Assessing the Burden of Dengue during the COVID-19 Pandemic in Mexico.

The transmission of the dengue virus in Mexico has historically been high, and its burden during the COVID-19 pandemic is currently not well understood. Our objective was to assess the burden of dengue-related disability-adjusted life years (DALYs) between 2020 and 2022. We conducted a cross-sectional analysis of databases resulting from an epidemiological surveillance of vector-borne diseases and computed DALYs using the protocol of the Global Burden of Disease (GBD) study 2019. Our results showed that there were 218,807 incident cases of dengue during the study period, resulting in 951 deaths. The calculated DALYs (and their 95% confidence intervals) were 8121 (7897-8396), 4733 (4661-4820), and 8461 (8344-8605) in 2020, 2021, and 2022, respectively. The DALY rates (per 100,000) were 6.5 (6.3-6.6), 3.8 (3.7-3.9), and 6.7 (6.6-6.8), respectively. The rates for 2020 and 2022 were similar to the historical mean (6.4, p = 0.884), whereas the rate for 2021 was lower than the mean. Premature mortality (years of life lost, YLL) contributed to 91% of the total burden. Our findings suggest that dengue fever remained a significant cause of disease burden during the COVID-19 pandemic, especially in terms of premature mortality.

Multicenter clinical evaluation of a novel transcription-mediated amplification assay for SARS-CoV-2 molecular testing.

INTRODUCTION: The onset and spread of COVID-19 pandemic has forced clinical laboratories to rapidly expand testing capacity for SARS-CoV-2. This study evaluates the clinical performance of the TMA Procleix SARS-CoV-2 assay in comparison to the RT-PCR assay Allplex™ SARS-CoV-2 for the qualitative detection of SARS-CoV-2 RNA. METHODS: Between November 2020 and February 2021, 610 upper-respiratory specimens received for routine SARS-CoV-2 molecular testing were prospectively collected and selected at the Hospital Universitari Vall d'Hebron and the Hospital Universitari Bellvitge in Barcelona, Spain. All samples were processed in parallel with the TMA and the RT-PCR assays, and results were compared. Discrepancies were retested by an additional RT-PCR method and the clinical history of these patients was reviewed. RESULTS: Overall, the level of concordance between both assays was 92.0% (κ, 0.772). Most discordant results (36/38, 94.7%) corresponded to samples testing positive with the TMA assay and negative with the RT-PCR method. Of these discrepant cases, most (28/36, 77.8%) were finally classified as confirmed or probable SARS-CoV-2 cases according to the discrepant analysis. CONCLUSION: In conclusion, the TMA Procleix SARS-CoV-2 assay performed well for the qualitative detection of SARS-CoV-2 RNA in a multisite clinical setting. This novel TMA assay demonstrated a greater sensitivity in comparison to RT-PCR methods for the molecular detection of SARS-CoV-2. This higher sensitivity but also the qualitative feature of this detection of SARS-CoV-2 should be considered when making testing algorithm decisions.

Predictors of Recurrent Laboratory-Confirmed Symptomatic SARS-CoV-2 Infections in a Cohort of Healthcare Workers.

BACKGROUND: Repeated SARS-CoV-2 infections are plausible and related published data are scarce. We aimed to identify factors associated with the risk of recurrent (three episodes) laboratory-confirmed symptomatic SARS-CoV-2 infections. METHODS: A retrospective cohort study was conducted, and 1,700 healthcare workers were enrolled. We used risk ratios (RR) and 95% confidence intervals (CI) to evaluate the factors associated with symptomatic SARS-CoV-2 infections. RESULTS: We identified 14 participants with recurrent illness episodes. Therefore, the incidence rate was 8.5 per 10,000 person months. In a multiple-model study, vaccinated adults (vs. unvaccinated, RR = 1.05 [1.03-1.06]) and those with a severe first illness episode (vs. mild disease, RR = 1.05 [1.01-1.10]) were at increased risk for repeated symptomatic SARS-CoV-2 reinfections. Increasing age showed a protective effect (per each additional year of age: RR = 0.98 [0.97-0.99]). CONCLUSIONS: Our results suggest that recurrent SARS-CoV-2 infections are rare events in adults, and they seem to be determined, partially, by vaccination status and age.

