POSSIBLE ROLE OF PEPTIDE EPITOPES OF COVID-19 BNT-162B2 MRNA VACCINE IN FOMENTING AUTOIMMUNITY: AN IN SILICO ANALYSIS

BackgroundFollowing the launch of the global COVID-19 vaccination campaign, there have been increased reports of autoimmune diseases developing de novo following vaccination. These cases include rheumatoid arthritis, autoimmune hepatitis, immune thrombotic thrombocytopenia, and connective tissue diseases. Nevertheless, COVID-19 vaccines are considered safe for patients with autoimmune diseases and are strongly recommended.ObjectivesThe aim of this in silico analysis is to investigate the presence of protein epitopes encoded by the BNT-162b2 mRNA vaccine, one of the most commonly administered COVID-19 vaccines, that could elicit an aberrant adaptive immune response in predisposed individuals.MethodsThe FASTA sequence of the protein encoded by the BNT-162b2 vaccine was retrieved from http://genome.ucsc.edu and used as a key input to the Immune Epitope Database and Analysis Resource (www.iedb.org). Linear peptides with 90% BLAST homology were selected, and T-cell, B-cell, and MHC ligand assays without MHC restriction were searched and evaluated. HLA-disease associations were screened on the HLA-SPREAD platform (https://hla-spread.igib.res.in) by selecting only positive markers.ResultsA total of 183 epitopes were found, corresponding to 178 SARS-CoV-2 and 5 SARS-CoV spike epitopes, respectively. Results were obtained from 22 T-cell assays, 398 B-cell assays, and 2 MHC ligand assays. Complementary receptors included 1080 T-cell receptors and 0 B-cell receptors.Specifically, the IEDB_epitope:1329790 (NATNVVIKVCEFQFCNDPFLGVYY) was shown to bind to HLA-DRB1*15:02 and HLA-DRB1*15:03 alleles, whereas the IEDB_epitope:1392457 (TKCTLKSFTVEKGIYQTSNFRVQPT) was reported to bind to HLA-DRB1*07:01, HLA-DRB1*03:01, HLA-DRB3*01:01, and HLA-DRB4*01:01 alleles. The HLA alleles detected were found to be positively associated with various immunological disorders (Table 1).Table 1.MHC-restricted epitopes of the BNT-162b2 vaccine and potentially associated immunological conditionsEpitopeAssayMHC moleculeAssociated disease (population)NATNVVIKVCEFQFCNDPFLGVYY + OX(C10)cellular MHC/mass spectrometry ligand presentationHLA-DRB1*15:02Takayasu arteritis (Japanese) Arthritis (Taiwanese) Scleroderma (Japanese) Colitis (Japanese)HLA-DRB1*15:03Systemic lupus erythematosus (Mexican American)TKCTLKSFTVEKGIYQTSNFRVQPT + SCM(K2)as aboveHLA-DRB1*07:01Allergy, hypersensitivity (Caucasian)HLA-DRB1*03:01Type 1 diabetes (African) Sarcoidosis, good prognosis (Finnish)HLA-DRB3*01:01Graves' disease (Caucasian) Thymoma (Caucasian) Sarcoidosis (Scandinavian) Autoimmune hepatitis (Caucasian)HLA-DRB4*01:01Vitiligo (Saudi Arabian)ConclusionSimilar to the SARS-CoV-2 spike protein, the protein product of the BNT-162b2 mRNA vaccine contains immunogenic epitopes that may trigger autoimmune phenomena in predisposed individuals. Genotyping for HLA alleles may help identify at-risk individuals. However, further research is needed to elucidate the underlying mechanisms and potential clinical implications.References[1]Vita R, Mahajan S, Overton JA et al. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 2019 Jan 8;47(D1):D339-D343. doi: 10.1093/nar/gky1006.[2]Dholakia D, Kalra A, Misir BR et al. HLA-SPREAD: a natural language processing based resource for curating HLA association from PubMed s. BMC Genomics 23, 10 (2022). https://doi.org/10.1186/s12864-021-08239-0[3]Parker R, Partridge T, Wormald C et al. Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells. Cell Rep. 2021 May 25;35(8):109179. doi: 10.1016/j.celrep.2021.109179.[4]Knierman MD, Lannan MB, Spindler LJ et al. The Human Leukocyte Antigen Class II Immunopeptidome of the SARS-CoV-2 Spike Glycoprotein. Cell Rep. 2020 Dec 1;33(9):108454. doi: 10.1016/j.celrep.2020.108454.Acknowledgements:NIL.Disclosure of InterestsNone Declared.

