWAS index variants were expression quantitative trait loci (eQTL) and had transcription factor binding sites, exonic splicing enhancers, or silencer activities. Furthermore, the proxy haplotype variants, rs4316, rs4353, rs4359, and three variants, namely rs2493133, rs2478543, and rs5051, were associated with blood metabolite and systolic blood pressure, respectively. These variants exerted more regulatory effects compared with other GWAS variants. The present study indicates that the genetic variants and candidate haplotypes of COVID-19 related genes are associated with blood pressure and blood metabolites. However, further observational studies are warranted to confirm these results. This article is protected by copyright. All rights reserved.

The Search of Association of HLA Class I and Class II Alleles with COVID-19 Mortality in the Russian Cohort.

HLA genes play a pivotal role in the immune response via presenting the pathogen peptides on the cell surface in a host organism. Here, we studied the association of HLA allele variants of class I (loci A, B, C) and class II (loci DRB1, DQB1, DPB1) genes with the outcome of COVID-19 infection. We performed high-resolution sequencing of class HLA I and class II genes based on the sample population of 157 patients who died from COVID-19 and 76 patients who survived despite severe symptoms. The results were further compared with HLA genotype frequencies in the control population represented by 475 people from the Russian population. Although the obtained data revealed no significant differences between the samples at a locus level, they allowed one to uncover a set of notable alleles potentially contributing to the COVID-19 outcome. Our results did not only confirm the previously discovered fatal role of age or association of DRB1*01:01:01G and DRB1*01:02:01G alleles with severe symptoms and survival, but also allowed us to single out the DQB1*05:03:01G allele and B*14:02:01G~C*08:02:01G haplotype, which were associated with survival. Our findings showed that not only separate allele, but also their haplotype, could serve as potential markers of COVID-19 outcome and be used during triage for hospital admission.

Implications of Haplotype Switching for the Origin and Global Spread of COVID-19

When analysed in patients at epicentres of outbreaks over the first three months of the 2020 pandemic, the virus responsible for COVID-19 cannot be classed as a rapidly mutating virus. It employs a haplotype-switching strategy most likely driven by APOBEC and ADAR cytosine and adenosine deamination events (C>U, A>I) at key selected sites in the ~ 30, 000 nt positive sense single-stranded RNA genome (Steele and Lindley 2020). Quite early on (China, through Jan 2020) the main haplotype was L with a minor proportion of the S haplotype. By the time of the explosive outbreaks in New York City (mid-to late-March 2020) the haplotype variants expanded to at least 13. The COVID-19 genomes analysed at the main sites of exponential increases in cases and deaths over a 2 week time period (explosive epicentres) such as Wuhan and New York City showed limited mutation per se of the main haplotypes engaged in disease. When mutation was detected it was usually conservative in terms of significant alterations to protein structure. The coronavirus haplotypes whether in Wuhan, West Coast USA, Spain or New York differ by no more than 2-9 coordinated nucleotide changes and all genomes are thus =99.98% identical to each other. Further, we show that the most similar SARS-like CoV animal virus sequences (bats, pangolins) could not have caused the assumed zoonotic event setting off this explosive pandemic in Wuhan and regions: zoonotic causation via a Chinese wild bat SLCoV reservoir jumping to humans by an intermediate amplifier (e.g. pangolins) is clearly not possible on the basis of the available data. We also discuss the evidence for airborne transmission of COVID-19 as the main infection route and highlight outbreaks on certain ships at sea consistent with their hypothesised cosmic origins. We conclude that the virus originated as a pure genetic strain in a life-bearing carbonaceous meteorite which was first deposited in the tropospheric jet stream over Wuhan. Over the next month or so this viral-laden dust cloud not only descended through the troposphere to target Wuhan and its environs, but was also transported in a Westerly direction through the mid-latitude northern jet stream causing explosive in-fall events sequentially over Iran, Italy, Spain and then New York City in the early months of the pandemic to the end of March 2020. © 2022 by World Scientific Publishing Co. Pte. Ltd.

A Novel Finding of an HLA Allele's and a Haplotype's Relationship with SARS-CoV-2 Vaccine-Associated Subacute Thyroiditis.

