Impact of scaling up SARS-CoV-2 vaccination on COVID-19 hospitalizations in Spain

A national population-based study of mortality and risk factors in COVID-19-hospitalized patients in Spain (2020-2021)

Objectives

The study aimed to analyze in-hospital mortality (IHM) among all COVID-19 patients hospitalized in Spain between March 1, 2020, and December 31, 2021, and to compare two distinct periods: the prevaccination period (March 1, 2020, to January 31, 2021) and the vaccination period (February 1, 2021, to December 31, 2021). The objective was to assess the impact of vaccination on IHM and identify associated risk factors, using data from Spain's national hospitalization registry.

Methods

This retrospective analysis used data from the Spanish National Surveillance System for Hospital Data. The primary outcome was in-hospital mortality (IHM). Multivariate logistic regression identified risk factors across the overall study period, as well as during the prevaccination and vaccination periods. Risk factors included age (in 20-year intervals), sex, comorbidities (e.g., hypertension, diabetes, chronic kidney failure, obesity, neurodegenerative disorders, and others), and admission to the intensive care unit.

Results

A total of 524,314 COVID-19 hospitalizations were recorded in Spain, with 329,690 during the prevaccination period and 194,624 during the vaccination period. Hospitalization rates dropped from 697/100,000 people to 411/100,000, and in-hospital mortality (IHM) decreased from 16.2 to 11.5% (adjusted odds ratio [AOR]: 0.71, 95% CI: 0.70-0.73, p < 0.001). IHM rose with age, from 0.8% in patients aged 18-39 to 31.7% in those ≥80 years (p < 0.001), but significant decreases were observed across all age groups after vaccination, especially in those ≥80 years (AOR: 0.76, 95% CI: 0.75-0.79, p < 0.001). Risk factors for IHM remained consistent, with leukemia, neoplasm, and lymphoma posing the highest risks, while female sex (AOR: 0.75, 95% CI: 0.74-0.77, p < 0.001) and dyslipidemia (AOR: 0.85, 95% CI: 0.32-0.86, p < 0.001) were protective factors.

Conclusion

During the vaccination period, the risk of in-hospital mortality (IHM) was 29% lower than in the prevaccination period, after adjusting for sex, age, and comorbidities. This reduced risk was observed across sexes, age groups, and comorbidities. The risk factors for IHM remained consistent between the two periods, with age as the main risk factor, while female sex and dyslipidemia were identified as protective factors.

Modeling COVID-19 dynamics in the Basque Country: characterizing population immunity profile from 2020 to 2022

BACKGROUND

COVID-19, caused by SARS-CoV-2, has spread globally, presenting a significant public health challenge. Vaccination has played a critical role in reducing severe disease and deaths. However, the waning of immunity after vaccination and the emergence of immune-escape variants require the continuation of vaccination efforts, including booster doses, to maintain population immunity. This study models the dynamics of COVID-19 in the Basque Country, Spain, aiming to characterize the population's immunity profile and assess its impact on the severity of outbreaks from 2020 to 2022.

METHODS

A SIR/DS model was developed to analyze the interplay of virus-specific and vaccine-induced immunity. The model includes three levels of immunity, with boosting effects from reinfection and/or vaccination. It was validated using empirical daily case data from the Basque Country. The model tracks shifts in immunity status and their effects on disease dynamics over time.

RESULTS

The COVID-19 epidemic in the Basque Country progressed through three distinct phases, each shaped by dynamic interactions between virus transmission, public health interventions, and vaccination efforts. The initial phase was marked by a rapid surge in cases, followed by a decline due to strict public health measures, with a seroprevalence of 1.3 % . In the intermediate phase, multiple smaller outbreaks emerged as restrictions were relaxed and new variants, such as Alpha and Delta, appeared. During this period, reinfection rates reached 20 % , and seroprevalence increased to 32 % . The final phase, dominated by the Omicron variant, saw a significant rise in cases driven by waning immunity and the variant's high transmissibility. Notably, 34 % of infections during this phase occurred in the naive population, with seroprevalence peaking at 43 % . Across all phases, the infection of naive and unvaccinated individuals contributed significantly to the severity of outbreaks, emphasizing the critical role of vaccination in mitigating disease impact.