A survival genome-wide association study to identify variants associated with COVID-19 risk of death

Background/Objectives: SARS-CoV-2 infection clinical manifestations hugely vary among patients, ranging from no symptoms, to life-threatening conditions. This variability is also due to host genetics: COVID-19 Host Genetics Initiative identified six loci associated with COVID-19 severity in a previous case-control genome-wide association study. A different approach to investigate the genetics of COVID-19 severity is looking for variants associated with mortality, e.g. by analyzing the association between genotypes and time-to-event data. Method(s): Here we perform a case-only genome-wide survival analysis, of 1,777 COVID-19 patients from the GEN-COVID cohort, 60 days after infection/hospitalization. Case-only studies has the advantage of eliminating selection biases and confounding related to control subjects. Patients were genotyped using Illumina Infinium Global Screening Arrays. PLINK software was used for data quality check and principal component analysis. GeneAbel R package was used for survival analysis and age, sex and the first four principal components were used as covariates in the Cox proportional hazard model. Result(s): We found four variants associated with COVID-19 patient survival at a nominal P < 1.0 x 10-6. Their minor alleles were associated with a higher mortality risk (i.e. hazard ratios (HR)>1). In detail, we observed: HR=1.03 for rs28416079 on chromosome 19 (P=1.34 x 10-7), HR=1.15 for rs72815354 on chromosome 10 (P=1.66 x 10-7), HR=2.12 for rs2785631 on chromosome 1 (P=5.14 x 10-7), and HR=2.27 for rs2785631 on chromosome 5 (P=6.65 x 10-7). Conclusion(s): The present results suggest that germline variants are COVID-19 prognostic factors. Replication in the remaining HGI COVID-19 patient cohort (EGAS00001005304) is ongoing at the time of submission.

The clinical significance of macrolide resistance in pediatric Mycoplasma pneumoniae infection during COVID-19 pandemic.

Background: Mycoplasma pneumoniae (MP) is a commonly occurring pathogen causing community-acquired pneumonia (CAP) in children. The global prevalence of macrolide-resistant MP (MRMP) infection, especially in Asian regions, is increasing rapidly. However, the prevalence of MRMP and its clinical significance during the COVID-19 pandemic is not clear. Methods: This study enrolled children with molecularly confirmed macrolide-susceptible MP (MSMP) and MRMP CAP from Beijing Children's Hospital Baoding Hospital, Capital Medical University between August 2021 and July 2022. The clinical characteristics, laboratory findings, chest imaging presentations, and strain genotypes were compared between patients with MSMP and MRMP CAP. Results: A total of 520 hospitalized children with MP-CAP were enrolled in the study, with a macrolide resistance rate of 92.7%. Patients with MRMP infection exhibited more severe clinical manifestations (such as dyspnea and pleural effusion) and had a longer hospital stay than the MSMP group. Furthermore, abnormal blood test results (including increased LDH and D-dimer) were more common in the MRMP group (P<0.05). Multilocus variable-number tandem-repeat analysis (MLVA) was performed on 304 samples based on four loci (Mpn13-16), and M3562 and M4572 were the major types, accounting for 74.0% and 16.8% of the strains, respectively. The macrolide resistance rate of M3562 strains was up to 95.1%. Conclusion: The prevalence of MRMP strains in hospitalized CAP patients was extremely high in the Baoding area, and patients infected with MRMP strains exhibited more severe clinical features and increased LDH and D-dimer. M3562 was the predominant resistant clone.

Development and authentication of Panax ginseng cv. Sunhong with high yield and multiple tolerance to heat damage, rusty roots and lodging.

