Comparison of the Risk of Hospitalization and Severe Disease Among Co-circulating Severe Acute Respiratory Syndrome Coronavirus 2 Variants.

BACKGROUND: We compare the risk of coronavirus disease 2019 (COVID-19) outcomes among co-circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants between January 2021 and May 2022 in Navarra, Spain. METHODS: We compared the frequency of hospitalization and severe disease (intensive care unit admission or death) due to COVID-19 among the co-circulating variants. Variants analyzed were nonvariants of concern (non-VOCs), Alpha, Delta, Omicron BA.1, and Omicron BA.2. Logistic regression models were used to estimate adjusted odds ratio (aOR). RESULTS: The Alpha variant had a higher risk of hospitalization (aOR, 1.86 [95 confidence interval {CI}, 1.282.71]) and severe disease (aOR, 2.40 [95 CI, 1.314.40]) than non-VOCs. The Delta variant did not show a significantly different risk of hospitalization (aOR, 0.73 [95 CI, .401.30]) and severe disease (aOR, 3.04 [95 CI, .5716.22]) compared to the Alpha variant. The Omicron BA.1 significantly reduced both risks relative to the Delta variant (aORs, 0.28 [95 CI, .16.47] and 0.23 [95 CI, .12.46], respectively). The Omicron BA.2 reduced the risk of hospitalization compared to BA.1 (aOR, 0.52 [95 CI, .29.95]). CONCLUSIONS: The Alpha and Delta variants showed an increased risk of hospitalization and severe disease, which decreased considerably with the Omicron BA.1 and BA.2. Surveillance of variants can lead to important differences in severity.

Risk reduction of hospitalisation and severe disease in vaccinated COVID-19 cases during the SARS-CoV-2 variant Omicron BA.1-predominant period, Navarre, Spain, January to March 2022.

BackgroundAs COVID-19 vaccine effectiveness against SARS-CoV-2 infection was lower for cases of the Omicron vs the Delta variant, understanding the effect of vaccination in reducing risk of hospitalisation and severe disease among COVID-19 cases is crucial.AimTo evaluate risk reduction of hospitalisation and severe disease in vaccinated COVID-19 cases during the Omicron BA.1-predominant period in Navarre, Spain.MethodsA case-to-case comparison included COVID-19 epidemiological surveillance data in adults ≥ 18 years from 3 January-20 March 2022. COVID-19 vaccination status was compared between hospitalised and non-hospitalised cases, and between severe (intensive care unit admission or death) and non-severe cases using logistic regression models.ResultsAmong 58,952 COVID-19 cases, 565 (1.0%) were hospitalised and 156 (0.3%) were severe. The risk of hospitalisation was reduced within the first 6 months after full COVID-19 vaccination (complete primary series) (adjusted odds ratio (aOR): 0.06; 95% CI: 0.04-0.09) and after 6 months (aOR: 0.16; 95% CI: 0.12-0.21; pcomparison < 0.001), as well as after a booster dose (aOR: 0.06: 95% CI: 0.04-0.07). Similarly, the risk of severe disease was reduced (aOR: 0.13, 0.18, and 0.06, respectively). Compared with cases fully vaccinated 6 months or more before a positive test, those who had received a booster dose had lower risk of hospitalisation (aOR: 0.38; 95% CI: 0.28-0.52) and severe disease (aOR: 0.38; 95% CI: 0.21-0.68).ConclusionsFull COVID-19 vaccination greatly reduced the risk of hospitalisation and severe outcomes in COVID-19 cases with the Omicron variant, and a booster dose improved this effect in people aged over 65 years.

Enhancing SARS-CoV-2 Surveillance through Regular Genomic Sequencing in Spain: The RELECOV Network.

Millions of SARS-CoV-2 whole genome sequences have been generated to date. However, good quality data and adequate surveillance systems are required to contribute to meaningful surveillance in public health. In this context, the network of Spanish laboratories for coronavirus (RELECOV) was created with the main goal of promoting actions to speed up the detection, analyses, and evaluation of SARS-CoV-2 at a national level, partially structured and financed by an ECDC-HERA-Incubator action (ECDC/GRANT/2021/024). A SARS-CoV-2 sequencing quality control assessment (QCA) was developed to evaluate the network's technical capacity. QCA full panel results showed a lower hit rate for lineage assignment compared to that obtained for variants. Genomic data comprising 48,578 viral genomes were studied and evaluated to monitor SARS-CoV-2. The developed network actions showed a 36% increase in sharing viral sequences. In addition, analysis of lineage/sublineage-defining mutations to track the virus showed characteristic mutation profiles for the Delta and Omicron variants. Further, phylogenetic analyses strongly correlated with different variant clusters, obtaining a robust reference tree. The RELECOV network has made it possible to improve and enhance the genomic surveillance of SARS-CoV-2 in Spain. It has provided and evaluated genomic tools for viral genome monitoring and characterization that make it possible to increase knowledge efficiently and quickly, promoting the genomic surveillance of SARS-CoV-2 in Spain.