CONCLUSION

The findings underscore the importance of continuous monitoring and adaptive public health strategies to mitigate the evolving epidemiological and immunological landscape of COVID-19. Dynamic interactions between immunity levels, reinfections, and vaccinations are critical in shaping outbreak severity and guiding evidence-based interventions.

Impact and Effectiveness of COVID-19 Vaccines Based on Machine Learning Analysis of a Time Series: A Population-Based Study

Background: Although confirmed cases of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been declining since late 2020 due to general vaccination, little research has been performed regarding the impact of vaccines against SARS-CoV-2 in Spain in terms of hospitalizations and deaths. Objective: Our aim was to identify the reduction in severity and mortality of coronavirus disease 2019 (COVID-19) at a nationwide level due to vaccination. Methods: We designed a retrospective, population-based study to define waves of infection and to describe the characteristics of the hospitalized population. We also studied the rollout of vaccination and its relationship with the decline in hospitalizations and deaths. Finally, we developed two mathematical models to estimate non-vaccination scenarios using machine learning modeling (with the ElasticNet and RandomForest algorithms). The vaccination and non-vaccination scenarios were eventually compared to estimate the number of averted hospitalizations and deaths. Results: In total, 498,789 patients were included, with a global mortality of 14.3%. We identified six waves or epidemic outbreaks during the observed period. We established a strong relationship between the beginning of vaccination and the decline in both hospitalizations and deaths due to COVID-19 in all age groups. We also estimated that vaccination prevented 170,959 hospitalizations (CI 95% 77,844-264,075) and 24,546 deaths (CI 95% 2548-46,543) in Spain between March 2021 and December 2021. We estimated a global reduction of 9.19% in total deaths during the first year of COVID-19 vaccination. Conclusions: Demographic and clinical profiles changed over the first months of the pandemic. In Spain, patients over 80 years old and other age groups obtained clinical benefit from early vaccination. The severity of COVID-19, in terms of hospitalizations and deaths, decreased due to vaccination. Our use of machine learning models provided a detailed estimation of the averted burden of the pandemic, demonstrating the effectiveness of vaccination at a population-wide level.

The molecular epidemiology of SARS-CoV-2 in the Pityusic Islands shows multiple introductions and fast replacements of variants in a touristic worldwide hot spot

The public health emergency caused by the Covid-19 outbreak in March 2020 encouraged worldwide initiatives to monitor the genetic diversity and features of the SARS-CoV-2 circulating variants, mainly based on the genomic surveillance. However, due to the impossibility to carry out extensive sequencing in resource-limited hospitals, other PCR-based strategies could be applied to efficiently monitor the circulating variants without the need to greatly expand the sequencing capacity. In our case, overpassing the technical limitations inherent to a second level hospital, we were able to characterize the weekly distribution of SARS-CoV-2 by the RT-qPCR amplification patterns visualization, single nucleotide polymorphism genotyping, and sequencing of randomly selected samples. All these molecular approaches allowed us to trace the epidemiology of SARS-CoV-2 viruses circulating in Ibiza and Formentera (Balearic Islands, Spain) during the third to the sixth pandemic waves (January 2021-July 2022), in which three major lineages that were considered as VOCs (Alpha, Delta, and Omicron), and many other non-VOC variants were detected and tracked.

Impact of the COVID-19 pandemic on hospital admissions due to viral hepatitis in Spain

BACKGROUND

Before the advent of COVID-19 vaccines, hospitalizations due to SARS-CoV-2 infection during 2020 collapsed most medical centers worldwide. Disruptions in health care for clinical conditions other than COVID-19 were not uniform. Herein, we report the impact of COVID-19 on hospitalizations due to viral hepatitis in Spain.

METHODS

Retrospective study of all hospitalizations in Spain during 10 months before (pre-pandemic period) and after (pandemic period) March 1st 2020. Admissions with a diagnosis of hepatitis B, C and/or delta were retrieved and compared using the Spanish National Registry of Hospital Discharges.

