Replication of SARS-CoV-2 in the human population is defined by distributions of mutants that are present at different frequencies within the infected host and can be detected by ultra-deep ...sequencing techniques. In this study, we examined the SARS-CoV-2 mutant spectra of amplicons from the spike-coding (S-coding) region of 5 nasopharyngeal isolates derived from patients with vaccine breakthrough. Interestingly, all patients became infected with the Alpha variant, but amino acid substitutions that correspond to the Delta Plus, Iota, and Omicron variants were present in the mutant spectra of the resident virus. Deep sequencing analysis of SARS-CoV-2 from patients with vaccine breakthrough revealed a rich reservoir of mutant types and may also identify tolerated substitutions that can be represented in epidemiologically dominant variants.
Background
The capacity of profilin to induce allergic symptoms in patients with respiratory allergy has been questioned. In this sense, the aim of this study was to investigate the correlation ...between profilin exposure and induction of symptoms in a prospective case‐control study.
Methods
The concentration of profilin as well as pollen levels in the air was measured. A diary score of symptoms was collected from allergic patients. Seventy‐nine individuals were included in the study; fifty cases and 28 controls were positive or negative to profilin, respectively. Conjunctival and bronchial provocation tests were performed with purified profilin (Pho d 2) in a subgroup of cases and controls.
Results
Profilin was detected in the environment on 133 days (maximum peak of 0.56 ng/m3). A positive correlation between profilin and pollen count of Olea and Poaceae was observed (ρ = 0.24; P < .001). Intensity of total, nasal and ocular symptoms was statistically higher in cases than in controls (P < .001). The risk of suffering symptoms, measured by the percentage of patients who presented any of the symptoms each day, was also higher in cases than in controls. The provocation test was positive in 95% of bronchial and 90% of conjunctival challenges in cases, and negative in all controls.
Conclusions
Profilin was detected in the environment and had the ability to induce a specific allergen response. Patients sensitized to this panallergen showed more symptoms and were more likely to have symptoms. Therefore, sensitization to profilin seems to be a marker of severity in patients with rhinoconjunctivitis and asthma mediated by pollen.
Profilin is detected in the environment and has the capacity to induce a specific allergen response as evidenced by bronchial and conjunctival challenges. Patients sensitized to profilin showed more and severe allergic symptoms and had more probability to develop allergic symptoms than the allergic control population negative to profilin. Sensitization to profilin seems to be a marker of severity in pollen allergic patients with rhinoconjunctivitis and asthma.
Populations of RNA viruses are composed of complex and dynamic mixtures of variant genomes that are termed mutant spectra or mutant clouds. This applies also to SARS-CoV-2, and mutations that are ...detected at low frequency in an infected individual can be dominant (represented in the consensus sequence) in subsequent variants of interest or variants of concern. Here we briefly review the main conclusions of our work on mutant spectrum characterization of hepatitis C virus (HCV) and SARS-CoV-2 at the nucleotide and amino acid levels and address the following two new questions derived from previous results: (i) how is the SARS-CoV-2 mutant and deletion spectrum composition in diagnostic samples, when examined at progressively lower cut-off mutant frequency values in ultra-deep sequencing; (ii) how the frequency distribution of minority amino acid substitutions in SARS-CoV-2 compares with that of HCV sampled also from infected patients. The main conclusions are the following: (i) the number of different mutations found at low frequency in SARS-CoV-2 mutant spectra increases dramatically (50- to 100-fold) as the cut-off frequency for mutation detection is lowered from 0.5% to 0.1%, and (ii) that, contrary to HCV, SARS-CoV-2 mutant spectra exhibit a deficit of intermediate frequency amino acid substitutions. The possible origin and implications of mutant spectrum differences among RNA viruses are discussed.
Mutant spectra of RNA viruses are important to understand viral pathogenesis and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses ...sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultradeep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of 30 nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low-frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype, and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three-dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19.
The study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low-frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.