Subacute thyroiditis (SAT) is a thyroid disease associated with viral infections. Its relationship with major histocompatibility complex (MHC) antigens was shown before. SAT cases triggered by different types of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines have been reported. In this study, human leukocyte antigen (HLA) genotypes of 27 SAT patients (13 vaccine-associated (V-SAT) and 14 non-SARS-CoV-2-infection non-vaccine-associated (non-V-SAT)) were compared with those of 362 healthy donors. HLA analyses were performed with low-resolution DNA-based sequence-specific oligonucleotide or sequence-specific primer methods. Statistical analyses were performed using IBM SPSS Statistics 25 and Stata/MP 14.1 with the hapipf function. Allele and haplotype frequencies were estimated by PyPop and gene[RATE] tool programs. The allele frequencies of HLA-A*11, HLA-B*35, and HLA-C*04 were higher in the patient groups. Both the allele frequency of HLA-A*11 and the haplotype frequency of A*11-B*35-C*04 were higher in the V-SAT group. The A*11-B*35-C*04 haplotype, including all three loci of MHC class I genes, is shown to be associated with the disease for the first time, especially in the V-SAT group. This finding will contribute to a better understanding of the etiopathogenesis of vaccine-associated SAT and the role of HLA genotypes in the functioning mechanisms of the SARS-CoV-2 vaccines.

Interleukin-38 promoter variants and risk of COVID-19 among Iraqis.

Coronavirus disease-19 (COVID-19) has recently emerged as a respiratory infection with a significant impact on health and society. The pathogenesis is primarily attributed to a dysregulation of cytokines, especially those with pro-inflammatory and anti-inflammatory effects. Interleukin-38 (IL-38) is a recently identified anti-inflammatory cytokine with a proposed involvement in mediating COVID-19 pathogenesis, while the association between IL38 gene variants and disease susceptibility has not been explored. Therefore, a pilot study was designed to evaluate the association of three gene variants in the promoter region of IL38 gene (rs7599662 T/A/C/G, rs28992497 T/C and rs28992498 C/A/T) with COVID-19 risk. DNA sequencing was performed to identify these variants. The study included 148 Iraqi patients with COVID-19 and 113 healthy controls (HC). Only rs7599662 showed a significant negative association with susceptibility to COVID-19. The mutant T allele was presented at a significantly lower frequency in patients compared to HC. Analysis of recessive, dominant and codominant models demonstrated that rs7599662 TT genotype frequency was significantly lower in patients than in HC. In terms of haplotypes (in order: rs7599662, rs28992497 and rs28992498), frequency of CTC haplotype was significantly increased in patients compared to HC, while TTC haplotype showed significantly lower frequency in patients. The three SNPs influenced serum IL-38 levels and homozygous genotypes of mutant alleles were associated with elevated levels. In conclusion, this study indicated that IL38 gene in terms of promoter variants and haplotypes may have important implications for COVID-19 risk.

A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2.

BACKGROUND: COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed to understand transmission, the cellular mechanism of pathogenicity, and the development of vaccines or drugs. OBJECTIVE: In this study, we intended to identify SARS-CoV-2 genome variants that may help understand the cellular and molecular foundation of coronavirus infections required to develop effective intervention strategies. METHODS: SARS-CoV-2 genome sequences were downloaded from an open-source public database, processed, and analyzed for variants in target detection sites and genes. RESULTS: We have identified six unique variants, G---AAC, T---AAC---T, AAC---T, AAC--------T, C----------T, and C--------C, at the nucleocapsid region and eleven major hotspot mutant genes: nsp3, surface glycoprotein, nucleocapsid phosphoprotein, ORF8, nsp6, nsp2, nsp4, helicase, membrane glycoprotein, 3'-5' exonuclease, and 2'-O-ribose methyltransferases. In addition, we have identified eleven major mutant genes that may have a crucial role in SARS-CoV-2 pathogenesis. CONCLUSION: Studying haplotype variants and 11 major mutant genes to understand the mechanism of action of fatal pathogenicity and inter-individual variations in immune responses is inevitable for managing target patient groups with identified variants and developing effective anti-viral drugs and vaccines.