RESULTS

Nationwide hospitalizations declined 14.6% during the pandemic period, from 3,144,164 to 2,684,845. This reduction was significantly more pronounced for admissions due to viral hepatitis (18.1% drop), falling from 46,521 to 38,115. During the pandemic period, patients admitted with viral hepatitis died significantly more frequently than during the pre-pandemic period (7.2% vs 6.1%; p < 0.001). Liver transplants significantly declined during the pandemic period. COVID-19 was diagnosed in 10.3% of patients hospitalized with viral hepatitis during the pandemic period. This subset of patients was older and died 2.4-fold more frequently than the rest, despite having advanced liver disease less frequently.

CONCLUSION

Hospitalizations due to viral hepatitis significantly declined in Spain during the COVID-19 pandemic. Patients admitted with viral hepatitis experienced a greater mortality during the pandemic period. Deaths were more pronounced when coinfected with SARS-CoV-2 despite having advanced liver disease less frequently.

COVID-19 in hospitalized solid organ transplant recipients in a nationwide registry study

OBJECTIVES

Underlying immunodeficiency has been associated with worse clinical presentation and increased mortality in patients with COVID-19. We evaluated the mortality of solid organ transplant (SOT) recipients (SOTR) hospitalized in Spain due to COVID-19.

METHODS

Nationwide, retrospective, observational analysis of all adults hospitalized because of COVID-19 in Spain during 2020. Stratification was made according to SOT status. The National Registry of Hospital Discharges was used, using the International Classification of Diseases, 10th revision coding list.

RESULTS

Of the 117,694 adults hospitalized during this period, 491 were SOTR: kidney 390 (79.4%), liver 59 (12%), lung 27 (5.5%), and heart 19 (3.9%). Overall, the mortality of SOTR was 13.8%. After adjustment for baseline characteristics, SOTR was not associated with higher mortality risk (odds ratio [OR] = 0.79, 95% confidence interval [CI] 0.60-1.03). However, lung transplantation was an independent factor related to mortality (OR = 3.26, 95% CI 1.33-7.43), while kidney, liver, and heart transplantation were not. Being a lung transplant recipient was the strongest prognostic factor in SOT patients (OR = 5.12, 95% CI 1.88-13.98).

CONCLUSION

This nationwide study supports that the COVID-19 mortality rate in SOTR in Spain during 2020 did not differ from the general population, except for lung transplant recipients, who presented worse outcomes. Efforts should be focused on the optimal management of lung transplant recipients with COVID-19.

Seven Epidemic Waves of COVID-19 in a Hospital in Madrid: Analysis of Severity and Associated Factors

(1) Background: COVID-19 has evolved during seven epidemic waves in Spain. Our objective was to describe changes in mortality and severity in our hospitalized patients. (2) Method: This study employed a descriptive, retrospective approach for COVID-19 patients admitted to the Hospital de Fuenlabrada (Madrid, Spain) until 31 December 2022. (3) Results: A total of 5510 admissions for COVID-19 were recorded. The first wave accounted for 1823 (33%) admissions and exhibited the highest proportion of severe patients: 65% with bilateral pneumonia and 83% with oxygen saturation under 94% during admission and elevated levels of CRP, IL-6, and D-dimer. In contrast, the seventh wave had the highest median age (79 years) and comorbidity (Charlson: 2.7), while only 3% of patients had bilateral pneumonia and 3% required intubation. The overall mortality rate was 10.3%. The first wave represented 39% of the total. The variables related to mortality were age (OR: 1.08, 1.07-1.09), cancer (OR: 1.99, 1.53-2.60), dementia (OR: 1.82, 1.20-2.75), the Charlson index (1.38, 1.31-1.47), the need for high-flow oxygen (OR: 6.10, 4.94-7.52), mechanical ventilation (OR: 11.554, 6.996-19.080), and CRP (OR: 1.04, 1.03-1.06). (4) Conclusions: The variables associated with mortality included age, comorbidity, respiratory failure, and inflammation. Differences in the baseline characteristics of admitted patients explained the differences in mortality in each wave. Differences observed between patients admitted in the latest wave and the earlier ones suggest that COVID-19 has evolved into a distinct disease, requiring a distinct approach.

