Respiratory syncytial virus outbreak DURING THE COVID-19 PANDEMIC. How has it changed?

INTRODUCTION: The epidemiology of respiratory syncytial virus (RSV) infection has changed during the COVID-19 pandemic. Our objectives were to describe the RSV epidemic in 2021 and compare it with the previous years to the pandemic. METHODS: Retrospective study performed in Madrid (Spain) in a large paediatric hospital comparing the epidemiology and clinical data of RSV admissions during 2021 and the two previous seasons. RESULTS: 899 children were admitted for RSV infection during the study period. During 2021, the outbreak peaked in June and the last cases were identified in July. Previous seasons were detected in autumn-winter. The number of admissions in 2021 was significantly lower than in previous seasons. There were no differences between seasons regarding age, sex or disease severity. CONCLUSION: RSV hospitalizations during 2021 in Spain moved to summer with no cases in autumn and winter 2020-2021. Unlike other countries, clinical data were similar between epidemics.

Respiratory syncytial virus outbreak during the COVID-19 pandemic. How has it changed?

INTRODUCTION: The epidemiology of respiratory syncytial virus (RSV) infection has changed during the COVID-19 pandemic. Our objectives were to describe the RSV epidemic in 2021 and compare it with the previous years to the pandemic. METHODS: Retrospective study performed in Madrid (Spain) in a large pediatric hospital comparing the epidemiology and clinical data of RSV admissions during 2021 and the two previous seasons. RESULTS: 899 children were admitted for RSV infection during the study period. During 2021, the outbreak peaked in June and the last cases were identified in July. Previous seasons were detected in autumn-winter. The number of admissions in 2021 was significantly lower than in previous seasons. There were no differences between seasons regarding age, sex or disease severity. CONCLUSION: RSV hospitalizations during 2021 in Spain moved to summer with no cases in autumn and winter 2020-2021. Unlike other countries, clinical data were similar between epidemics.

First wave of the COVID-19 pandemic in Madrid: handling the unexpected in a tertiary hospital.

Introduction: The COVID-19 pandemic was declared on March 11th, 2020. By the end of January, the first imported cases were detected in Spain and, by March, the number of cases was growing exponentially, causing the implementation of a national lockdown. Madrid has been one of the most affected regions in terms of both cases and deaths. The aim of this study is to describe the epidemic curve and the epidemiological features and outcomes of COVID-19 patients hospitalized in La Paz University Hospital, a tertiary hospital located in Madrid. Methods: We included confirmed and probable COVID-19 cases admitted to our centre from February 26th to June 1st, 2020. We studied trends in hospitalization and ICU admissions using joinpoint regression analysis. Results: A sample of 2970 patients was obtained. Median age was 70 years old (IQR 55-82) and 54.8% of them were male. ICU admission rate was 8.7% with a mortality rate of 45.7%. Global CFR was 21.8%. Median time from symptom onset to death was 14 days (IQR 9-22). Conclusions: We detected an admissions peak on March 21st followed by a descending trend, matching national and regional data. Age and sex distribution were comparable to further series nationally and in western countries.

Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease.

BACKGROUND: SARS-CoV-2 infections have a wide spectrum of clinical manifestations whose causes are not completely understood. Some human conditions predispose to severe outcome, like old age or the presence of comorbidities, but many other facets, including coinfections with other viruses, remain poorly characterized. METHODS: In this study, the eukaryotic fraction of the respiratory virome of 120 COVID-19 patients was characterized through whole metagenomic sequencing. RESULTS: Genetic material from respiratory viruses was detected in 25% of all samples, whereas human viruses other than SARS-CoV-2 were found in 80% of them. Samples from hospitalized and deceased patients presented a higher prevalence of different viruses when compared to ambulatory individuals. Small circular DNA viruses from the Anneloviridae (Torque teno midi virus 8, TTV-like mini virus 19 and 26) and Cycloviridae families (Human associated cyclovirus 10), Human betaherpesvirus 6, were found to be significantly more abundant in samples from deceased and hospitalized patients compared to samples from ambulatory individuals. Similarly, Rotavirus A, Measles morbillivirus and Alphapapilomavirus 10 were significantly more prevalent in deceased patients compared to hospitalized and ambulatory individuals. CONCLUSIONS: Results show the suitability of using metagenomics to characterize a broader peripheric virological landscape of the eukaryotic virome in SARS-CoV-2 infected patients with distinct disease outcomes. Identified prevalent viruses in hospitalized and deceased patients may prove important for the targeted exploration of coinfections that may impact prognosis.

Psychological impact of the COVID-19 pandemic on primary care workers: a cross-sectional study.