IMMUNO-PSYCHIATRY AND INFLAMMATION

: The discovery that the immune system can influence brain function and structure has profoundly changed the landscape of psychiatry. Repeated report of association of pro-inflammatory cytokines with major psychiatric disorders led to exploration of the causes and consequences of this inflammatory background. This low-grade inflammation has been shown to be the consequence of interaction between environmental factors such as infections, stress, pollution, unhealthy lifestyle with immune-genetic background. Association with particular immune-genetic variants of Toll-like receptor genes possibly explain diminished response to infections (TLR, NOD), association with mitochondrial genes contribute to maintenance of inflammation, while association with particular HLA haplotypes explains induction of auto-immune phenomena and/or exaggerated synaptic pruning. For example, association with the complement genes can induce abnormal pruning and microglial activation thereby increasing the risk of neurodevelopmental disorders such as early onset schizophrenia. In the context of the SARS-Cov2 pandemic, increased severity of COVID-19 in psychiatric patients is probably due to their reduced ability to fight infection. Systemic inflammation and persistent infections induce different pathways paving the way to biomarker-guided personalized medicine. One of the best examples is the identification of “autoimmune psychosis” defined by presence of anti-neuronal antibodies that has been confounded for long with atypical, mild, or attenuated forms of autoimmune encephalitis. Persistent infections are associated to activation of Human endogenous retrovirus (HERV). Systemic inflammation induced by microbial infection or psychosocial factors can also be at the origin of the activation of human endogenous retrovirus. Inflammation is also known to be associated with gut dysbiosis and disturbance of the integrity of the digestive barrier leading to behavioral abnormalities. One last example can be found in the immune-metabolic abnormalities that pave the way to metabolic syndrome associated with psychiatric disorders. Although many aspects of the complex relationship between immunity and brain function are not yet fully elucidated, the findings that have accumulated so far have transformed our understanding of psychiatric disorders and favored the consideration of other possible cellular and molecular targets for their treatment than just alterations in neuronal transmitters. Disclosure: Nothing to disclose.

'rEACTIVE' MYOSITIS FOLLOWING ANTI-SARS-2 VACCINATION in TWO PATIENTS CARRYING HLA-B∗35 HAPLOTYPE

Background: The anti-SARS2 vaccination is considered the best way to reduce the frequency and the subsequent effects of COVID19 pandemic. To this aim, the most used in western countries are mRNA vaccines BNT16162b2 (Pfzer-Bi-oNT) and mRNA-1273 (Moderna). With both these vaccines the risk/benefts balance is largely favorable and severe adverse effects are almost rare. In keeping, although transient myalgia and arthralgia are frequently seen, myositis have been until now rarely reported. Objectives: To report two cases of myositis occurring in two patients after BNT16162b2 vaccine administration evaluated at the Center for Rheumatic Diseases in Venice, Italy. Methods: In these patients clinical examination, blood and instrumental investigations for myositis and, in addition HLA typing, were performed. Patients were followed for at least six months after the onset of symptoms. Results: The frst patient, a 54-year-old male, complained of high-grade fever 4 days after the I dose of BNT16162b2 (Pfzer-BioNT) followed, by mild fatigue, muscle soreness and increasing weakness. He was sent to the emergency department of the local Hospital. The physical examination confrmed the muscle weakness. Blood investigation revealed an increase of AST: 509 U/L (NV< 37), ALT:189 U/L (NV <78), LDH 609, CPK 11394 U/L (NV<, 309), Myoglobin 3571 ng/ml (VN <96), CRP 1. 6 mg/dl. Prednisone (PN) was started (50 mg orally day) and tapered to 5 mg in two weeks. At high doses, the symptoms slightly improved, but when < 10 mg, all the symptoms reappeared. Thus, he was hospitalized again. The new examination confrmed the increase of all indices of myositis;antinuclear antibodies and myositis antibodies were absent and PN was restarted at 10 mg/day without beneft;echo-cardiography and TC scan were negative. He was then sent to our observation. We increased the dose of PN at 1 mg/PN/kg and we required HLA typing. Two weeks later symptoms disappared almost completely and then we tapered PN 5 mg/day weekly. At present the patients is completely well and muscle indices negative since two months. HLA typing revealed the presence of B∗35 and DRB1∗15. The second case was a 29-year-old female presented with a history of complaints appeared two days after the vaccination with BNT16162b2 administration (Pfzer-BioNT) characterized by three days of high-degree fever, followed by sever weakness, especially in the arms. The family doctor decide to hear our advise. At the initial presentation arm strenght was very decrease and the patient was accompanied. We required a serie of investigations which revealed: CPK 8950 U/L (NV 250), CRP 3.5 mg/dl increased;antinuclear and anti-myositis antibodies absent;cardiac (Ultrasound) and thoracic (CT) investigation and electro-myography negative. HLA typing revealed the presence of haplotypes B∗35 and DRB1∗15. PN (50 mg orally day) was started;two weeks later she improved and both muscle indices and CRP negative. Thus, we reduce the dosage at 25 mg/day with tapering 5 mg weekly. She was completely remitted at end of PN cycle. At present, three month later she is well. Conclusion: The rare occurrence of some particular side effects is not predictable. Our cases of severe myositis which in both cases completely remitted in some months are associated with haplotypes HLA-B∗35 and DRB1∗15. These are both binding sites linked to high-affinity interactions to S-protein T-cell epitope which account for high potentials to trigger immunogenic responses to the S protein of SARS-CoV-2 (1). Furthermore classically, HLA-B35 is associated with reactive arthritis and self-limiting, unclassifed rheumatism (2).