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.

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 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.

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.

Reemerging Influenza Virus Infections during the Dominance of the Omicron SARS-CoV-2 Variant in Mexico.

The burden of influenza in Mexico has been high. We aimed to characterize its epidemiological patterns before and during the coronavirus disease 2019 (COVID-19) pandemic. A retrospective cohort study was conducted and 5652 PCR-confirmed cases of influenza (October 2019-April 2022) were analyzed. The highest incidence (144 per million) was observed in December 2019 and rapidly decreased right before the start of the pandemic (February 2020). No cases were documented in the 2020-2021 season, and infections reemerged at a low level (8 per million) in December 2021. The case-fatality rates were around 5% in both seasons (p = 0.591). The dominant strains were AH1N1 and AH3N2 in the 2019-2020 and 2021-2022 seasons, respectively. In multiple analysis, males and older patients were at increased risk of a fatal outcome. Flu vaccination and infection by B lineages (vs. AH1N1) showed a protective effect. Our results suggest that the spread of the influenza virus reemerged in the 2021-2022 season when the SARS-CoV-2 Omicron variant (B.1.1.529) was dominant. Efforts focusing on the prevention of transmission of respiratory viral pathogens, together with flu vaccination, may be useful to reduce the risk of an influenza outbreak.

Antimicrobial use and aetiology of bloodstream infections in critically ill patients during early stages of SARS-CoV-2 pandemic.

Background: During early stages of COVID-19 pandemic, antimicrobials were commonly prescribed. Aim: To describe clinical, microbiological and antimicrobial use changes in bloodstream infections (BSI) of ICU patients during the first wave of COVID-19 pandemic compared to pre-COVID-19 era. Methods: Observational cohort study of patients admitted to ICU of Bellvitge University Hospital was conducted during the COVID-19 pandemic (March-June 2020) and before COVID-19 pandemic (March-June 2019). Differences in clinical characteristics, antimicrobial consumption and incidence and aetiology of BSI were measured. Findings: COVID-19 patients had significantly less comorbidities with obesity the only risk factor that increased in frequency. COVID-19 patients more frequently required invasive supportive care measures, had longer median ICU stay and higher mortality rates. The incidence of BSIs was higher in COVID-19 period (RR 3.2 [95%CI 2.2-4.7]), occurred in patients who showed prolonged median ICU stay (21days) and was associated with high mortality rate (47%). The highest increases in the aetiological agents were observed for AmpC-producing bacteria (RR 11.1 [95%CI 2.6-47.9]) and non-fermenting rods (RR 7.0 [95%CI 1.5-31.4]). The emergence of bacteraemia caused by Gram-negative rods resistant to amoxicillin-clavulanate, which was used as empirical therapy during early stages of the pandemic, led to an escalation towards broader-spectrum antimicrobials such as meropenem and colistin which was also associated with the emergence of resistant isolates. Conclusions: The epidemiological shift towards resistant phenotypes in critically ill COVID-19 patients was associated with the selective use of antimicrobials. Our study provides evidence of the impact of empirical therapy on the selection of bacteria and their consequences on BSI over the subsequent months.

COVID-19 Pneumonia in Fully Vaccinated Adults during the Dominance of the Omicron Sublineages BA.1.1 and BA.2 in Mexico.