Effectiveness of influenza vaccination in preventing influenza in primary care, Navarre, Spain, 2021/22.

Compared with individuals unvaccinated in the current and three previous influenza seasons, in 2021/22, influenza vaccine effectiveness at primary care level was 37% (95% CI: 16 to 52) for current season vaccination, regardless of previous doses, and 35% (95% CI: -3 to 45) for only previous seasons vaccination. Against influenza A(H3N2), estimates were 39% (95% CI: 16 to 55) and 24% (95% CI: -8 to 47) suggesting moderate effectiveness of current season vaccination and possible remaining effect of prior vaccinations.

Seroprevalence of antibodies against SARS-CoV-2 and risk of COVID-19 in Navarre, Spain, May to July 2022.

In Navarre, Spain, in May 2022, the seroprevalence of anti-nucleocapsid (N) and anti-spike (S) antibodies of SARS-CoV-2 was 58.9% and 92.7%, respectively. The incidence of confirmed COVID-19 thereafter through July was lower in people with anti-N antibodies (adjusted odds ratio (aOR) = 0.08; 95% confidence interval (CI): 0.05-0.13) but not with anti-S antibodies (aOR = 1.06; 95% CI: 0.47-2.38). Hybrid immunity, including anti-N antibodies induced by natural exposure to SARS-CoV-2, seems essential in preventing Omicron COVID-19 cases.

Effect of Influenza Vaccination in Preventing Laboratory-Confirmed Influenza Hospitalization in Patients With Diabetes Mellitus.

BACKGROUND: People with diabetes are at high risk of severe influenza complications. The influenza vaccination effect among diabetic patients remains inconclusive. We estimated the average effect of influenza vaccination status in the current and prior seasons in preventing laboratory-confirmed influenza hospitalization in diabetic patients. METHODS: Patients attended in hospitals and primary healthcare centers with influenza-like illness were tested for influenza from the 2013-2014 to 2018-2019 seasons in Navarre, Spain. A test-negative case-control design in diabetic inpatients compared the influenza vaccination status in the current and 5 prior seasons between laboratory-confirmed influenza cases and negative controls. Vaccination status of influenza-confirmed cases was compared between diabetic inpatients and outpatients. Influenza vaccination effect was compared between diabetic patients and older (≥ 60 years) or chronic nondiabetic patients. RESULTS: Of 1670 diabetic inpatients tested, 569 (34%) were confirmed for influenza and 1101 were test-negative controls. The average effect in preventing influenza hospitalization was 46% (95% confidence interval [CI], 28%-59%) for current-season vaccination and 44% (95% CI, 20%-61%) for vaccination in prior seasons only in comparison to unvaccinated patients in the current and prior seasons. Among diabetic patients with confirmed influenza, current-season vaccination reduced the probability of hospitalization (adjusted odds ratio, 0.35; 95% CI, .15-.79). In diabetic patients, vaccination effect against influenza hospitalizations was not inferior to that in older or chronic nondiabetic patients. CONCLUSIONS: On average, influenza vaccination of diabetic population reduced by around half the risk of influenza hospitalization. Vaccination in prior seasons maintained a notable protective effect. These results reinforce the recommendation of influenza vaccination for diabetic patients.

Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021.

With the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the acquisition of novel mutations in existing lineages, the need to implement methods capable of monitoring viral dynamics arises. We report the emergence and spread of a new SARS-CoV-2 variant within the B.1.575 lineage, containing the E484K mutation in the spike protein (named B.1.575.2), in a region in northern Spain in May and June 2021. SARS-CoV-2-positive samples with cycle threshold values of ≤30 were selected to screen for presumptive variants using the TaqPath coronavirus disease 2019 (COVID-19) reverse transcription (RT)-PCR kit and the TaqMan SARS-CoV-2 mutation panel. Confirmation of variants was performed by whole-genome sequencing. Of the 200 samples belonging to the B.1.575 lineage, 194 (97%) corresponded to the B.1.575.2 sublineage, which was related to the presence of the E484K mutation. Of 197 cases registered in the Global Initiative on Sharing Avian Influenza Data (GISAID) EpiCoV database as lineage B.1.575.2, 194 (99.5%) were identified in Pamplona, Spain. This report emphasizes the importance of complementing surveillance of SARS-CoV-2 with sequencing for the rapid control of emerging viral variants.