BACKGROUND: The COVID-19 pandemic has had a major impact on the mental health of healthcare workers, yet studies in primary care workers are scarce. AIM: To investigate the prevalence of and associated factors for psychological distress in primary care workers during the first COVID-19 outbreak. DESIGN AND SETTING: This was a multicentre, cross-sectional, web-based survey conducted in primary healthcare workers in Spain, between May and September 2020. METHOD: Healthcare workers were invited to complete a survey to evaluate sociodemographic and work-related characteristics, COVID-19 infection status, exposure to patients with COVID-19, and resilience (using the Connor-Davidson Resilience Scale), in addition to being screened for common mental disorders (depression, anxiety disorders, post-traumatic stress disorder, panic attacks, and substance use disorder). Positive screening for any of these disorders was analysed globally using the term 'any current mental disorder'. RESULTS: A total of 2928 primary care professionals participated in the survey. Of them, 43.7% (95% confidence interval [CI] = 41.9 to 45.4) tested positive for a current mental disorder. Female sex (odds ratio [OR] 1.61, 95% CI = 1.25 to 2.06), having previous mental disorders (OR 2.58, 95% CI = 2.15 to 3.10), greater occupational exposure to patients with COVID-19 (OR 2.63, 95% CI = 1.98 to 3.51), having children or dependents (OR 1.35, 95% CI = 1.04 to 1.76 and OR 1.59, 95% CI = 1.20 to 2.11, respectively), or having an administrative job (OR 2.24, 95% CI = 1.66 to 3.03) were associated with a higher risk of any current mental disorder. Personal resilience was shown to be a protective factor. CONCLUSION: Almost half of primary care workers showed significant psychological distress. Strategies to support the mental health of primary care workers are necessary, including designing psychological support and resilience-building interventions based on risk factors identified.

Genomic Characterization of SARS-CoV-2 Isolated from Patients with Distinct Disease Outcomes in Mexico.

The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has shown a wide spectrum of clinical manifestations ranging from asymptomatic infections to severe disease and death. Pre-existing medical conditions and age have been mainly linked to the development of severe disease; however, the potential association of viral genetic characteristics with different clinical conditions remains unclear. SARS-CoV-2 variants with increased transmissibility were detected early in the pandemics, and several variants with potential relevance for public health are currently circulating around the world. In this study, we characterized 57 complete SARS-CoV-2 genomes during the exponential growth phase of the early epidemiological curve in Mexico, in April 2020. Patients were categorized under distinct disease severity outcomes: mild disease or ambulatory care, severe disease or hospitalized, and deceased. To reduce bias related to risk factors, the patients were less than 60 years old and with no diagnosed comorbidities A trait-association phylogenomic approach was used to explore genotype-phenotype associations, represented by the co-occurrence of mutations, disease severity outcome categories, and clusters of Mexican sequences. Phylogenetic results revealed a higher genomic diversity compared to the initial viruses detected during the early stage of the local epidemic. We identified a total of 90 single nucleotide variants compared to the Wuhan-Hu-1 genome, including 54 nonsynonymous mutations. We did not find evidence for the co-occurrence of mutations associated with specific disease outcomes. Therefore, in the group of patients studied, disease severity was likely mainly driven by the host genetic background and other demographic factors. IMPORTANCE The genetic association of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with different clinical conditions remains unclear and needs further investigation. In this study, we characterized 57 complete SARS-CoV-2 genomes from patients in Mexico with distinct disease severity outcomes: mild disease or ambulatory care, severe disease or hospitalized, and deceased. To reduce bias related to risk factors the patients were less than 60 years old and with no diagnosed comorbidities. We did not find evidence for the co-occurrence of mutations associated with specific disease outcomes. Therefore, in the group of patients studied, disease severity was likely mainly driven by the host genetic background and other demographic factors.

Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic.

During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most common circulating lineages during this period. We defined six different geographical regions with particular dynamics of lineage circulation. The Northeast and Northwest regions were the ones that exhibited the highest lineage diversity, while the Central south and South/Southeast regions presented less diversity with predominance of a certain lineage. Additionally, by late February 2021, lineage B.1.1.519 represented more than 89% of all circulating lineages in the country.

Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico.

SARS-CoV-2 variants emerged in late 2020, and at least three variants of concern (B.1.1.7, B.1.351, and P1) have been reported by WHO. These variants have several substitutions in the spike protein that affect receptor binding; they exhibit increased transmissibility and may be associated with reduced vaccine effectiveness. In the present work, we report the identification of a potential variant of interest, harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.1.1.519, that rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021.

Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico.

The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.IMPORTANCE Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the initial virus strains introduced in Mexico came from Europe and the United States and that the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region.

Full genome sequence of the first SARS-CoV-2 detected in Mexico.

SARS-CoV-2 was first detected in the city of Wuhan, Hubei Province, China. In this report, we describe the complete genome sequence of the first imported SARS-CoV-2, detected in a Mexican patient who had traveled to Bergamo, Italy. Phylogenetic analysis showed that this isolate belongs to subclade A2a (lineage G) and is closely related to isolates from Finland, Germany and Brazil, all of which were from patients with a history of travel to Italy. This is the first report of the complete genome sequence of this virus in Mexico.