Background and Objectives: A nationwide retrospective cohort study was conducted to evaluate the factors associated with the risk of laboratory-confirmed coronavirus disease 2019 (COVID-19)-related pneumonia in fully vaccinated adults during the dominance of the Omicron sublineages in Mexico. Materials and Methods: Fully COVID-19-vaccinated adults with laboratory-positive illness and symptom onset from April to mid-June 2022 were eligible. We computed the eta-squared (η2) to evaluate the effect size of the study sample. The characteristics predicting pneumonia were evaluated through risk ratios (RRs), and the 95% confidence intervals (CIs) were computed through generalized linear models. Results: The data from 35,561 participants were evaluated, and the overall risk of pneumonia was 0.5%. In multiple analyses, patients aged ≥ 60 years old were at increased risk of developing pneumonia (vs. 20-39 years old: RR = 1.031, 95% CI = 1.027-1.034). Chronic pulmonary obstructive disease, type 2 diabetes mellitus, arterial hypertension, chronic kidney disease (any stage), and immunosuppression (any cause) were also associated with a higher pneumonia risk. The η2 of all the variables included in the multiple models was <0.06. Conclusions: Our study suggests that, even when fully COVID-19-vaccinated, older adults and those with chronic conditions were at increased risk of pneumonia during the dominance of the Omicron sublineages BA.1.1 and BA.2.

Decreased survival in children inpatients with COVID-19 and antibiotic prescription.

BACKGROUND: The empirical prescription of antibiotics to inpatients with Coronavirus Disease 2019 (COVID-19) is frequent despite uncommon bacterial coinfections. Current knowledge of the effect of antibiotics on the survival of hospitalized children with COVID-19 is limited. OBJECTIVE: To characterize the survival experience of children with laboratory-positive COVID-19 in whom antibiotics were prescribed at hospital admission. METHODS: A retrospective cohort study was conducted in Mexico, with children hospitalized due to COVID-19 from March 2020 to December 2021. Data from 1601 patients were analyzed using the Kaplan-Meier method and the log-rank test. We computed hazard ratios (HR) and 95% confidence intervals (CI) to evaluate the effect of the analyzed exposures on disease outcomes. RESULTS: Antibiotics were prescribed to 13.2% ([Formula: see text] = 211) of enrolled children and a higher mortality rate [14.9 (95% CI 10.1-19.8) vs. 8.3 (95% CI 6.8-9.8)] per 1000 person-days, [Formula: see text] < 0.001) was found among them. At any given cut-off, survival functions were lower in antibiotic-positive inpatients ([Formula: see text] < 0.001). In the multiple model, antibiotic prescription was associated with a 50% increase in the risk of fatal outcome (HR = 1.50, 95% CI 1.01-2.22). A longer interval between illness onset and healthcare-seeking and pneumonia at hospital admission was associated with a poorer prognosis. CONCLUSIONS: Our results suggest that antibiotic prescription in children hospitalized due to COVID-19 is associated with decreased survival. If later replicated, these findings highlight the need for rational antibiotics in these patients.

Empirical Antibiotic Prescribing in Adult COVID-19 Inpatients over Two Years in Mexico.

Background and Objectives: Empirical antibiotic prescribing in patients with coronavirus disease 2019 (COVID-19) has been common even though bacterial coinfections are infrequent. The overuse of antibacterial agents may accelerate the antibiotic resistance crisis. We aimed to evaluate factors predicting empirical antibiotic prescribing to adult COVID-19 inpatients over 2 years (March 2020-February 2021) in Mexico. Materials and Methods: A cross-sectional analysis of a nationwide cohort study was conducted. Hospitalized adults due to laboratory-confirmed COVID-19 were included (n = 214,171). Odds ratios (OR) and 95% confidence intervals (CI), computed by using logistic regression models, were used to evaluate factors predicting empirical antibiotic prescribing. Results: The overall frequency of antibiotic usage was 25.3%. In multiple analysis, the highest risk of antibiotic prescription was documented among patients with pneumonia at hospital admission (OR = 2.20, 95% CI 2.16-2.25). Male patients, those with chronic comorbidities (namely obesity and chronic kidney disease) and longer interval days from symptoms onset to healthcare seeking, were also more likely to receive these drugs. We also documented that, per each elapsed week during the study period, the odds of receiving antibiotic therapy decreased by about 2% (OR = 0.98, 95% CI 0.97-0.99). Conclusion: Our study identified COVID-19 populations at increased risk of receiving empirical antibiotic therapy during the first two years of the pandemic.