Differences in Trends in Admissions and Outcomes among Patients from a Secondary Hospital in Madrid during the COVID-19 Pandemic: A Hospital-Based Epidemiological Analysis (2020-2022)

Spain had some of Europe's highest incidence and mortality rates for coronavirus disease 2019 (COVID-19). This study highlights the impact of the COVID-19 pandemic on daily health care in terms of incidence, critical patients, and mortality. We describe the characteristics and clinical outcomes of patients, comparing variables over the different waves. We performed a descriptive, retrospective study using the historical records of patients hospitalized with COVID-19. We describe demographic characteristics, admissions, and occupancy. Time series allowed us to visualize and analyze trends and patterns, and identify several waves during the 27-month period. A total of 3315 patients had been hospitalized with confirmed COVID-19. One-third of these patients were hospitalized during the first weeks of the pandemic. We observed that 4.6% of all hospitalizations had been admitted to the intensive care unit, and we identified a mortality rate of 9.4% among hospitalized patients. Arithmetic- and semi-logarithmic-scale charts showed how admissions and deaths rose sharply during the first weeks, increasing by 10 every few days. We described a single hospital's response and experiences during the pandemic. This research highlights certain demographic profiles in a population and emphasizes the importance of identifying waves when performing research on COVID-19. Our results can extend the analysis of the impact of COVID-19 and can be applied in other contexts, and can be considered when further analyzing the clinical, epidemiological, or demographic characteristics of populations with COVID-19. Our findings suggest that the pandemic should be analyzed not as a whole but rather in different waves.

Hospitalization burden and epidemiology of the COVID-19 pandemic in Spain (2020-2021)

BACKGROUND

Spain had some of Europe's highest incidence and mortality rates for coronavirus disease 2019 (COVID-19). Here we describe the epidemiology and trends in hospitalizations, the number of critical patients, and deaths in Spain in 2020 and 2021.

METHODS

We performed a descriptive, retrospective, nationwide study using an administrative database, the Minimum Basic Data Set at Hospitalization, which includes 95-97% of discharge reports for patients hospitalized in Spain in 2020 and 2021. We analyzed the number of hospitalizations, admissions to intensive care units, and deaths and their geographic distribution across regions of Spain.

RESULTS

As of December 31, 2021, a total of 498,789 patients (1.04% of the entire Spanish population) had needed hospitalization. At least six waves of illness were identified. Men were more prone to hospitalization than women. The median age was 66. A total of 54,340 patients (10.9% of all hospitalizations) had been admitted to the intensive care unit. We identified 71,437 deaths (mortality rate of 14.3% among hospitalized patients). We also observed important differences among regions, with Madrid being the epicenter of hospitalizations and mortality.

CONCLUSIONS

We analyzed Spain's response to COVID-19 and describe here its experiences during the pandemic in terms of hospitalizations, critical illness, and deaths. This research highlights changes over several months and waves and the importance of factors such as vaccination, the predominant variant of the virus, and public health interventions in the rise and fall of the outbreaks.

Increased incidence of giant cell arteritis and associated stroke during the COVID-19 pandemic in Spain: A nation-wide population study

INTRODUCTION

SARS-CoV-2 infection and COVID-19 vaccines might have increased the incidence of giant-cell arteritis (GCA) and the risk of associated stroke in Spain.

METHODS

Retrospective nation-wide observational analysis of all adults hospitalized with GCA in Spain during 5 years (Jan-2016 and Dec-2021. The incidence and proportion of admissions with or because of GCA and GCA-associated stroke were compared between pre-pandemic (2016-2019) and pandemic (2020 and 2021) years. Sensitivity analyses were conducted for the different COVID-19 waves and vaccine timing schedules.