Ginseng (Panax ginseng) has been used as a valuable medicinal plant in Asia, and the demand for ginseng production for health functional food is increasing worldwide after the COVID-19 crisis. Although a number of cultivars have been developed to increase ginseng production, none of them were widely cultivated in Korea because they could not resist various environmental stresses while being grown in one place for at least 4 years. To address this, Sunhong was developed as a ginseng cultivar with high yield and multiple stress tolerance by pure line selection. Sunhong showed high yield and heat tolerance comparable to Yunpoong, a representative high-yielding cultivar, and exhibited 1.4 times lower prevalence of rusty roots than Yunpoong, suggesting that Sunhong can keep its high yield and quality during long-term cultivation. In addition, distinct color and lodging resistance were expected to increase the convenience of cultivation. To supply pure seeds to farmers, we also established a reliable high-throughput authentication system for Sunhong and seven ginseng cultivars through genotyping-by-sequencing (GBS) analysis. The GBS approach enabled to identify a sufficient number of informative SNPs in ginseng, a heterozygous and polyploid species. These results contribute to the improvement of yield, quality, and homogeneity, and therefore promote the ginseng industry. Supplementary Information: The online version contains supplementary material available at 10.1007/s13580-023-00526-x.

Tb Genomics for Public Health

Mycobacterium tuberculosis complex (MTBC), the causative organisms of tuberculosis (TB), has afflicted man for millennia. TB was declared a global health emergency by the World Health Organization in 1993. Before the 2020 Covid pandemic, it was responsible for 10 million new cases annually and was the leading infectious disease killer worldwide. MTBC strain typing represents an important complementary tool to guide TB control measures. TB programmes can use genotyping results in combination with epidemiological information to determine if recent transmission has likely occurred, and hence identify outbreaks that require targeted public health action. MTBC genotyping also can differentiate between relapse or re-infection, detect false-positive cases, and identify and monitor the circulating TB strains in the population over time. Restriction Fragment Length Phenotyping (RFLP), introduced in the 1990s, was labour intensive, required large amounts of DNA and was not easily comparable between laboratories. These disadvantages are overcome by the PCR-based MIRU-VNTR and spoligotyping methods. More recently, whole genome sequencing (WGS) of MTBC has been shown to provide high resolution identification of recent transmission chains and their direction, as well as drug resistance prediction. Its increasing reliability and affordability has enabled this technology to transition from the research arena to clinical care and public health functions. Its application in high TB burden countries will hopefully revitalize global TB control efforts which have set back by the Covid pandemic.Copyright © 2023

Molecular genetics and genomics of the ABO blood group system

The A and B oligosaccharide antigens of the ABO blood group system are produced from the common precursor, H substance, by enzymatic reactions catalyzed by A and B glycosyltransferases (AT and BT) encoded by functional A and B alleles at the ABO genetic locus, respectively. In 1990, my research team cloned human A, B, and O allelic cDNAs. We then demonstrated this central dogma of ABO and opened a new era of molecular genetics. We identified four amino acid substitutions between AT and BT and inactivating mutations in the O alleles, clarifying the allelic basis of ABO. We became the first to achieve successful ABO genotyping, discriminating between AA and AO genotypes and between BB and BO, which was impossible using immunohematological/serological methods. We also identified mutations in several subgroup alleles and also in the cis-AB and B(A) alleles that specify the expression of the A and B antigens by single alleles. Later, other scientists interested in the ABO system characterized many additional ABO alleles. However, the situation has changed drastically in the last decade, due to rapid advances in next-generation sequencing (NGS) technology, which has allowed the sequencing of several thousand genes and even the entire genome in individual experiments. Genome sequencing has revealed not only the exome but also transcription/translation regulatory elements. RNA sequencing determines which genes and spliced transcripts are expressed. Because more than 500,000 human genomes have been sequenced and deposited in sequence databases, bioinformaticians can retrieve and analyze this data without generating it. Now, in this era of genomics, we can harness the vast sequence information to unravel the molecular mechanisms responsible for important biological phenomena associated with the ABO polymorphism. Two examples are presented in this review: the delineation of the ABO gene evolution in a variety of species and the association of single nucleotide variant (SNV) sites in the ABO gene with diseases and biological parameters through genome-wide association studies (GWAS).Copyright © Annals of Blood. All rights reserved.

Mannose-binding lectin gene 2 variant DD (rs 5030737) is associated with susceptibility to COVID-19 infection in the urban population of Patna City (India).

