Search

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 non–variants 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}, 1.28–2.71]) and severe disease (aOR, 2.40 [95% CI, 1.31–4.40]) than non-VOCs. The Delta variant did not show a significantly different risk of hospitalization (aOR, 0.73 [95% CI, .40–1.30]) and severe disease (aOR, 3.04 [95% CI, .57–16.22]) 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.

Background As 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. Aim To evaluate risk reduction of hospitalisation and severe disease in vaccinated COVID-19 cases during the Omicron BA.1-predominant period in Navarre, Spain. Methods A 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. Results Among 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 Conclusions Full 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.

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.

Many factors might affect SARS-CoV-2 transmission, but their relevance is not well established. The objectives were to assess the secondary attack rate (SAR) and the risk factors for SARS-CoV-2 transmission from confirmed index cases to their close contacts in household and non-household settings.This cohort study included the close contacts of SARS-CoV-2 infected cases confirmed between May and December 2020 in Navarre, Spain. Epidemiological and clinical variables of the index case and close contacts were collected. The SAR was calculated, and the independent effect of each variable on the transmission risk was evaluated by logistic regression.A total of 59,900 close contacts of 20,048 index cases were studied, and 53.6% were household contacts. SAR was 34.9% overall, 46.8% in household contacts and 21.1% in non-household contacts. The risk of transmission was higher in household setting (adjusted odds ratio (aOR) 2.96, 95% CI 2.84-3.07), from symptomatic index cases (aOR 1.50, 95% CI 1.43-1.58), immigrants (aOR 1.44, 95% CI 1.36-1.52), and increased with age. A higher susceptibility of close contacts was associated with 5-14 years of age, immigrants (aOR 1.54), very low or low-income level (aOR 1.27, and aOR, 1.17, respectively), healthcare work (aOR 1.21), and diagnosis of diabetes (aOR 1.14, 95%CI 1.03-1.25), chronic kidney disease (aOR 1.18, 95%CI 1.04-1.35), hypertension (aOR 1.11, 95% CI 1.03-1.19), and severe obesity (aOR 1.18, 95% CI 1.00-1.38). Transmission increased progressively from May to September 2020 as the B.1.177 variant became dominant.The risk of SARS-CoV-2 infection was considerable among close contacts of infected persons. The higher risk associated with household contacts, immigrants, older index cases, close contacts with lower income level and comorbidities should be considered to address preventive interventions.

Simple Summary Malignant pleural mesothelioma (MPM) is an aggressive and still incurable cancer. There is an urgent need to identify effective and reliable tools for detecting and diagnosing the early onset of MPM. In our study, we investigated the whole miRNAs expression profile from serum extracellular vesicles to identify early changes related to MPM development. miR-11400, miR-148a-3p, and miR-409-3p levels were increased in pre-clinical MPM patients up to five years before their diagnosis. The three-miRNA pattern showed a good discrimination capacity to distinguish pre-clinical MPM from cancer-free controls. The three miRNAs also displayed high diagnostic capabilities for differentiating between MPM patients and controls. This study identified a potential EV miRNA signature in preclinical MPM up to five years before diagnosis and raises the possibility of early intervention. Malignant pleural mesothelioma (MPM) is an aggressive cancer with a dismal prognosis. Early therapeutic interventions could improve patient outcomes. We aimed to identify a pattern of microRNAs (miRNAs) as potential early non-invasive markers of MPM. In a case-control study nested in the European Prospective Investigation into Cancer and Nutrition cohort, we screened the whole miRNome in serum extracellular vesicles (EVs) of preclinical MPM cases. In a subgroup of 20 preclinical samples collected five years prior MPM diagnosis, we observed an upregulation of miR-11400 (fold change (FC) = 2.6, adjusted p-value = 0.01), miR-148a-3p (FC = 1.5, p-value = 0.001), and miR-409-3p (FC = 1.5, p-value = 0.04) relative to matched controls. The 3-miRNA panel showed a good classification capacity with an area under the receiver operating characteristic curve (AUC) of 0.81 (specificity = 0.75, sensitivity = 0.70). The diagnostic ability of the model was also evaluated in an independent retrospective cohort, yielding a higher predictive power (AUC = 0.86). A signature of EV miRNA can be detected up to five years before MPM; moreover, the identified miRNAs could provide functional insights into the molecular changes related to the late carcinogenic process, preceding MPM development.