RESULTS

A total of 17,268 hospital admissions in patients diagnosed with GCA were identified. During 2020 there were 79.3 and 8.1 per 100,000 admissions of GCA and GCA-associated stroke, respectively. During 2021 these figures were 80.8 and 7.7 per 100,00 admissions, respectively. As comparison, yearly admissions due to GCA and GCA-associated stroke were 72.4 and 5.7 per 100,00, respectively, during the pre-pandemic period (p < 0.05). Coincident with the third wave of COVID-19 (and first vaccine dosing), the rate of GCA-associated stroke admissions increased significantly (from 6.6 to 12%; p < 0.001). Likewise, there was an increase in GCA-associated stroke (6.6% vs 4.1%, p = 0.016) coincident with the third dose vaccination (booster) in patients older than 70 at the end of 2021. In multivariate analysis, only patients admitted during the third COVID-19 wave (and first vaccine dosing) (OR = 1.89, 95% CI 1.22-2.93), and during the third vaccination dosing in patients older than 70 (booster) (OR = 1.66, CI 1.11-2.49), presented a higher GCA-associated stroke risk than the same months of previous years after adjustment by age, sex, classical cardiovascular risk factors and COVID-19 diagnosis.

CONCLUSIONS

The COVID-19 pandemic led to an increased incidence of GCA during 2020 and 2021. Moreover, the risk of associated stroke significantly risen accompanying times of COVID-19 vaccine dosing, hypothetically linked to an increased thrombotic risk of mRNA-SARS-CoV-2 vaccines. Hence, forthcoming vaccine policies and indications must weigh the risk of severe COVID-19 with the risk of flare or stroke in patients with GCA.

Healthcare resource use and associated costs in a cohort of hospitalized COVID-19 patients in Spain: A retrospective analysis from the first to the third pandemic wave. EPICOV study

OBJECTIVES

Describe healthcare resource use and costs per hospitalized coronavirus disease-2019 (COVID-19) patient during the three main outbreak waves.

METHODS

A retrospective observational study. COVID-19 patient data were collected from a dataset from 17 hospitals in the HM Hospitals Group. Mean total costs per hospitalized patient and per day were estimated in each wave, as defined by the Spanish National Health System perspective. In addition, costs were estimated for both patients admitted and those not admitted to the intensive care unit (ICU) and were stratified by age groups.

RESULTS

A total of 3756 COVID-19 patients were included: 2279 (60.7%) for the first, 740 (19.7%) for the second, and 737 (19.6%) for the and third wave. Most (around 90%) did not require ICU treatment. For those patients, mean ± SD cost per patient ranged from €10 196.1 ± €7237.2 (mean length of stay [LOS] ± SD: 9.7 ± 6.2 days) for the second wave to €9364.5 ± €6321.1 for the third wave (mean 9.0 ± 5.7 days). Mean costs were around €1000 per day for all the waves. For patients admitted to the ICU, cost per patient ranged from €81 332.5 ± €63 725.8 (mean 31.0 ± 26.3 days) for the second wave to €36 952.1 ± €24 809.2 (mean 15.7 ± 8.2 days) for the third wave. Mean costs per day were around €3000 for all the waves. When estimated by age, mean LOS and costs were greater in patients over 80 when not admitted to the ICU and for patients aged 60 to 79 when admitted to the ICU.

CONCLUSIONS

LOS was longer for patients admitted to the ICU (especially in the first two waves) and for older patients in our study cohort; these populations incurred the highest hospitalization costs.

Psychometric Properties of the COVID-19 Pandemic Fatigue Scale: Cross-sectional Online Survey Study

Background

Pandemic fatigue is defined as feelings of demotivation to follow preventive measures against COVID-19, together with decreased trust in government and frequency of information-seeking behaviors.

Objective

This study aims to analyze the psychometric properties of the COVID-19–specific pandemic fatigue scale according to classical test theory (CTT) and Rasch model approaches in the general Spanish population.