The study aimed to measure plasma levels of Mannose-Binding Lectin (MBL) and MBL-associated serine protease-2 (MASP-2) and their polymorphisms in COVID-19 patients and controls to detect association. As MBL is a protein of immunological importance, it may contribute to the first-line host defence against SARS-CoV-2. MBL initiates the lectin pathway of complement activation with help of MASP-1 and MASP-2. Hence, appropriate serum levels of MBL and MASPs are crucial in getting protection from the disease. The polymorphisms of MBL and MASP genes affect their plasma levels, impacting their protective function and thus may manifest susceptibility, extreme variability in the clinical symptoms and progression of COVID-19 disease. The present study was conducted to find plasma levels and genetic variations in MBL and MASP-2 in COVID-19 patients and controls using PCR-RFLP and ELISA, respectively.The present study was conducted to find plasma levels and genetic variations in MBL and MASP-2 in COVID-19 patients and controls using PCR-RFLP and ELISA, respectively. Our results indicate that median serum levels of MBL and MASP-2 were significantly low in diseased cases but attained normal levels on recovery. Only genotype DD was found to be associated with COVID-19 cases in the urban population of Patna city.

Evolutionary adaptation of bovine coronavirus (BCoV): Screening of natural recombinations across the complete genomes.

Bovine coronavirus (BCoV) is a member of pathogenic Betacoronaviruses that has been circulating for several decades in multiple host species. Given the similarity between BCoV and human coronaviruses, the current study aimed to review the complete genomes of 107 BCoV strains available on the GenBank database, collected between 1983 and 2017 from different countries. The maximum-likelihood based phylogenetic analysis revealed three main BCoV genogroups: GI, GII, and GIII. GI is further divided into nine subgenogroups: GI-a to GI-i. The GI-a to GI-d are restricted to Japan, and GI-e to GI-i to the USA. The evolutionary relationships were also inferred using phylogenetic network analysis, revealing two major distinct networks dominated by viruses identified in the USA and Japan, respectively. The USA strains-dominated Network Cluster includes two sub-branches: France/Germany and Japan/China in addition to the United States, while Japan strains-dominated Network Cluster is limited to Japan. Twelve recombination events were determined, including 11 intragenogroup (GI) and one intergenogroup (GII vs. GI-g). The breakpoints of the recombination events were mainly located in ORF1ab and the spike glycoprotein ORF. Interestingly, 10 of 12 recombination events occurred between Japan strains, one between the USA strains, and one from intercontinental recombination (Japan vs. USA). These findings suggest that geographical characteristics, and population density with closer contact, might significantly impact the BCoV infection and co-infection and boost the emergence of more complex virus lineages.

Efficient SARS-CoV-2 Surveillance during the Pandemic-Endemic Transition Using PCR-Based Genotyping Assays.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOC) pose an increased risk to public health due to higher transmissibility and/or immune escape. In this study, we assessed the performance of a custom TaqMan SARS-CoV-2 mutation panel consisting of 10 selected real-time PCR (RT-PCR) genotyping assays compared to whole-genome sequencing (WGS) for identification of 5 VOC circulating in The Netherlands. SARS-CoV-2 positive samples (N = 664), collected during routine PCR screening (15 ≤ CT ≤ 32) between May-July 2021 and December 2021-January 2022, were selected and analyzed using the RT-PCR genotyping assays. VOC lineage was determined based on the detected mutation profile. In parallel, all samples underwent WGS with the Ion AmpliSeq SARS-CoV-2 research panel. Among 664 SARS-CoV-2 positive samples, the RT-PCR genotyping assays classified 31.2% as Alpha (N = 207); 48.9% as Delta (N = 325); 19.4% as Omicron (N = 129), 0.3% as Beta (N = 2), and 1 sample as a non-VOC. Matching results were obtained using WGS in 100% of the samples. RT-PCR genotyping assays enable accurate detection of SARS-CoV-2 VOC. Furthermore, they are easily implementable, and the costs and turnaround time are significantly reduced compared to WGS. For this reason, a higher proportion of SARS-CoV-2 positive cases in the VOC surveillance testing can be included, while reserving valuable WGS resources for identification of new variants. Therefore, RT-PCR genotyping assays would be a powerful method to include in SARS-CoV-2 surveillance testing. IMPORTANCE The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genome changes constantly. It is estimated that there are thousands of variants of SARS-CoV-2 by now. Some of those variants, variants of concern (VOC), pose an increased risk to public health due to higher transmissibility and/or immune escape. Pathogen surveillance helps researchers, epidemiologists, and public health officials to monitor the evolution of infectious diseases agents, alert on the spread of pathogens, and develop counter measures like vaccines. The technique used for the pathogen surveillance is called sequence analysis which makes it possible to examine the building blocks of SARS-CoV-2. In this study, a new PCR method based on the detection of specific changes of those building blocks is presented. This method enables a fast, accurate and cheap determination of different SARS-CoV-2 VOC. Therefore, it would be a powerful method to include in SARS-CoV-2 surveillance testing.

