Hospitalisations and Deaths Averted by COVID-19 Vaccination in Navarre, Spain, 2021-2022.

In 2021-2022, most of the Spanish population received COVID-19 vaccines and a high proportion of them had SARS-CoV-2 infection. We estimated the rate of hospitalisations and deaths that were averted by risk reduction among vaccinated COVID-19 cases. Hospitalisations and deaths were analysed among COVID-19 cases confirmed in 2021 and 2022 in Navarre, Spain. To calculate the number of prevented outcomes by sex, age, comorbidities, and semester, the difference in the risk of each outcome between unvaccinated and vaccinated cases was multiplied by the number of vaccinated cases. COVID-19 vaccination coverage with any dose reached 88%, 86% with full vaccination, and 56% with a booster dose. The cumulative rates per 1000 inhabitants were 382 COVID-19 confirmed cases, 6.70 hospitalisations, and 1.15 deaths from COVID-19. The estimated rates of prevented events by vaccination were 16.33 hospitalisations and 3.39 deaths per 1000 inhabitants, which was 70.9% and 74.7% of expected events without vaccination, respectively. People aged 80 years and older or with major chronic conditions accounted for the majority of hospitalizations and deaths prevented by COVID-19 vaccination. One hospitalisation and death due to COVID-19 were averted for every 53 and 258 people vaccinated, respectively. The high COVID-19 vaccine effect in reducing the risk of severe outcomes and the high vaccination coverage in risk populations prevented three out of four hospitalisations and deaths due to COVID-19 during a period of intense circulation of SARS-CoV-2.

Whole Genome Sequencing for Studying Helicobacter pylori Antimicrobial Resistance.

Antibiotic resistance (AMR) is an alarming concern worldwide and Helicobacter pylori, one of the most prevalent bacteria, is not an exception. With antibiotics being its primary therapy, increasing resistance leads to a higher rate of treatment failure. Understanding the genomic mechanisms of resistance to clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline, and rifampicin through next-generation sequencing-based molecular tools, such as whole genome sequencing (WGS), can be of great value, not only to direct a patient's treatment, but also to establish and optimize treatment guidelines according to the local epidemiology and to avoid the use of inappropriate antibiotics. WGS approaches allow us to gain insight into the genomic determinants involved in AMR. To this end, different pipelines and platforms are continuously being developed. In this study, we take a more detailed view of the use and progression of WGS for in-depth study of H. pylori's AMR.

Effect of COVID-19 vaccination on the SARS-CoV-2 transmission among social and household close contacts: A cohort study.

BACKGROUND: COVID-19 vaccination was expected to reduce SARS-CoV-2 transmission, but the relevance of this effect remains unclear. We aimed to estimate the effectiveness of COVID-19 vaccination of the index cases and their close contacts in reducing the probability of SARS-CoV-2 transmission. METHODS: Transmission of SARS-CoV-2 infection was evaluated in two cohorts of adult close contacts of COVID-19 confirmed cases (social and household settings) by COVID-19 vaccination status of the index case and the close contact, from April to November 2021 in Navarre, Spain. The effects of vaccination of the index case and the close contact were estimated as (1-adjusted relative risk) × 100%. RESULTS: Among 19,631 social contacts, 3257 (17%) were confirmed with SARS-CoV-2. COVID-19 vaccination of the index case reduced infectiousness by 44% (95% CI, 27-57%), vaccination of the close contact reduced susceptibility by 69% (95% CI, 65-73%), and vaccination of both reduced transmissibility by 74% (95% CI, 70-78%) in social settings, suggesting some synergy of effects. Among 20,708 household contacts, 6269 (30%) were infected, and vaccine effectiveness estimates were 13% (95% CI, -5% to 28%), 61% (95% CI, 58-64%), and 52% (95% CI, 47-56%), respectively. These estimates were lower in older people and had not relevant differences between the Alpha (April-June) and Delta (July-November) variant periods. CONCLUSIONS: COVID-19 vaccination reduces infectiousness and susceptibility; however, these effects are insufficient for complete control of SARS-CoV-2 transmission, especially in older people and household setting. Relaxation of preventive behaviors after vaccination may counteract part of the vaccine effect on transmission.

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.

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.

Are molecular methods helpful for the diagnosis of Helicobacter pylori infection and for the prediction of its antimicrobial resistance?

Infections produced by Helicobacter pylori (H. pylori), a spiral Gram-negative bacterium, can cause chronic gastritis, peptic ulcer, and gastric cancer. Antibiotic therapy is the most effective treatment for H. pylori infection at present. However, owing to the increasing antibiotic resistance of H. pylori strains, it has become a serious threat to human health. Therefore, the accurate diagnosis of H. pylori infections and its antibiotic resistance markers is of great significance. Conventional microbiological diagnosis of H. pylori is based on culture; however, successful isolation of H. pylori from gastric biopsy specimens is a challenging task affected by several factors and has limitations in terms of the time of response. To improve conventional methods, some molecular techniques, such as PCR, have been recently used in both invasive and non-invasive H. pylori diagnosis, enabling simultaneous detection of H. pylori and point mutations responsible for frequent antibiotic resistance. The advantages and disadvantages of molecular methods, mainly PCR, versus conventional culture for the H. pylori identification and the detection of antibiotic resistance are discussed. As expected, the combination of both diagnostic methods will lead to the most efficient identification of the H. pylori strains and the resistance patterns.