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.

With the emergence of new SARS-CoV-2 variants and the acquisition of novel mutations in exiting 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 B.1.575 lineage containing the E484K mutation in the spike protein (named B.1.575.2) in a region of Northern Spain between May and June 2021. SARS-CoV-2 positive samples with cycle threshold value less than or equal to 30 were selected to screen of presumptive variants using the TaqPath™ COVID-19 RT-PCR kit and 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 sub-lineage, which was related to the presence of the E484K mutation. Of 197 cases registered in 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.

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.

To the Editor,The gold standard technique used in diagnostics of SARS-CoV-2 infection is the reverse transcription quantitative real-time porlymerase chain reaction (RTqPCR). A problem in routine u...

The independent role of hypertension for COVID-19 outcomes in the population remains unclear. We aimed to estimate the independent effect of hypertension and hypertension-related conditions, i.e., cardiovascular, cerebrovascular and chronic kidney diseases, as potential risk factors for COVID-19 hospitalization and severe COVID-19 (i.e., intensive care unit admission or death) in the population. The risk for severe COVID-19 among hospitalized patients was also evaluated. A Spanish population-based cohort of people aged 25–79 years was prospectively followed from March to May 2020 to identify hospitalizations for laboratory-confirmed COVID-19. Poisson regression was used to estimate the adjusted relative risk (aRR) for COVID-19 hospitalization and severe COVID-19 among the whole cohort, and for severe COVID-19 among hospitalized patients. Of 424,784 people followed, 1106 were hospitalized by COVID-19 and 176 were severe cases. Hypertension was not independently associated with a higher risk of hospitalization (aRR 0.96, 95% CI 0.83–1.12) nor severe COVID-19 (aRR 1.12, 95% CI 0.80–1.56) in the population. Persons with cardiovascular, cerebrovascular and chronic kidney diseases were at higher risk for COVID-19 hospitalization (aRR 1.33, 95% CI 1.13–1.58, aRR 1.41, 95% CI 1.04–1.92, and aRR 1.52, 95% CI 1.21–1.91, respectively) and severe COVID-19 (aRR 1.61, 95% CI 1.13–2.30, aRR 1.91, 95% CI 1.13–3.25, and aRR 1.78, 95% CI 1.14–2.76, respectively). COVID-19 hospitalized patients with cerebrovascular diseases were at higher risk of mortality (aRR 1.80, 95% CI 1.00–3.23). The current study shows that, in the general population, persons with cardiovascular, cerebrovascular and chronic kidney diseases, but not those with hypertension only, should be considered as high-risk groups for COVID-19 hospitalization and severe COVID-19.

BackgroundAfter the first pandemic wave, a nationwide seroepidemiological survey assessed the seroprevalence of SARS-CoV-2 antibodies in the population of Spain and found notable differences among provinces whose causes remain unclear. The present study aimed to examine the influence of environmental factors on SARS-CoV-2 infection. MethodsThis ecological study analyzed the association between environmental and demographic factors and SARS-CoV-2 infection by province. Environmental temperature and humidity were obtained from the Spanish Meteorological Agency and province extension, and latitude and altitude above sea level of their capital cities from the Geographical Institute. The seroprevalence SARS-CoV-2 antibodies by province was obtained from a nationwide representative survey performed in June 2020, after the first pandemic wave in Spain. Linear regression was used in the analysis.ResultsThe seroprevalence of SARS-CoV-2 antibodies of the 50 provinces ranged from 0.2% to 13.6%. Altitude explained nearly half of differences in seroprevalence (determination coefficient [R2]=0.46, p2=0.55, p2 of increase in population density, the seroprevalence increased by 0.84 and 0.63 percentage points, respectively.ConclusionsEnvironmental conditions related to higher altitude in winter-spring, as lower temperature and absolute humidity, may be relevant to SARS-CoV-2 transmission. Places with such adverse conditions may require additional efforts for pandemic control.