Epidemiology and Molecular Characterizations of Coronavirus from Companion Animals Living in Chengdu, Southwest China

The recent COVID-19 pandemic has once again caught the attention of people on the probable zoonotic transmission from animals to humans, but the role of companion animals in the coronavirus (CoV) epidemiology still remains unknown. The present study was aimed to investigate epidemiology and molecular characterizations of CoVs from companion animals in Chengdu city, Southwest China. 523 clinical samples from 393 animals were collected from one veterinary hospital between 2020 and 2021, and the presence of CoVs was detected by end-point PCR using pan-CoV assay targeting the RdRp gene. Partial and complete S genes were sequenced for further genotyping and genetic diversity analysis. A total of 162 (31.0%, 162/523) samples and 146 (37.2%, 146/393) animals were tested positive for CoVs. The positive rate in rectal swabs was higher than that in eye/nose/mouth swabs and ascitic fluid but was not statistically different between clinically healthy and diseased ones. Genotyping identified twenty-two feline enteric coronavirus (FCoV) I, four canine enteric coronavirus (CECoV) I, fourteen CECoV IIa, and one CECoV IIb, respectively. Eight complete S genes, including one canine respiratory coronavirus (CRCoV) strain, were successfully obtained. FCoV strains (F21071412 and F21061627) were more closely related to CECoV strains than CRCoV, and C21041821-2 showed potential recombination event. In addition, furin cleavage site between S1 and S2 was identified in two strains. The study supplemented epidemiological information and natural gene pool of CoVs from companion animals. Further understanding of other functional units of CoVs is needed, so as to contribute to the prevention and control of emerging infectious diseases.

KIR2DL2/C1: A potential predictive immunogenetic marker to COVID-19 severity in Spanish patients

COVID-19 has aspects on its pathogenesis that still need elucidating and an analysis of clinical and immunogenetic factors in each cohort of patients is paramount to understanding how genetic variability can explain the multiple clinical spectra seen in patients infected with SARS-CoV-2. The aim of this study was to correlate the KIR polymorphism/HLA class I ligand interactions from patients and healthy subjects with either the susceptibility or severity to COVID-19. Genotyping of HLA-A, -B, -C and KIR genes were carried out from 459 symptomatic as well as 667 non-infected Spanish Caucasian individuals using Lifecodes HLA-SSO and KIR-SSO kits (ImmucorTM, USA) and analyzed in the Luminex in this uni-centre case-control study performed at the University Hospital of Salamanca, Spain. Comparative KIR gene analysis showed that KIR2DS4 was significantly more representative in healthy versus infected individuals. When comparing subgroups of infected patients, KIR2DS3 had a higher frequency in those who progressed to a more severity disease and yet with higher mortality rate. Three functional combinations were significant on univariate analysis: KIR2DL2/C1, KIR2DS2/C1, and KIR2DS3/C1. However, in the multivariate analysis, only the KIR2DL2/C1 interaction remained significant (OR = 15.2 (95% CI 1.5-147), p = 0.0189). Compared with the solo-clinical characteristics predictive model, that included well-known comorbidity variables such as hypertension, age, sex, diabetes, C-reactive protein, dyslipidemia, smoking, ferritin, and fibrinogen, the clinical-and-KIR-based model showed a better ability to discriminate between severe and nonsevere patients with higher sensitivity and specificity. Our results support a fundamental role of KIR/ligand interaction in the clinical course of COVID-19. Since the KIR2DL2 gene has a high frequency in Spain (60%), the analysis of the KIR2DL2/C1 in symptomatic patients who require hospitalization could be helpful to better determine their prognosis.

Decreased Neisseria gonorrhoeae genotypic diversity following COVID-19 restrictions in Queensland, Australia 2020.

