Unraveling the Effects of the COVID-19 Pandemic on the Burden of Respiratory Syncytial Virus in a Tertiary Hospital in Catalonia, Spain: Season 2022-2023 Analysis (preprint)

Purpose: Respiratory Syncytial Virus (RSV) associated infections have historically been the cause of seasonal paediatric hospital departments’ saturation. During the COVID-19 pandemic, the community incidence of RSV was reduced, thus the hospital burden. The last RSV season broke out in early October 2022, 4-6 weeks earlier than in pre-pandemic years, and was thought to be the most demanding to date. Our aim was to assess the burden of RSV-related hospitalizations on a referral hospital (Catalonia, Spain) during the pre-pandemic years and the most recent 2022-2023 season. Methods: We analysed the paediatric hospital and intensive care (PICU) admissions data (January 2016 – January 2023) of a tertiary referral hospital in Catalonia, Spain. All-cause pediatric admissions, admissions related to confirmed RSV infections, and occupancy-related variables were collected. Results and conclusion: RSV-related hospitalizations incidence was lower during the pandemic years, particularly in 2020. The majority of RSV cases within an epidemic peak primarily affected children ≤3 months. Although the number of daily admissions during the last RSV 2022-2023 season was not higher than in the pre-pandemic years, the mean occupancy of the hospital was significantly higher (p= 0.04) due to a longer period of days with more than 20 RSV infected children inpatients per day.

The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants (preprint)

The SARS-CoV-2 Omicron variant emerged showing higher transmissibility and possibly higher resistance to current COVID-19 vaccines than other variants dominating the global pandemic. In a March 2020 study performed in clinical samples, we found that a portion of genomes in the SARS-CoV-2 viral population accumulated deletions at the S1/S2 cleavage site (PRRAR/S) of the spike gene, generating a frameshift and appearance of a premature stop codon. The main aim of this study was to determine the frequency of defective deletions in prevalent variants from the first to sixth pandemic waves in our setting and discuss whether the differences observed might support epidemiological proposals.The complete SARS-CoV-2 spike gene was deeply studied by next-generation sequencing using the MiSeq platform. More than 90 million reads were obtained from respiratory swab specimens of 78 COVID-19 patients with mild infection caused by the predominant variants circulating in the Barcelona city area during the six pandemic waves: B.1.5, B.1.1, B.1.177, Alpha, Beta, Delta, and Omicron.The frequency of defective genomes found in variants dominating the first and second waves was similar to that seen in Omicron, but differed from the frequencies seen in the Alpha, Beta and Delta variants.Our results support the notion cited in epidemiological reports that Omicron did not emerge from continuous evolution of the Alpha, Beta or Delta variant.

Epidemiological dynamics of the incidence of COVID-19 in children and the relationship with the opening of schools in Catalonia (Spain) (preprint)

Here we analyse the epidemiological trend of the incidence of COVID-19 in children in Catalonia (Spain) during the first 20 weeks of the 2020-2021 school year. This study demonstrates that while schools were open the incidence rate among children remained significantly lower than in general population, despite a greater diagnostic effort in children. These results suggest that schools have not played a significant role in the SARS-CoV-2 dissemination in Catalonia.

Peripheral and lung resident T cell responses against SARS-CoV-2 (preprint)

Considering that SARS-CoV-2 interacts with the host at the respiratory tract mucosal interface, T cells strategically placed within these surfaces, namely resident memory T cells, will be essential to limit viral spread and disease. Importantly, these cells are mostly non-recirculating, which reduces the window of opportunity to examine circulating lymphocytes in blood as they home to the lung parenchyma. Here, we demonstrate that viral specific T cells can migrate and establish in the lung as resident memory T cells remaining detectable up to 10 months after initial infection. Moreover, focusing on the acute phase of the infection, we identified virus-specific T cell responses in blood with functional, migratory and apoptotic patterns modulated by viral proteins and associated with clinical outcome. Our study highlights IL-10 secretion by virus-specific T cells associated to a better outcome and the persistence of resident memory T cells as key players for future protection against SARS-CoV-2 infection.

Functional profile, homing and residency of protective T cell immune responses against SARS-CoV-2 (preprint)

Considering that SARS-CoV-2 interacts with the host at the respiratory tract mucosal interface, T cells strategically placed within these surfaces, namely resident memory T cells, will be essential to limit viral spread and disease. Importantly, these cells are mostly non-recirculating, which reduces the window of opportunity to examine circulating lymphocytes in blood as they home to the lung parenchyma. Here, we demonstrate that viral specific T cells can migrate and establish in the lung as resident memory T cells, being detectable beyond 7 months in convalescent COVID-19 patients. Moreover, focusing on the acute phase of the infection, we identified virus-specific T cell responses in blood with functional, migratory and apoptotic patterns modulated by viral proteins and associated with clinical outcome. Our study highlights IL-10 secretion by virus-specific T cells associated to a better outcome and the persistence of resident memory T cells as key players for future protection against SARS-CoV-2 infection.

Nasopharyngeal microbial communities of patients infected with SARS-COV-2 that developed COVID-19. (preprint)

BackgroundSARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however studies focused on the patients microbiota are still lacking. In this study, we investigated the nasopharyngeal microbiome composition of patients who developed different severity levels of COVID-19. We performed Rdna-SSU (16S) sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization) and severe (admission to ICU). We compared the microbiome diversity and OTU composition among severity groups using Similarity Percentage (SIMPER) analysis and Maaslin2. We also built bacterial co-abundance networks for each group using Fastpar. ResultsStatistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidetes (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthemore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms. ConclusionsOur preliminary study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. These microbes with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results. IMPORTANCEThis work has studied the microbiota of the nasopharyngeal tract in COVID19 patients using advanced techniques of molecular microbiology. Diverse microorganisms, most of which are harmless or even beneficial to the host, colonize the nasopharyngeal tract. These microorganisms are the microbiota, and they are present in every people. However, changes in this microbiota could be related to different diseases as cancer, gastrointestinal pathologies or even COVID19. This study has been performed to investigate the microbiota from patients with COVID19, in order to determinate its implication in the pathology severity. The results obtained showed that it is possible that several specific microorganisms are present only in patients with severe COVID19. These data, could be used as a prognostic biomarker to early detect whose patients will develop a severe COVID19 and improve their clinical management.

A complete analysis of the epidemiological scenario around a SARS-CoV-2 reinfection: previous infection events and subsequent transmission (preprint)

The first descriptions of reinfection by SARS-CoV-2 have been recently reported. However, these studies focus exclusively on the reinfected case, without considering the epidemiological context of the event. We present the first complete analysis of the epidemiological scenario around a reinfection by SARS-CoV-2, including three cases preceding the reinfection, the reinfected case per se, and the subsequent transmission to another seven cases. Our analysis is supported by host genetics, viral whole genome sequencing, phylogenomic population analysis, and refined epidemiological data obtained from in-depth interviews with the involved subjects. The reinfection involved a 53-year-old woman with asthma, with a first COVID-19 episode in April 2020 and a much more severe second episode four months and a half later, with COVID-19 seroconversion in August, and requiring hospital admission.