POS-011 PRIMARY ATYPICAL HEMOLYTIC-UREMIC SYNDROME ASSOCIATED WITH COVID-19: A BRIEF REVIEW

Introduction: Since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was diagnosed in December 2019, coronavirus disease 2019 (COVID-19) has spread tremendously. We now know that infected individuals can experience a wide range of systemic complications, including thrombotic microangiopathy (TMA). Among the total of 45 published cases of COVID-19-associated TMA, there were 4 cases of primary atypical hemolytic-uremic syndrome (aHUS). COVID-19 likely represents a second hit of primary aHUS that manifests in genetically predisposed individuals. Methods: We reviewed the global literature reported from the first mention of COVID-19 in 2019 to February 2022, including individual case reports and case series of adult patients with COVID-19-associated TMAs. Electronic searches were conducted in the PubMed database using keywords and their combinations: »thrombotic microangiopathy, COVID-19, thrombotic thrombocytopenic purpura, atypical hemolytic-uremic syndrome«. Results: Among the total of 45 published cases of COVID-19-associated TMA, there were 18 cases reported as acquired thrombotic thrombocytopenic purpura (TTP) and 19 cases presented as mixed forms of TMA associated with multifactorial triggers (without proven abnormalities of ADAMTS13 activity or proven inhibitors of ADAMTS13 or proven Shiga toxin). The remaining 8 cases were complement-mediated TMAs: • 2 cases of hereditary aHUS (patient 1 and 2);• 1 case of probable hereditary aHUS, where the patient had a heterozygous variant with unknown significance in complement factor I and was heterozygous for the complement factor H H3 haplotype reported as a risk factor of aHUS (patient 3);• 1 case of aHUS with significantly elevated factor H autoantibodies in the absence of genetic testing (patient 4);• 4 cases with decreased complement levels in the absence of genetic testing. We focused on the 4 patients with primary aHUS. Among those, there were 2 females and 2 males with an average age of 28.75 +/- 6.18 years. Although in all cases nasopharyngeal swab was positive for SARS-CoV-2 infection by a polymerase chain reaction-based test, none of the patients had any respiratory symptoms. Patients 2 and 3 underwent renal biopsies, which confirmed the diagnosis of TMA. Patients 2, 3, and 4 required treatment with hemodialysis (HD). Patient 3 did not receive any specific treatment due to delayed diagnosis and lack of availability of eculizumab, while patients 2 and 4 underwent therapeutic plasma exchange and received steroids and eculizumab (patient 2 received only the initial dose of eculizumab because further doses were not granted). Patients 2 and 3 remained HD-dependent, while the renal function of patient 4 partially recovered. Patient 1, who did not need HD, was treated with eculizumab and had partial recovery of renal function. Conclusions: In conclusion, different types of TMA may occur during the course of COVID-19, including aHUS. COVID-19 likely represents a second hit of primary aHUS that manifests in genetically predisposed individuals (e.g., those with an underlying complement risk factor). Early identification of COVID-19-associated primary aHUS is needed in order to promptly start treatment with eculizumab. No conflict of interest