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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.

ABSTRACT 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. IMPORTANCE 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.

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.

The genetic basis of severe COVID-19 has been thoroughly studied, and many genetic risk factors shared between populations have been identified. However, reduced sample sizes from non-European groups have limited the discovery of population-specific common risk loci. In this second study nested in the SCOURGE consortium, we conducted a genome-wide association study (GWAS) for COVID-19 hospitalization in admixed Americans, comprising a total of 4702 hospitalized cases recruited by SCOURGE and seven other participating studies in the COVID-19 Host Genetic Initiative. We identified four genome-wide significant associations, two of which constitute novel loci and were first discovered in Latin American populations (BAZ2B and DDIAS). A trans-ethnic meta-analysis revealed another novel cross-population risk locus in CREBBP. Finally, we assessed the performance of a cross-ancestry polygenic risk score in the SCOURGE admixed American cohort. This study constitutes the largest GWAS for COVID-19 hospitalization in admixed Latin Americans conducted to date. This allowed to reveal novel risk loci and emphasize the need of considering the diversity of populations in genomic research.

Abstract Rare variants affecting host defense against pathogens could be involved in COVID-19 severity and may help explain fatal outcomes in young and middle-aged patients. Our aim was to report the presence of rare genetic variants in certain genes, by using whole exome sequencing, in a selected group of COVID-19 patients under 65 years who required intubation or resulting in death (n = 44). To this end, different etiopathogenic mechanisms were explored using gene prioritization-based analysis in which genes involved in immune response, immunodeficiencies or blood coagulation were studied. We detected 44 different variants of interest, in 29 different patients (66%). Some of these variants were previously described as pathogenic and were located in genes mainly involved in immune response. A network analysis, including the 42 genes with candidate variants, showed three main components, consisting of 25 highly interconnected genes related to immune response and two additional networks composed by genes enriched in carbohydrate metabolism and in DNA metabolism and repair processes. In conclusion, we have detected candidate variants that may potentially influence COVID-19 outcome in our cohort of patients. Further studies are needed to confirm the ultimate role of the genetic variants described in the present study on COVID-19 severity.

Resumen: La pandemia de COVID-19 ha supuesto un desafío tanto clínico como jurídico y bioético. Se desarrollan estos tres pilares fundamentales en el abordaje de la priorización de recursos sanitarios en pandemia: criterios clínicos, marco legal correspondiente y principios éticos aplicables. Inicialmente se aplicaron criterios clínicos para identificar a los pacientes con mejor pronóstico de supervivencia, combinando una evaluación clínica y el uso de variables de pronóstico a corto y largo plazo. Sin embargo, la decisión de priorizar la atención de un paciente sobre otro tiene una carga jurídico-política, que presenta el riesgo de caer en la discriminación ya que están en juego derechos fundamentales. Los criterios de priorización deben basarse en principios que reflejen como filosofía vehicular la que hemos asumido constitucionalmente como Estado social y democrático de Derecho, que no responde al utilitarismo, sino al personalismo. Cualquier filosofía de distribución de recursos tiene que tener presente la perspectiva científica, constitucional y, con ellas, las de los derechos fundamentales y los principios bioéticos. En la priorización de los recursos deberían consolidarse principios éticos como el respeto a la dignidad de las personas, el principio de necesidad (igual necesidad, igual acceso al recurso), el principio de equidad (que aconseja priorizar a los grupos de población más vulnerables), la transparencia (fundamental en la confianza de la sociedad) y el principio de reciprocidad (que exige proteger a los sectores de la población que asumen más riesgos), entre otros. Abstract: The COVID-19 pandemic has been a clinical challenge, but also a legal and bioethical one. These three fundamental pillars are developed in the approach to prioritizing health resources in pandemic, clinical criteria, corresponding legal framework and applicable ethical principles. Initially, clinical criteria were applied to identify patients with the best survival prognosis, combining a clinical evaluation and the use of short-term and long-term prognostic variables. But the decision to prioritize the care of one patient over another has a legal–political burden, which poses a risk of falling into discrimination since fundamental rights are at stake. The prioritization criteria must be based on principles that reflect as a vehicle philosophy that which we have constitutionally assumed as a social and democratic State of Law, which did not respond to utilitarianism but to personalism. Any philosophy of resource distribution must bear in mind the scientific and constitutional perspective and, with them, those of fundamental rights and bioethical principles. In the prioritization of resources, ethical principles must be consolidated such as respect for the human dignity, the principle of necessity (equal need, equal access to the resource), the principle of equity (which advises prioritizing the most vulnerable population groups), transparency (fundamental in society's trust) and the principle of reciprocity (which requires protecting the sectors of the population that take more risks), among others.

Objectives: Each new wave of the COVID-19 pandemic invites the possible obligation to prioritize individuals' access to vital resources, and thereby leads to unresolved and important bioethical concerns. Governments have to make decisions to protect access to the health system with equity. The prioritization criteria during a pandemic are both a clinical and legal-administrative decision with ethical repercussion. We aim to analyse the prioritization protocols used in Spain during the pandemic which, in many cases, have not been updated.Method: We carried out a narrative review of 27 protocols of prioritization proposed by healthcare ethics committees, scientific societies and institutions in Spain for this study. The review evaluated shared aspects and unique differences and proffered a bioethical reflection.Results: The research questions explored patient prioritization, the criteria applied and the relative weight assigned to each criterion. There was a need to use several indicators, being morbidity and mortality scales the most commonly used, followed by facets pertaining to disease severity and functional status. Although age was initially considered in some protocols, it cannot be the sole criterion used when assigning care resources.Conclusions: In COVID-19 pandemic there is a need for a unified set of criteria that guarantees equity and transparency in decision-making processes. Establishing treatment indications is not the aim of such criteria, but instead prioritizing access to care resources. In protocols of prioritization, the principle of efficiency must vary according to the principle of equity and the criteria used to guarantee such equity.

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.