Independent risk factors of COVID-19 pneumonia in vaccinated Mexican adults.

OBJECTIVES: To evaluate host factors associated with the risk of coronavirus disease 2019 (COVID-19) pneumonia in vaccinated adults. METHODS: A cohort study was conducted in Mexico, and data from 1607 adults with confirmed illness, with a positive history of COVID-19 vaccination, were analyzed. Risk ratios (RR) and 95% confidence intervals (CI) were computed as a measure of the significance of the associations between putative risk factors and the prevalence of COVID-19 pneumonia in vaccinated subjects. RESULTS: The overall risk of pneumonia was 1.98 per 1000 person-days. In the multiple regression analysis, older subjects, those with a history of smoking (current), obesity, and type 2 diabetes mellitus were at increased risk of pneumonia. CONCLUSIONS: Our results suggest that the effectiveness of COVID-19 vaccines may be reduced in a subset of adults who are older aged, smokers, obese, or have type 2 diabetes mellitus.

Impact on the Nutritional and Functional Status of Older Mexican Adults in the Absence of Recreational Activities due to COVID-19: A Longitudinal Study From 2018 to 2021.

A longitudinal study, from 2018 to 2021, identified impacts on the nutritional and functional status of older adults when face-to-face activities at a social assistance center in Mexico were suspended due to the COVID-19 pandemic. A total of 71 older adults were evaluated at three different periods: 18 months prior, three months before the pandemic, and 12 months after the onset of the pandemic. Seventy-one older adults completed follow up. Anthropometric measurements, dietary intake, physical tests, and health screening for malnutrition, dependence, and physical frailty, were evaluated. There was a significant decrease in lean body mass and body water in the older adults assessed, in addition to a significant reduction in the frailty scale and gait speed. Finally, a significant reduction in ingested energy and several nutrients such as protein, and carbohydrates, was found, yet an increase in sugar and cholesterol intake was noted.

COVID-19 vaccines provide better protection against related pneumonia than previous symptomatic infection.

OBJECTIVES: To compare, in a real-world scenario, the protective effect of vaccination and previous laboratory-confirmed symptomatic infection on the risk of COVID-19 pneumonia. METHODS: A retrospective study was conducted and 46,998 adults with laboratory-confirmed COVID-19 were enrolled. Risk ratios (RRs) and 95% confidence intervals (CIs) were used to evaluate the effect of the evaluated exposures on the risk of pneumonia. RESULTS: In multiple analysis and after adjusting by reinfection status, vaccinated participants were at reduced risk of developing pneumonia (RR = 0.974, 95% CI 0.965-0.983). The association of having had a previous infection was not significant (RR = 1.001, 95% CI 0.969-1.034). CONCLUSION: Our results suggest, and if later replicated, that COVID-19 vaccines provide better protection against pneumonia than previous symptomatic infections. Therefore, offering vaccination to all eligible subjects despite past COVID-19 infections might be relevant to reducing the pandemic-related burden.

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.

SARS-CoV-2 outbreak in a nursing home after vaccination with BNT162b2: A role for the quantification of circulating antibodies.

We describe an outbreak of SARS-CoV-2 (B.1.351) in a nursing home. At the outbreak onset 96% of residents and 76% of HCW had received two doses of BNT162b2. Twenty-eight residents (28/53) and six HCW (6/33) were infected. Infected residents had lower levels of anti-S antibodies compared to those who were not infected (157 vs 552 U/mL). Among 50 residents with available serological status, nineteen (19/25) with serum concentration < 300 U/mL and seven (7/25) with concentration > 300 U/mL acquired SARS-CoV-2 (RR 2.7 [95 %CI 1.4-5.3]). The quantification of circulating antibodies could be useful in detecting people with an impaired immune response who are at high risk of acquiring and spreading SARS-CoV-2.