Effect of influenza vaccination in patients with asthma.

BACKGROUND: Although annual influenza vaccination is recommended for persons with asthma, its effectiveness in this patient population is not well described. We evaluated the effect of influenza vaccination in the current and previous seasons in preventing influenza among people with asthma. METHODS: Using population health data from the Navarre region of Spain for the 2015/16 to 2019/20 influenza seasons, we conducted a test-negative case-control study to assess the effect of influenza vaccination in the current and 5 previous seasons. From patients presenting to hospitals and primary health care centres with influenza-like illness who underwent testing for influenza, we estimated the effects of influenza vaccination among patients with asthma overall and between those presenting as inpatients or outpatients, as well as between patients with and without asthma. RESULTS: Of 1032 patients who had asthma and were tested, we confirmed that 421 had influenza and the remaining 611 were test-negative controls. We found that the average effect of influenza vaccination was 43% (adjusted odds ratio [OR] 0.57, 95% confidence interval [CI] 0.40 to 0.80) for current-season vaccination regardless of previous doses, and 38% (adjusted OR 0.62, 95% CI 0.39 to 0.96) for vaccination in previous seasons only. Effects were similar for outpatients and inpatients. Among patients with asthma and confirmed influenza, current-season vaccination did not reduce the odds of hospital admission (adjusted OR 1.05, 95% CI 0.51 to 2.18). Influenza vaccination effects were similar for patients with and without asthma. INTERPRETATION: We estimated that, on average, current or previous influenza vaccination of people with asthma prevented almost half of influenza cases. These results support recommendations that people with asthma receive influenza vaccination.

Simple models to include influenza vaccination history when evaluating the effect of influenza vaccination.

BackgroundMost reports of influenza vaccine effectiveness consider current-season vaccination only.AimWe evaluated a method to estimate the effect of influenza vaccinations (EIV) considering vaccination history.MethodsWe used a test-negative design with well-documented vaccination history to evaluate the average EIV over eight influenza seasons (2011/12-2018/19; n = 10,356). Modifying effect was considered as difference in effects of vaccination in current and previous seasons and current-season vaccination only. We also explored differences between current-season estimates excluding from the reference category people vaccinated in any of the five previous seasons and estimates without this exclusion or only for one or three previous seasons.ResultsThe EIV was 50%, 45% and 38% in people vaccinated in the current season who had previously received none, one to two and three to five doses, respectively, and it was 30% and 43% for one to two and three to five prior doses only. Vaccination in at least three previous seasons reduced the effect of current-season vaccination by 12 percentage points overall, 31 among outpatients, 22 in 9-65 year-olds, and 23 against influenza B. Including people vaccinated in previous seasons only in the unvaccinated category underestimated EIV by 9 percentage points on average (31% vs 40%). Estimates considering vaccination of three or five previous seasons were similar.ConclusionsVaccine effectiveness studies should consider influenza vaccination in previous seasons, as it can retain effect and is often an effect modifier. Vaccination status in three categories (current season, previous seasons only, unvaccinated) reflects the whole EIV.

Effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 infection and hospitalisation, Navarre, Spain, January to April 2021.

COVID-19 vaccine effectiveness was evaluated in close contacts of cases diagnosed during January-April 2021. Among 20,961 contacts, 7,240 SARS-CoV-2 infections were confirmed, with 5,467 being symptomatic and 559 leading to hospitalisations. Non-brand-specific one and two dose vaccine effectiveness were respectively, 35% (95% confidence interval (CI): 25 to 44) and 66% (95% CI: 57 to 74) against infections, 42% (95% CI: 31 to 52) and 82% (95% CI: 74 to 88) against symptomatic infection, and 72% (95% CI: 47 to 85) and 95% (95% CI: 62 to 99) against COVID-19 hospitalisation. The second dose significantly increased effectiveness. Findings support continuing complete vaccination.

Product-specific COVID-19 vaccine effectiveness against secondary infection in close contacts, Navarre, Spain, April to August 2021.

COVID-19 vaccine effectiveness by product (two doses Comirnaty, Spikevax or Vaxzevria and one of Janssen), against infection ranged from 50% (95% CI: 42 to 57) for Janssen to 86% (70 to 93) for Vaxzevria-Comirnaty combination; among ≥ 60 year-olds, from 17% (-26 to 45) for Janssen to 68% (48 to 80) for Spikevax; and against hospitalisation from 74% (43 to 88) for Janssen to > 90% for other products. Two doses of vaccine were highly effective against hospitalisation, but suboptimal for infection control.