We investigated the potential effects of COVID-19 public health restrictions on the prevalence and distribution of Neisseria gonorrhoeae (NG) genotypes in our Queensland isolate population in the first half of the year 2020. A total of 763 NG isolates were genotyped to examine gonococcal strain distribution and prevalence for the first 6 months of 2020, with 1 January 2020 to 31 March 2020 classified as 'pre' COVID-19 restrictions (n = 463) and 1 April 2020 to 30 June 2020 classified as 'post' COVID-19 restrictions (n = 300). Genotypes most prevalent 'pre' restrictions remained proportionally high 'post' restrictions, with some significantly increasing 'post' restrictions. However, genotype diversity was significantly reduced 'post' restrictions. Overall, it seems public health restrictions (9-10 weeks) were not sufficient to affect rates of infection or reduce the prevalence of well-established genotypes in our population, potentially due to reduced access to services or health-seeking behaviours.

TNF, TNFRSF1A, and TNFRSF1B variants affect TNFR1 and TNFR2 levels in patients with severe COVID-19

Background: TNF and its receptors (TNFR1 and TNFR2) have been implicated in the severity of COVID-19. But it has not been explored the association of genetic variants with cytokine levels. Aim(s): We assessed the association of TNF (rs1800629, rs361525), TNFRSF1A (rs767455, rs1800693), and TNFRSF1B (rs1061622, rs3397) single nucleotide variants with TNF, TNFR1, and TNFR2 plasma levels in patients with severe COVID-19. Method(s): The study included 334 severe COVID-19 hospitalized patients in Mexico's Instituto Nacional de Enfermedades Respiratorias. Blood sampling was performed among the first seven days since patients' admission. Cytokine levels were determined using ELISA and Taqman assays for genotyping. Kruskal-Wallis test was performed in RStudio v.1.3.1073. Result(s): Patients with TT or GT genotype (TNFRSF1B rs1061622) exhibited higher sTNFR1 levels than those carrying GG (1,580 and 1,499 pg/ml vs 1,031 pg/mL). For TNF rs1800629 and rs361525 the higher TNFR2 levels were observed among patients homozygous for the common allele (rs1800629 GG=3,993 pg/mL vs AG+AA=2,881 pg/mL;rs361525 GG=3,996 pg/mL, AG=3,919 pg/mL, and AA=1,935 pg/mL). Higher levels of both receptors were related with more severe forms of COVID-19. Conclusion(s): TNFRSF1B rs1061622, and TNF rs1800629 and rs361525 affect the TNFR1 and TNFR2 levels implicated in the severity of COVID-19.

COVID-19 Mortality and the Cytokine Storm: An Added Value for APOE Genotyping

The new COVID-19 presents some comorbidities, such as obesity, Alzheimer's, and coronary risk, among others. We argue that the current understanding of some of these clinical conditions may illuminate the design of future COVID-19 studies to account for a bias that may be the cause of the para-doxical associations between COVID-19 mortality and cytokine storm. Given that we know some of the genetic mechanisms behind these diseases, it is possible to circumscribe these studies to some key genes that help us understand why some patients experience a cytokine storm and what the treatment strategies might be. In this paper, we discuss the role of A2M and APOE genes. A2M encodes a multifaceted protein which is highly expressed in the liver and released to the bloodstream associated with the apolipopro-tein E. This association depends on the APOE genotype. A2M has protease-clearing activity binding of a broad range of proteases, such as thrombin and Factor Xa. It also presents the ability to bind to proin-flammatory ligands, like cytokines. Further, A2M acts as chaperone of misfolded substrates, like beta-amyloid peptide. The last two molecular functions grant it a key role in regulating both inflammatory processes, as well as extracellular protein homeostasis. For these reasons, we conclude that A2M-APOE association will have prophylactic, therapeutic, and prognostic implications;and the proper understanding of the physiological role of APOE and A2M in controlling inflammatory processes can shed further light on the putative treatment of COVID-19-derived cytokine storm.Copyright © 2022 Bentham Science Publishers.