Multicenter clinical evaluation of a novel transcription-mediated amplification assay for SARS-CoV-2 molecular testing.

INTRODUCTION: The onset and spread of COVID-19 pandemic has forced clinical laboratories to rapidly expand testing capacity for SARS-CoV-2. This study evaluates the clinical performance of the TMA Procleix SARS-CoV-2 assay in comparison to the RT-PCR assay AllplexTM SARS-CoV-2 for the qualitative detection of SARS-CoV-2 RNA. METHODS: Between November 2020 and February 2021, 610 upper-respiratory specimens received for routine SARS-CoV-2 molecular testing were prospectively collected and selected at the Hospital Universitari Vall d'Hebron and the Hospital Universitari Bellvitge in Barcelona, Spain. All samples were processed in parallel with the TMA and the RT-PCR assays, and results were compared. Discrepancies were retested by an additional RT-PCR method and the clinical history of these patients was reviewed. RESULTS: Overall, the level of concordance between both assays was 92.0% (κ, 0.772). Most discordant results (36/38, 94.7%) corresponded to samples testing positive with the TMA assay and negative with the RT-PCR method. Of these discrepant cases, most (28/36, 77.8%) were finally classified as confirmed or probable SARS-CoV-2 cases according to the discrepant analysis. CONCLUSION: In conclusion, the TMA Procleix SARS-CoV-2 assay performed well for the qualitative detection of SARS-CoV-2 RNA in a multisite clinical setting. This novel TMA assay demonstrated a greater sensitivity in comparison to RT-PCR methods for the molecular detection of SARS-CoV-2. This higher sensitivity but also the qualitative feature of this detection of SARS-CoV-2 should be considered when making testing algorithm decisions.

Multicenter clinical evaluation of a novel transcription-mediated amplification assay for SARS-CoV-2 molecular testing

Introducción: El inicio y la expansión de la pandemia por COVID-19 han forzado a los laboratorios clínicos a ampliar rápidamente la capacidad de detección de SARS-CoV-2. Evaluamos el rendimiento clínico del ensayo de TMA Procleix SARS-CoV-2 en comparación con ensayo de RT-PCR AllplexTM SARS-CoV-2 para la detección cualitativa de ARN de SARS-CoV-2. Métodos: Entre noviembre de 2020 y febrero de 2021, se seleccionaron prospectivamente 610 muestras del tracto respiratorio superior recibidas de rutina en el Hospital Universitario Vall d´Hebron y el Hospital Universitario de Bellvitge en Barcelona, España, para el diagnóstico molecular de SARS-CoV-2. Todas las muestras fueron procesadas en paralelo con los ensayos de TMA y RT-PCR, y se compararon los resultados. Las discrepancias se estudiaron por un método adicional de RT-PCR y se revisaron las historias clínicas de los pacientes. Resultados: En general, la concordancia entre ambos ensayos fue del 92.0% (κ, 0.772). La mayoría de casos discrepantes (36/38, 94.7%) correspondían a muestras positivas con el ensayo de TMA y negativas con el método de RT-PCR. De estos, la mayoría (28/36, 77,8%) fueron finalmente clasificados como casos confirmados o probables de SARS-CoV-2 de acuerdo al análisis de discrepantes. Conclusión: El ensayo de TMA Procleix SARS-CoV-2 funcionó bien para la detección cualitativa de ARN de SARS-CoV-2 en un entorno clínico multicéntrico. Este ensayo TMA demostró una mayor sensibilidad en comparación con métodos de RT-PCR para la detección molecular de SARS-CoV-2. Esta mayor sensibilidad, pero también el carácter cualitativo de esta detección de SARS-CoV-2, se deben considerar en el diagnóstico de la infección.

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.

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.