Methods

This was a cross-sectional study in a representative sample of 1018 adults who completed an online survey in November 2020 in the framework of the COVID-19 Snapshot Monitoring (COSMO)-Spain project. The assessments included the 6-item COVID-19 Pandemic Fatigue Scale (CPFS) and other COVID-19–related variables: COVID-19 infection, adherence to preventive behaviors, information-seeking behavior, self-efficacy, worry, and cognitive and affective risk perception. Data quality, acceptability, reliability, and validity were analyzed according to CTT, and the fit to the Rasch model, unidimensionality, appropriateness of the response scale, item local independency, reliability (person-separation index [PSI]), and item-person distribution were also calculated.

Results

The mean CPFS score was 17.06 (SD 5.04, range 6-30), with higher scores for women, younger participants, participants who never seek information on COVID-19, those who think they would contract a mild disease in case of infection, those with higher level of worry about coronavirus/COVID-19, and those who felt depressed or felt the coronavirus/COVID-19 is spreading slowly (all P<.01). The Cronbach alpha for the CPFS was 0.74. In the confirmatory factor analysis, one factor was identified (root mean square error of approximation [RMSEA]=.02; comparative fit index [CFI]=.99; χ²₅=8.06, P=.15). The CPFS showed good fit to the Rasch model (χ ²₂₄=42.025, P=.01, PSI=.642), unidimensionality (binomial 95% CI –.005 to .045), and item local independency.

Conclusions

Our results suggest that the CPFS has moderate reliability and internal consistency and it is composed of a single dimension. It is a useful tool to ascertain the level of pandemic fatigue in the general population, which may help to guide the communication and information strategies to face the COVID-19 pandemic.

Systemic Autoimmune Diseases in Patients Hospitalized with COVID-19 in Spain: A Nation-Wide Registry Study

We aimed to evaluate the clinical outcome of Systemic Autoimmune Diseases (SADs) patients hospitalized with COVID-19 in Spain, before the introduction of SARS-CoV-2 vaccines. A nationwide, retrospective and observational analysis of the patients admitted during 2020, based on the ICD10 codes in the National Registry of Hospital Discharges, was performed. Among 117,694 patients, only 892 (0.8%) presented any type of SAD before COVID-19-related admission: Sjogren’s Syndrome constituted 25%, Systemic Vasculitides 21%, Systemic Lupus Erythematosus 19%, Sarcoidosis 17%, Systemic Sclerosis 11%, Mixed and Undifferentiated Connective Tissue Disease 4%, Behçet’s Disease 4% and Inflammatory Myopathies 2%. The in-hospital mortality rate was higher in SAD individuals (20% vs. 16%, p < 0.001). After adjustment by baseline conditions, SADs were not associated with a higher mortality risk (OR = 0.93, 95% CI 0.78−1.11). Mortality in the SADs patients was determined by age (OR = 1.05, 95% CI 1.04−1.07), heart failure (OR = 1.67, 95% CI 1.10−2.49), chronic kidney disease (OR = 1.29, 95% CI 1.05−1.59) and liver disease (OR = 1.97, 95% CI 1.13−3.44). In conclusion, the higher COVID-19 mortality rate seen in SADs patients hospitalized in Spain in 2020 was related to the higher burden of comorbidities, secondary to direct organ damage and sequelae of their condition. Whilst further studies should evaluate the impact of baseline immunosuppression on COVID-19 outcomes in this population, efforts should be focused on the optimal management of SAD to minimize the impact of the organ damage that has been shown to determine COVID-19 prognosis.

SARS-CoV-2 Omicron variant escapes neutralizing antibodies and T cell responses more efficiently than other variants in mild COVID-19 convalescents

Coronavirus disease 2019 (COVID-19) convalescents living in regions with low vaccination rates rely on post-infection immunity for protection against re-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We evaluate humoral and T cell immunity against five variants of concern (VOCs) in mild-COVID-19 convalescents at 12 months after infection with ancestral virus. In this cohort, ancestral, receptor-binding domain (RBD)-specific antibody and circulating memory B cell levels are conserved in most individuals, and yet serum neutralization against live B.1.1.529 (Omicron) is completely abrogated and significantly reduced for other VOCs. Likewise, ancestral SARS-CoV-2-specific memory T cell frequencies are maintained in >50% of convalescents, but the cytokine response in these cells to mutated spike epitopes corresponding to B.1.1.529 and B.1.351 (Beta) VOCs were impaired. These results indicate that increased antigen variability in VOCs impairs humoral and spike-specific T cell immunity post-infection, strongly suggesting that COVID-19 convalescents are vulnerable and at risk of re-infection with VOCs, thus stressing the importance of vaccination programs.