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.

A nasopharyngeal swab is a sample used for the diagnosis of SARS-CoV-2 infection. Saliva is a sample easier to obtain and the risk of contagion for the professional is lower. This study aimed to evaluate the utility of saliva for the diagnosis of SARS-CoV-2 infection. This prospective study involved 674 patients with suspected SARS-CoV-2 infection. Paired nasopharyngeal and saliva samples were processed by RT-qPCR. Sensitivity, specificity, and kappa coefficient were used to evaluate the results from both samples. We considered the influence of age, symptoms, chronic conditions, and sample processing with lysis buffer. Of the 674 patients, 636 (94.4%) had valid results from both samples. The virus detection in saliva compared to a nasopharyngeal sample (gold standard) was 51.9% (95% CI: 46.3%&ndash, 57.4%) and increased to 91.6% (95% CI: 86.7%&ndash, 96.5%) when the cycle threshold (Ct) was &le, 30. The specificity of the saliva sample was 99.1% (95% CI: 97.0%&ndash, 99.8%). The concordance between samples was 75% (&kappa, = 0.50, 95% CI: 0.45&ndash, 0.56). The Ct values were significantly higher in saliva. In conclusion, saliva sample utility is limited for clinical diagnosis, but could be a useful alternative for the detection of SARS-CoV-2 in massive screening studies, when the availability of trained professionals for sampling or personal protection equipment is limited.

After the first pandemic wave, a nationwide survey assessed the seroprevalence of SARS-CoV-2 antibodies in Spain and found notable differences among provinces whose causes remained unclear. This ecological study aimed to analyze the association between environmental and demographic factors and SARS-CoV-2 infection by province. The seroprevalence of SARS-CoV-2 antibodies by province was obtained from a nationwide representative survey performed in June 2020, after the first pandemic wave in Spain. Linear regression was used in the analysis. The seroprevalence of SARS-CoV-2 antibodies of the 50 provinces ranged from 0.2% to 13.6%. The altitude, which ranged from 5 to 1131 m, explained nearly half of differences in seroprevalence (R2 = 0.47, p &lt, 0.001). The seroprevalence in people residing in provinces above the median altitude (215 m) was three-fold higher (6.5% vs. 2.1%, p &lt, 0.001). In the multivariate linear regression, the addition of population density significantly improved the predictive value of the altitude (R2 = 0.55, p &lt, 0.001). Every 100 m of altitude increase and 100 inhabitants/km2 of increase in population density, the seroprevalence rose 0.84 and 0.63 percentage points, respectively. Environmental conditions related to higher altitude in winter–spring, such as lower temperatures and absolute humidity, may be relevant to SARS-CoV-2 transmission. Places with such adverse conditions may require additional efforts for pandemic control.

Background The World Health Organization (WHO) recommended RT-qPCR tests as the reference technique for SARS-CoV-2 molecular detection, however with the rapid spread of the infection, mutations in specific RT-qPCR target regions have been widely described could allow the presumptive identification. Objective In this study, we evaluated the analytical performance of the Allplex™SARS-CoV-2/FluA/FluB/RSV assay for the additional presumptive identification of SARS-CoV-2 variants in a real-life setting. Results We observed gene-specific changes in the cycle threshold (Ct) of the N and RdRp genes compared with the Ct yielded for the S gene when the SARS-CoV-2 testing was performed Allplex™SARS-CoV-2/FluA/FluB/RSV assay. Seventeen samples showed Ct variations in the N and/or RdRp. In 10 cases, the N gene was affected, delayed or negative and in 14 cases, the RdRp gene showed a delay or negative concerning the S gene. A delay in the Ct of both genes (RdRp and N) was observed in six cases. Sequencing determined that all samples identified as B.1.1.7 showed changes in the PCR curves of the N and RdRp. However, samples identified as B.1.177 only showed variations for the RdRp gene. Conclusions Allplex™SARS-CoV-2/FluA/FluB/RSV assay, the diagnosis could presumably allow the rapid assignment of lineages B.1.1.7 and B.1.177, and emphasizes the importance of exhaustive surveillance for circulating variants of the SARS-CoV-2 virus to reduce community transmission.