Repeat Doses of Sotrovimab for Recurrence of COVID-19 in a High-Risk Pregnancy

Background: Myasthenia gravis (MG) is an autoimmune disorder leading to variable degrees of skeletal muscle weakness. During pregnancy, infections can trigger exacerbations and should be treated promptly and aggressively.(1) Sotrovimab is a monoclonal antibody used as monotherapy in high-risk, symptomatic non-hospitalized patients at risk of developing COVID-19 disease. (2) It is thought to have retained activity against SARS-CoV-2 omicron variant. (3) Limited data are available on its use in pregnancy. Case: A 39-year-old woman with severe generalized MG, was referred to our joint neuro-obstetric multidisciplinary service. Her two previous pregnancies were complicated by severe exacerbations of MG necessitating intensive care admissions, and preterm labour. Her long-term therapy included high dose steroids, intravenous immune globulin (IVIG) and plasma exchanges. In this pregnancy, she additionally received rituximab in the first-trimester, allowing her prednisolone to be weaned to 20 mg daily, with ongoing 3-weekly IVIG. She received 3 doses of the Pfizer COVID-19 vaccine. At 19 weeks she developed mild coryzal symptoms, sore throat and myalgia. Lateral flow and polymerase chain reaction tests in the community confirmed infection with SARS-CoV-2. She was treated with sotrovimab with uneventful recovery at home. At 31 weeks, she again tested positive for SARS-CoV-2, after reporting mild COVID-19 symptoms. She received a second dose of sotrovimab and had a quick recovery. Subsequent SARS-CoV-2 genotyping indicated she had contracted the Omicron-BA.2 variant. Fetal surveillance for growth (SARS-CoV-2) and arthrogryposis (MG) did not raise concerns. At 35+3 weeks, she went into spontaneous labour and was delivered by caesarean section for evolving chorioamnionitis, with uneventful recovery for mother and baby. Discussion(s): We report a case of repeated treatment with sotrovimab (in second and third trimesters) of a high-risk, non-hospitalized pregnant woman, who was re-infected with SARS-CoV-2. We identified no immediate maternal, fetal or neonatal complications following two doses of sotrovimab for mild COVID-19.

OPTIMIZATION OF MOLECULAR METHODS FOR SARS-CoV-2 QUALITATIVE DETECTION AND GENOTYPING IN RESPIRATORY SPECIMENS FROM PATIENTS WITH LIVER DISEASE

Introduction and Objectives: SARS-CoV-2 active infection diagnosis is currently performed through RT-qPCR. Despite the fact that PCR-based assays can provide results relatively fast, these techniques require capable professionals, specific equipment and adequate infrastructure. In order to facilitate COVID-19 diagnosis in remote areas, an alternative to RT-qPCR would be loop-mediated isothermal (RT-LAMP) amplification. SARS-CoV-2 variant genotyping through high-throughput sequencing (HTS) allows SARS-CoV-2 genomic surveillance, especially for patients with a higher vulnerability. This study aimed to optimize RT-LAMP and HTS methods for SARS-CoV-2 RNA detection and genotyping, respectively, in respiratory samples from patients with liver disease. Material(s) and Method(s): A total of 142 respiratory secretions were obtained from individuals with SARS-CoV-2 RNA detectable by RT-qPCR (N1 Ct <= 30), divided into groups with (n=18) or without (n=124) liver disease. The study also enrolled 55 individuals who had SARS-CoV-2 RNA undetectable at RT-qPCR. For RT-LAMP methodology, primers were used for ORF1 gene amplification. As for HTS genotyping, the steps of cDNA synthesis, complete SARS-CoV-2 genome PCR amplification, preparation of genomic libraries and sequencing in MinION device were performed for 26 swab samples. Result(s): Samples with viral RNA detectable by RT-qPCR had a mean Ct value of 24.3 +/- 3.75. Referring to RT-LAMP, it was observed a sensitivity of 71.1% (101/142). When considering RT-qPCR mean Ct value, RT-LAMP sensitivity was 88.9% (16/18), associated with a mean Ct of 23.3 +/- 3.5 for patients with COVID and hepatitis. A specificity of 100% (55/55) was observed since all negative swabs tested by RT-qPCR were negative at RT-LAMP. Through sequencing by MinION, SARS-CoV-2 lineages gamma (7/26;27%), zeta (1/26;3.9%), delta (6/26;23%) and omicron (12/26;46.1%) were genotyped and detected by RT-LAMP. Conclusion(s): RT-LAMP demonstrated high sensitivity for molecular detection of SARS-CoV-2 RNA for patients with high viral load. Besides, RT-LAMP was capable of detecting all SARS-CoV-2 lineages genotyped by MinION in both groups.Copyright © 2023

The effect of COVID-19 pandemics on the comprehensive laboratory diagnostic of alpha-1 antitrypsin deficiency in Europe - report from the AATD LABNet