•

Most mild COVID-19 convalescents maintain immunity at 12 months after disease onset

•

B.1.1.529 escapes antibodies in convalescents infected with ancestral SARS-CoV-2

•

SARS-CoV-2 VOCs can partially avoid recognition by antigen-specific T cells

•

Antigenic drift in SARS-CoV-2 VOCs significantly challenges convalescent immunity

Evolution of SARS-CoV-2 in Spain during the First Two Years of the Pandemic: Circulating Variants, Amino Acid Conservation, and Genetic Variability in Structural, Non-Structural, and Accessory Proteins

Monitoring SARS-CoV-2’s genetic diversity and emerging mutations in this ongoing pandemic is crucial to understanding its evolution and ensuring the performance of COVID-19 diagnostic tests, vaccines, and therapies. Spain has been one of the main epicenters of COVID-19, reaching the highest number of cases and deaths per 100,000 population in Europe at the beginning of the pandemic. This study aims to investigate the epidemiology of SARS-CoV-2 in Spain and its 18 Autonomous Communities across the six epidemic waves established from February 2020 to January 2022. We report on the circulating SARS-CoV-2 variants in each epidemic wave and Spanish region and analyze the mutation frequency, amino acid (aa) conservation, and most frequent aa changes across each structural/non-structural/accessory viral protein among the Spanish sequences deposited in the GISAID database during the study period. The overall SARS-CoV-2 mutation frequency was 1.24 × 10−5. The aa conservation was >99% in the three types of protein, being non-structural the most conserved. Accessory proteins had more variable positions, while structural proteins presented more aa changes per sequence. Six main lineages spread successfully in Spain from 2020 to 2022. The presented data provide an insight into the SARS-CoV-2 circulation and genetic variability in Spain during the first two years of the pandemic.

Resilience of Spike-Specific Immunity Induced by COVID-19 Vaccines against SARS-CoV-2 Variants

The outbreak of SARS-CoV-2 leading to the declaration of the COVID-19 global pandemic has led to the urgent development and deployment of several COVID-19 vaccines. Many of these new vaccines, including those based on mRNA and adenoviruses, are aimed to generate neutralizing antibodies against the spike glycoprotein, which is known to bind to the receptor angiotensin converting enzyme 2 (ACE2) in host cells via the receptor-binding domain (RBD). Antibodies binding to this domain can block the interaction with the receptor and prevent viral entry into the cells. Additionally, these vaccines can also induce spike-specific T cells which could contribute to providing protection against the virus. However, the emergence of new SARS-CoV-2 variants can impair the immunity generated by COVID-19 vaccines if mutations occur in cognate epitopes, precluding immune recognition. Here, we evaluated the chance of five SARS-CoV-2 variants of concern (VOCs), Alpha, Beta, Gamma, Delta and Omicron, to escape spike-specific immunity induced by vaccines. To that end, we examined the impact of the SARS-CoV-2 variant mutations on residues located on experimentally verified spike-specific epitopes, deposited at the Immune Epitope Database, that are targeted by neutralizing antibodies or recognized by T cells. We found about 300 of such B cell epitopes, which were largely overlapping, and could be grouped into 54 B cell epitope clusters sharing ≥ 7 residues. Most of the B cell epitope clusters map in the RBD domain (39 out of 54) and 20%, 50%, 37%, 44% and 57% of the total are mutated in SARS-CoV-2 Alpha, Beta, Gamma, Delta and Omicron variants, respectively. We also found 234 experimentally verified CD8 and CD4 T cell epitopes that were distributed evenly throughout the spike protein. Interestingly, in each SARS-CoV-2 VOC, over 87% and 79% of CD8 and CD4 T cell epitopes, respectively, are not mutated. These observations suggest that SARS-CoV-2 VOCs—particularly the Omicron variant—may be prone to escape spike-specific antibody immunity, but not cellular immunity, elicited by COVID-19 vaccines.