Analysis of polymorphic microsatellite markers (STR) is a helpful genotyping technique to differentiate Candida parapsilosis sensu stricto isolates. The aim of this study is to develop and perform an initial validation of an alternative protocol for the reliable and accurate microsatellite genotyping of C. parapsilosis sensu stricto isolates using high-throughput multiplex PCR. To achieve this, the results obtained using the new protocol were compared to the ones obtained using a previously described reference method. To that end, diagnostic accuracy, informativeness and discrimination parameters were estimated., This work was supported by the Consejeria de Educacion, Universidades e Investigacion of the Gobierno Vasco-Eusko Jaurlaritza [GIC 15/78 IT-990-16] and the Universidad del Pais Vasco/Euskal Herriko Unibertsitatea [UFI 11/25]. CTS has been supported by a research grant of the Fundacion Jesus de Gangoiti Barrera.

Vaccines may induce positive non-specific immune responses to other pathogens. This study aims to evaluate if influenza vaccination in the 2019–2020 season had any effect on the risk of SARS-CoV-2 confirmed infection in a cohort of health workers. During the first SARS-CoV-2 epidemic wave in Spain, between March and May 2020, a cohort of 11,201 health workers was highly tested by RT-qPCR and/or rapid antibody test when the infection was suspected. Later in June, 8665 of them were tested for total antibodies in serum. A total of 890 (7.9%) health workers were laboratory-confirmed for SARS-CoV-2 infection by any type of test, while no case of influenza was detected. The adjusted odds ratio between 2019–2020 influenza vaccination and SARS-CoV-2 confirmed infection was the same (1.07; 95% CI, 0.92–1.24) in both comparisons of positive testers with all others (cohort design) and with negative testers (test-negative design). Among symptomatic patients tested by RT-qPCR, the comparison of positive cases and negative controls showed an adjusted odds ratio of 0.86 (95% CI, 0.68–1.08). These results suggest that influenza vaccination does not significantly modify the risk of SARS-CoV-2 infection. The development of specific vaccines against SARS-CoV-2 is urgent.

Introduction In July and August 2021, the SARS-CoV-2 Delta variant dominated in Europe. Aim Using a multicentre test-negative study, we measured COVID-19 vaccine effectiveness (VE) against symptomatic infection. Methods Individuals with COVID-19 or acute respiratory symptoms at primary care/community level in 10 European countries were tested for SARS-CoV-2. We measured complete primary course overall VE by vaccine brand and by time since vaccination. Results Overall VE was 74% (95% CI: 69–79), 76% (95% CI: 71–80), 63% (95% CI: 48–75) and 63% (95% CI: 16–83) among those aged 30–44, 45–59, 60–74 and ≥ 75 years, respectively. VE among those aged 30–59 years was 78% (95% CI: 75–81), 66% (95% CI: 58–73), 91% (95% CI: 87–94) and 52% (95% CI: 40–61), for Comirnaty, Vaxzevria, Spikevax and COVID-19 Vaccine Janssen, respectively. VE among people 60 years and older was 67% (95% CI: 52–77), 65% (95% CI: 48–76) and 83% (95% CI: 64–92) for Comirnaty, Vaxzevria and Spikevax, respectively. Comirnaty VE among those aged 30–59 years was 87% (95% CI: 83–89) at 14–29 days and 65% (95% CI: 56–71%) at ≥ 90 days between vaccination and onset of symptoms. Conclusions VE against symptomatic infection with the SARS-CoV-2 Delta variant varied among brands, ranging from 52% to 91%. While some waning of the vaccine effect may be present (sample size limited this analysis to only Comirnaty), protection was 65% at 90 days or more between vaccination and onset.