Prevalence and detection of undiagnosed active hepatitis C virus infections in Navarre, Spain, 2017-2019.

BACKGROUND: undiagnosed active hepatitis C virus (HCV) infection remains an obstacle towards its eradication. This study aimed to estimate the prevalence of HCV infection and to describe the diagnostic advances in Navarre, Spain. METHODS: HCV-infection diagnostic performance was analyzed in Navarre's primary and specialized health care between 2017 and 2019. The prevalence of undiagnosed infections was estimated for patients with programmed surgeries unrelated to HCV infection, who underwent a routine HCV antibody (anti-HCV) determination. HCV-RNA (viral load) was quantified in anti-HCV positive cases. The prevalence was standardized according to the sex and age distribution in the general population. RESULTS: from the 63,405 subjects examined for anti-HCV, 84 (five per 100,000 person-years) were diagnosed with an active infection. In Primary Health Care, 20,363 patients were analyzed and 47 active infections were detected, i.e. one case for every 433 people tested, implying 56 % of all identified active infections. On the other hand, 9,399 surgical patients were analyzed and 120 anti-HCV positive cases were detected (adjusted prevalence: 1.47 %; 95 % CI: 1.24-1.52). A positive viral load had been determined at any time in 66 cases (0.61 %), of which five were undiagnosed active infections (adjusted prevalence: 0.04 %; 95 % CI: 0.01-0.11). Preoperative screening allowed the detection of one undiagnosed infection per 795 people analyzed aged between 45 and 64 years. CONCLUSIONS: Primary Health Care efficiently contributes to the detection of undiagnosed HCV active infections. This may be speeded up by performing population screening, targeting subjects between 45 and 64 years of age.

Remaining Effect of Influenza Vaccines Received in Prior Seasons.

This study evaluates the remaining effect of influenza vaccines received in the 5 prior seasons. During 7 influenza seasons, 8933 patients were enrolled and 47% were confirmed for influenza. Compared with unvaccinated individuals in the current and 5 prior seasons, vaccination was protective when the last dose had been received in the current season (40% [95% confidence interval {CI}, 32%-47%]), and 1 (42% [95% CI, 27%-54%]), 2-3 (35% [95% CI, 16%-49%]), or 4-5 seasons (31% [95% CI, 4%-51%]) prior. This effect lasted for fewer seasons in the elderly and in patients with chronic conditions. On average, several recent prior doses were as protective as current-season vaccination.

Detection of Respiratory Viruses in Deceased Persons, Spain, 2017.

During the 2016-17 influenza season in Spain, we tested specimens from 57 elderly deceased persons for respiratory viruses. Influenza viruses were detected in 18% of the specimens and any respiratory virus in 47%. Only 7% of participants had received a diagnosis of infection with the detected virus before death.

Interim effectiveness of trivalent influenza vaccine in a season dominated by lineage mismatched influenza B, northern Spain, 2017/18.

The 2017/18 interim estimate of trivalent influenza vaccine effectiveness (VE) was 39% (95% confidence interval: 20-54) in Navarre. Compared with individuals unvaccinated in the current and five previous seasons, VE against influenza B was 41% for current and any prior doses, 67% for current vaccination only, and 22% for any prior doses, and 43%, 51% and 54%, respectively against influenza A(H3N2). This suggests moderate VE despite predominance of lineage mismatched influenza B.

Comparison of influenza vaccine effectiveness in preventing outpatient and inpatient influenza cases in older adults, northern Spain, 2010/11 to 2015/16.

IntroductionWe compared trivalent inactivated influenza vaccine effectiveness (VE) in preventing outpatient and inpatient influenza cases in Navarre, Spain. Methods: During seasons 2010/11 to 2015/16, community-dwelling patients with influenza-like illness aged 50 years or older were tested for influenza when attended by sentinel general practitioners or admitted to hospitals. The test-negative design was used to estimate and compare the VE by healthcare setting. Results: We compared 1,242 laboratory-confirmed influenza cases (557 outpatient and 685 inpatient cases) and 1,641 test-negative controls. Influenza VE was 34% (95% confidence interval (CI): 6 to 54) in outpatients and 32% (95% CI: 15 to 45) in inpatients. VE in outpatients and inpatients was, respectively, 41% (95% CI: -1 to 65) and 36% (95% CI: 12 to 53) against A(H1N1)pdm09, 5% (95% CI: -58 to 43) and 22% (95% CI: -9 to 44) against A(H3N2), and 49% (95% CI, 6 to 73) and 37% (95% CI: 2 to 59) against influenza B. Trivalent inactivated influenza vaccine was not associated with a different probability of hospitalisation among influenza cases, apart from a 54% (95% CI: 10 to 76) reduction in hospitalisation of influenza A(H3N2) cases. Conclusions: On average, influenza VE was moderate and similar in preventing outpatient and inpatient influenza cases over six influenza seasons in patients above 50 years of age. In some instances of low VE, vaccination may still reduce the risk of hospitalisation in older adults with vaccine failure.