How to Deal With Vaccine Breakthrough Infection With SARS-CoV-2 Variants

Novel Coronary Pneumonia is the most infectious disease with the highest number of morbidity and mortality in 100 years. Despite aggressive and effective COVID-19 prevention and control measures, countries have been unable to stop its outbreaks. With the widespread use of vaccines, the occurrence of COVID-19 has declined markedly. April 21, 2021, New York scholars reported Vaccine Breakthrough Infections with SARS-CoV-2 Variants, which immediately attracted widespread attention. In this mini-review, we focus on the characteristics of SARS-CoV-2 and its mutant strains and vaccine breakthrough infections. We have found that outbreaks of vaccine-breaking SARS-CoV-2 Delta infections in many countries are primarily the result of declining vaccine-generated antibody titers and relaxed outbreak management measures. For this reason, we believe that the main response to vaccine-breaking infections with the SARS-CoV-2 variant is to implement a rigorous outbreak defense policy and vaccine application. Only by intensifying the current vaccination intensity, gradually improving the vaccine and its application methods, and strengthening non-pharmaceutical measures such as travel restrictions, social distancing, masking and hand hygiene, can the COVID-19 outbreak be fully controlled at an early date.

Oral antivirals for the prevention and treatment of SARS-CoV-2 infection

Vaccines and antivirals are the classical weapons deployed to contain, prevent, and treat life-threatening viral illnesses. Specifically, for SARS-CoV-2 infection, vaccines protect against severe COVID-19 disease manifestations and complications. However, waning immunity and emergence of vaccine escape mutants remains a growing threat. This is highlighted by the current surge of the omicron COVID-19 variant. Thus, there is a race to find treatment alternatives. We contend that oral small molecule antivirals that halt SARSCoV- 2 infection are essential. Compared to currently available monoclonal antibodies and remdesivir, where parenteral administration is required, oral antivirals offer treatments in an outpatient setting with dissemination available on a larger scale. In response to this need at 2021's end, regulatory agencies provided emergency use authorization for both molnupiravir and nirmatrelvir. These medicines act on the viral polymerase and protease, respectively. Each is given for 5 days and can reduce disease progression by 30% and 89%, respectively. The advent of additional oral antivirals, the assessment of combination therapies, the formulation of extended-release medications, and their benefit for both early treatment and prophylaxis will likely transform the landscape of the COVID-19 pandemic.

Mortality by Covid-19 Prior to Vaccination - One Year Experience of Hospitalized Patients in Madrid

Objectives

The aim of the study was to analyze the mortality and characteristics of deceased patients with COVID-19 during the first year of the pandemic.

Methods

All admissions owing to COVID-19 at a tertiary hospital in Madrid were analyzed. Three waves were considered: March 2020 to June 2020, July 2020 to November 2020, and December 2020 to April 2021.

Results

A total of 3,676 patients were identified. Among inpatients, no differences regarding age, sex, length of admission, or mortality were found between the 3 waves (p >0.05). The overall mortality rate was 12.9%. Among deceased patients, the median age was 82 years and the median Charlson Comorbidity Index was 6. Considering the main predictors for mortality by COVID-19 (age, sex, and concomitant comorbidities), only patients with previous lung disease were more prevalent in the third period (p <0.01). Finally, higher intensive care unit admission rates, a lower rate of patients coming from nursing homes, and a lower rate of patients with dementia were noted in the third period (p <0.05) among deceased patients.

Conclusion

One year after the onset of the pandemic, the mortality rate of hospitalized patients and the profile of non-survivors have not changed significantly. In the absence of vaccine benefits, advanced age and multiple pathologies are uniform characteristics of non-survivors.