Diagnosis of alpha1-antitrypsin deficiency, a rare genetic disorder, consists of biochemical serum analysis to evaluate protein deficiency and electrophoretic abnormalities, as well as genetic analysis to identify SERPINA1 gene variants responsible for the protein deficiency. In majority of European countries diagnostic is centralized, blood and/or DNA samples are referred to dedicated reference laboratories. We aimed at analyzing data reported by the 8 leading European centers (AATD LABnet part of the EARCO ERS CRC and ERN-LUNG activities) to assess the effect of COVID-19 pandemic and healthcare disruption on the AATD diagnostic provision. In total, the number of tests dropped in 2020 vs 2019 by -20,43% (+/-13,25) for AAT concentration analysis, -25,5% (+/-12,79) for AAT phenotyping and -23,57% (+/-10,28) for SERPINA1 genotyping, while in 2021 vs 2019 by respectively -16,86% (+/-21,34), -9,2% (+/-30,38), -13,57% (+/-40,82). Specifically, diagnostics in Poland and Italy were affected the most with -48% and -28% fewer samples analyzed (2021 vs 2019, phenotyping), while in France and Portugal referrals recovered by the end of 2021, with + 18% and +29% respectively (2021 vs 2019, genotyping). Disorganization of healthcare provision due to the COVID-19 pandemic severely disrupted AATD diagnostics in Europe. In some countries the detrimental effect was temporary, while in others it continued in 2021.

SARS-CoV-2: Evaluation and Evolution

The emerging new COVID 2019 pandemic, which started in 2019 in China (Wuhan) and is caused by SARS-CoV-2, raises critical concerns due to high morbidity and mortality. As many patients are infected and the numbers still increase, this may suggest that there are different variants of the virus and some of them are more pathogenic. Besides, the virus is suspected to have various evolutionary pathways since SARS-CoV-2 belongs to the RNA viruses' family, which is characterized by a high mutation rate. Additionally, it is crucial to understand the life cycle of the virus to be able to urge antiviral studies. Genotyping studies about viruses are also important in order to understand the transmission and evolution of the virus. The genome of SARS-CoV-2 has a furin-like cleavage site in its S protein that may affect its pathogenicity. It was found that insertions and deletions in S protein have an impact on the transmission and fusion of the virus. The single nucleotide polymorphisms (SNP) genotypes are used to track the relationship of virus isolates. Se-quence alignment revealed the presence of hundreds of inter-host mutations during person-to-per-son transmission. Furthermore, genetic recombination provided a second mechanism for virus evo-lution. In this review, we highlight the life cycle of the virus and methods of virus evolution caused by mutations or recombination of viral genomes.Copyright © 2021 Bentham Science Publishers.

Molecular epidemiological analysis of COVID-19 imported cases in Ruili from July to November, 2021.

Objective To analyze the epidemiological and genomic characteristics of COVID-19 cases imported by land in Ruili, and to provide reference for border epidemic prevention and control in Yunnan Province. Methods We collected information about SARS-CoV-2 infected individuals from overseas land in Ruili, Yunnan from July to November, 2021. The epidemiological characteristics were statistically analyzed. The second-generation sequencing platform of Illumina was used to conduct high-through-put sequencing on the selected 40 positive samples and to analyze their genotyping and variation characteristics. Results During the study period,Ruili City reported 796 COVID-19 cases from abroad.The median age of COVID-19 cases was 28.5 years (Interquantile range 10, range 1-85). The gender ratio between men and women was 4.61 : 1, Most of these infected individuals engaged in business services, accounting for 49.75% (396/796) , 95.60% of COVID-19 cases were mild and moderate cases. The sequencing results of 34 cases can be divided into three clades according to Nextstrain typing method, including 24 cases belong to 21A(Delta) clade, 9 cases belong to 21I(Delta) clade and 1 case belongs to 20I (Alpha V1) clade. Conclusions The virus genotypes of the cases in this study were mainly divided into three branches and there were some differences among them, most of which were Delta mutants.We should continue to implement border control measures and continue to monitor the virus mutation of imported cases, so as to evaluate the threat of the mutant strain to the current situation of epidemic prevention and control in Yunnan Province.Copyright © 2023, Publication Centre of Anhui Medical University. All rights reserved.