Effect of Repeated Vaccination With the Same Vaccine Component Against 2009 Pandemic Influenza A(H1N1) Virus.

Background: The 2009 pandemic influenza A(H1N1) (A[H1N1]pdm09) vaccine component has remained unchanged from 2009. We estimate the effectiveness of current and prior inactivated influenza A(H1N1)pdm09 vaccination from influenza seasons 2010-2011 to 2015-2016. Methods: Patients attended with influenza-like illness were tested for influenza. Four periods with continued A(H1N1)pdm09 circulation were included in a test-negative design. Results: We enrolled 1278 cases and 2343 controls. As compared to individuals never vaccinated against influenza A(H1N1)pdm09, the highest effectiveness (66%; 95% confidence interval, 49%-78%) was observed in those vaccinated in the current season who had received 1-2 prior doses. The effectiveness was not statistically lower in individuals vaccinated in the current season only (52%) or in those without current vaccination and >2 prior doses (47%). However, the protection was lower in individuals vaccinated in the current season after >2 prior doses (38%; P = .009) or those currently unvaccinated with 1-2 prior doses (10%; P < .001). Current-season vaccination improved the effect in individuals with 1-2 prior doses and did not modify significantly the risk of influenza in individuals with >2 prior doses. Conclusion: Current vaccination or several prior doses were needed for high protection. Despite the decreasing effect of repeated vaccination, current-season vaccination was not inferior to no current-season vaccination.

Source identification of autochthonous-introduced Plasmodium vivax Malaria, Spain.

In 2014, an autochthonous case of introduced malaria caused by Plasmodium vivax was identified in Spain. The strain that infected this patient was identical to that of a prior imported case from Pakistan. This is the first case where the source of infection could be identified since elimination in Spain.

Combined effectiveness of prior and current season influenza vaccination in northern Spain: 2016/17 mid-season analysis.

The 2016/17 mid-season vaccine effectiveness estimate against influenza A(H3N2) was 15% (95% confidence interval: -11 to 35) in Navarre. Comparing to individuals unvaccinated in the current and four prior seasons, effectiveness was 24% for current and 3-4 prior doses, 61% for current and 1-2 prior doses, 42% for only current vaccination, and 58% for 3-4 prior doses. This suggests moderate effectiveness for different combinations of vaccination in the current and prior seasons.

Direct, indirect and total effects of 13-valent pneumococcal conjugate vaccination on invasive pneumococcal disease in children in Navarra, Spain, 2001 to 2014: cohort and case-control study.

We estimated the direct, indirect and total effects of the 13-valent pneumococcal conjugate vaccine (PCV13) on invasive pneumococcal disease (IPD) in children. A population-based cohort study followed children aged between 2.5 and 59 months between 2001 and 2014 in Navarra, Spain. IPD incidence was compared by PCV status and period. All cases diagnosed from July 2010 to December 2014 and eight matched controls per case were analysed to estimate the adjusted direct effect of PCV13. A total of 120,980 children were followed and 206 IPD cases were detected. Compared with unvaccinated children in the baseline period (2001-2004), overall IPD incidence in 2011-2014 (76% average PCV coverage) declined equally in vaccinated (total effect: 76%; hazard ratio (HR): 0.24; 95% confidence interval (CI): 0.14-0.40) and unvaccinated children (indirect effect: 78%; HR: 0.22; 95% CI: 0.09-0.55). IPD incidence from non-PCV13 serotypes increased among vaccinated children (HR: 2.84; 95% CI: 1.02-7.88). The direct effect of one or more doses of PCV13 against vaccine serotypes was 95% (odds ratio: 0.05; 95% CI: 0.01-0.55). PCV13 was highly effective in preventing vaccine-serotype IPD. The results suggest substantial and similar population-level vaccine benefits in vaccinated and unvaccinated children through strong total and indirect effects.