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.

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.

Differences in Transmission between SARS-CoV-2 Alpha (B.1.1.7) and Delta (B.1.617.2) Variants.

The present study aimed to compare the susceptibility and infectivity between the Alpha and Delta variants of SARS-CoV-2 and to investigate characteristics of the index case and the contact that may affect transmission. The risk of SARS-CoV-2 infection was compared between close contacts of COVID-19 cases with Alpha and Delta variants during June 2021 to August 2021. In index cases, Spike gene target failure (TaqPath) was used as a proxy of Alpha variant and the L452R mutation (TaqMan) for Delta variant. Cox regression models were used to estimate adjusted relative risks (RR). We compared close contacts of index cases with Alpha (n = 2139) and Delta variants (n = 5439). Delta variant was more transmissible overall (relative risk [RR] 1.32, 95% CI = 1.13 to 1.53), and in non-household contacts (RR 1.71, 95% CI = 1.35 to 2.16), but not in household contacts (RR 1.10, 95% CI = 0.91 to 1.34; Pinteraction < 0.001). Delta variant excess transmission was observed when the index cases were 12 to 39 years old (RR 1.51, 95% CI = 1.27 to 1.79) and the close contacts were 18 to 39 years old (RR 1.62, 95% CI = 1.29 to 2.03), but not among those younger or older than such ages. Differences in transmissibility between variants disappeared with vaccination of the index case (RR 0.68, 95% CI = 0.46 to 1.02), but not with vaccination of the close contact. This report shows that the Delta variant is more transmissible than Alpha variant mainly among young adults. Vaccination of the index cases reduced the excess transmission, which reinforces the recommendation of vaccination to reduce transmission of the Delta variant. IMPORTANCE The higher transmissibility of the Delta variant of SARS-CoV-2 in comparison with the Alpha variant has been reported. We compared the transmission of the Alpha and Delta variants by characteristics and COVID-19 vaccination status of index cases and their close contacts. Interestingly, the Delta variant showed increased transmissibility when the index case was an adolescent or young adult and when the close contact was a young adult; however, in index cases and close contacts of other age groups, transmission did not differ between variants. This may explain the increased proportion of young people who have been infected in the surges due to the Delta variant. The Delta variant was more transmissible than the Alpha variant when the index cases were unvaccinated against COVID-19, and their vaccination equaled the transmissibility of both variants, which suggests a higher impact of vaccination in controlling transmission of the Delta variant.

Utility of a commercial RT-qPCR assay to detect SARS-CoV-2 gene variations as an indicator of lineages.

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.

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.

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.

Risk Factors of Infection, Hospitalization and Death from SARS-CoV-2: A Population-Based Cohort Study.

We conducted a prospective population-based cohort study to assess risk factors for infection, hospitalization, and death from SARS-CoV-2. The study comprised the people covered by the Health Service of Navarre, Spain. Sociodemographic variables and chronic conditions were obtained from electronic healthcare databases. Confirmed infections, hospitalizations, and deaths from SARS-CoV-2 were obtained from the enhanced epidemiological surveillance during the second SARS-CoV-2 epidemic surge (July-December 2020), in which diagnostic tests were widely available. Among 643,757 people, 5497 confirmed infections, 323 hospitalizations, 38 intensive care unit admissions, and 72 deaths from SARS-CoV-2 per 100,000 inhabitants were observed. A higher incidence of confirmed infection was associated with people aged 15-29 years, nursing home residents, healthcare workers, people born in Latin America or Africa, as well as in those diagnosed with diabetes, cardiovascular disease, chronic obstructive pulmonary disease (COPD), chronic kidney disease, dementia, severe obesity, hypertension and functional dependence. The risk of hospitalization in the population was associated with males, higher age, nursing home residents, Latin American or African origin, and those diagnosed with immunodeficiency, diabetes, cardiovascular disease, COPD, asthma, kidney disease, cerebrovascular disease, cirrhosis, dementia, severe obesity, hypertension and functional dependence. The risk of death was associated with males, higher age, nursing home residents, Latin American origin, low income level, immunodeficiency, diabetes, cardiovascular disease, COPD, kidney disease, dementia, and functional dependence. This study supports the prioritization of the older population, nursing home residents, and people with chronic conditions and functional dependence for SARS-CoV-2 prevention and vaccination, and highlights the need for additional preventive support for immigrants.

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.

[Cerebrospinal fluid shunt-associated meningitis caused by Gordonia sputi: case report and review of the literature].

We report the first known case of cerebrospinal fluid (CSF) shunt-associated meningitis caused by Gordonia sputi and review published cases of Gordonia CNS infections.