Background
Ample evidence indicates a sex‐related difference in severity of COVID‐19, with less favorable outcomes observed in men. Genetic factors have been proposed as candidates to explain this ...difference. The polyglutamine (polyQ) polymorphism in the androgen receptor gene has been recently described as a genetic biomarker of COVID‐19 severity.
Objective
To test the association between the androgen receptor polyQ polymorphism and COVID‐19 severity in a large cohort of COVID‐19 male patients.
Materials and methods
This study included 1136 male patients infected with SARS‐CoV‐2 as confirmed by positive PCR. Patients were retrospectively and prospectively enrolled from March to November 2020. Patients were classified according to their severity into three categories: oligosymptomatic, hospitalized and severe patients requiring ventilatory support. The number of CAG repeats (polyQ polymorphism) at the androgen receptor was obtained by PCR and patients were classified as either short (<23 repeats) or long (≥23 repeats) allele carriers. The association between polyQ alleles (short or long) and COVID‐19 severity was assessed by Chi‐squared (Chi2) and logistic regression analysis.
Results
The mean number of polyQ CAG repeats was 22 (±3). Patients were classified as oligosymptomatic (15.5%), hospitalized (63.2%), and severe patients (21.3%) requiring substantial respiratory support. PolyQ alleles distribution did not show significant differences between severity classes in our cohort (Chi2 test p > 0.05). Similar results were observed after adjusting by known risk factors such as age, comorbidities, and ethnicity (multivariate logistic regression analysis).
Discussion
Androgen sensitivity may be a critical factor in COVID‐19 disease severity. However, we did not find an association between the polyQ polymorphism and the COVID‐19 severity. Additional studies are needed to clarify the mechanism underlying the association between androgens and COVID‐19 outcome.
Conclusions
The results obtained in our study do not support the role of this polymorphism as biomarker of COVID‐19 severity.
Use of Inhalation Devices in Pediatric Population Seoane-Rodriguez, Marta, MD; Ruiz-Hornillos, Javier, MD; Blanco-Bermejo, Sandra, MD ...
Journal of allergy and clinical immunology,
02/2017, Volume:
139, Issue:
2
Journal Article
Peer reviewed
Open access
Rationale The aim was: to determine the number of children that use the optimal inhalation device according to their age, and how many of them perform a correct technique; to determine the efficacy ...of our training strategy for improving inhaler technique.
Background
Sensitization to Finales (Cupressaceae and Pinaceae) has increased dramatically in recent years. The prevalence of sensitization in different geographic areas is related to exposure to ...specific pollens.
Objectives
To investigate the prevalence of allergy to different conifer pollens, describe the characteristics of patients with such allergy, and identify the involved allergens.
Methods
Patients were recruited at five hospitals near Madrid. Extracts from conifer pollen were prepared and used in skin-prick testing. Wheal sizes were recorded, and serum samples obtained from patients with positive reactions to Cupressus arizonica and/or Pinus pinea. The specific immunoglobulin E value to C. arizonica and Cup a 1 was determined. Individual immunoblots for each patient and with a pool of sera were performed. Allergenic proteins were sequenced by using liquid chromatography-tandem mass spectrometry.
Results
Of 499 individuals included in the study, 17 (14%) had positive skin-prick test results to some conifer pollen extracts. Sixty-four patients had positive results to C. arizonica (prevalence 12.8%) and 11 had positive results to P. pinea (2.2%). All the patients had respiratory symptoms (61.4% during the C. arizonica pollination period), and 62.9% had asthma. Approximately 86% of the patients had positive specific immunoglobulin E results to C. arizonica and 923% had positive results to Cup a 1. Fourteen different bands were recognized by immunoblot; the most frequent bands were those detected at 43, 18, 16, and 14 kDa. All sequenced proteins corresponded to Cup a 1.
Conclusion
Allergy to conifer pollen could be considered a relevant cause of respiratory allergy in central Spain. Asthma was more frequent than in other studies. We only identified Cup a 1 as involved in sensitization.
PDF
