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Objetivo. Conocer el impacto de los niveles de polen de gramíneas en la utilización de las consultas de atención primaria por episodios de rinitis alérgica y asma en Santiago de Compostela durante un año.Método. Se realizó un estudio ecológico descriptivo. Se comparó la variable dicotómica “sobreconsulta” (semanas con un número de consultas mayor al esperado) con los niveles de polen. Además, se correlacionaron los episodios de asma o rinitis alérgica con los recuentos de polen, los contaminantes atmosféricos y las condiciones atmosféricas. Las variables que mostraron asociación se analizaron mediante regresión logística.Resultados. Las sobreconsultas por rinitis alérgica se asocian significativamente con los niveles altos de gramíneas. Existe fuerte asociación directa del número de episodios de rinitis alérgica con el recuento de polen y con los niveles de ozono. Los niveles de polen influyen significativamente en la existencia de sobreconsultas pero no existe relación entre estas y los niveles de ozono. Existe un número significativamente mayor de consultas por asma cuando los niveles de polen de gramíneas son altos. Se observa fuerte asociación directa de los episodios de asma con el polen y con los niveles de ozono. Estos influyen significativamente en la existencia de sobreconsultas pero no existe relación entre estas y los niveles de gramíneas.Conclusiones. El nivel de polen de gramíneas parece aumentar la probabilidad de sobreconsultas en atención primaria por rinitis alérgica. No existe evidencia de que los niveles de polen de gramíneas aumenten el número de consultas en atención primaria por asma.Objective. To find out the impact of grass pollen levels on the use of primary care consultations for episodes of allergic rhinitis and asthma in Santiago de Compostela throughout a year.Method. A descriptive ecological study was carried out. The dichotomous variable “overconsultation” (weeks with a higher than expected number of consultations) was compared with pollen levels. In addition, episodes of asthma or allergic rhinitis were correlated with pollen counts, air pollutants and atmospheric conditions. The variables that were found to be associated were analysed by logistic regression.Results. “Overconsultation” caused by allergic rhinitis was significantly associated with high levels of grass pollen. A strong direct association was found between the number of episodes of allergic rhinitis and both pollen count and ozone levels. Pollen levels significantly influenced the existence of “overconsultation”, but no relationship was found between “overconsultation” and ozone levels. There was a significantly higher number of visits for asthma when grass pollen levels were high. A strong direct association was observed between episodes of asthma and both pollen count and ozone levels. These two factors significantly influenced the existence of “overconsultation”, but no relationship was found between “overconsultation” and grass pollen levels.Conclusions. The grass pollen level appears to increase the likelihood of primary care “overconsultation” for allergic rhinitis. However, no evidence was found that high grass pollen levels increase the number of primary care consultations caused by asthma.Objetivo: Conhecer o impacto dos níveis de pólen de gramíneas na utilização de consultas de cuidados primários de saúde por episódios de rinite alérgica e asma, em Santiago de Compostela durante um ano.Método: Foi realizado um estudo ecológico descritivo. Comparou-se a variável dicotómica sobreconsulta (semanas com um número de consultas superior ao esperado) com os níveis de pólen. Também, se correlacionaram os episódios de asma ou rinite alérgica com a contagem de pólen, os contaminantes atmosféricos e as condições atmosféricas. As variáveis que comprovaram associação foram analisadas por regressão logística.Resultados: As sobreconsultas por rinite alérgica estão significativamente associadas com os altos níveis de gramíneas. Existe uma forte associação direta do número de episódios de rinite alérgica com a contagem de pólen e os níveis de ozono. Os níveis de pólen influenciam significativamente a existência de sobreconsultas mas não existe relação entre estas e os níveis de ozono. Existe um número significativamente maior de consultas para a asma quando os níveis de pólen de gramíneas são elevados. Observa-se uma forte associação direta dos episódios de asma com os níveis de pólen e com os níveis de ozono. Estes influenciam significativamente a existência de sobreconsultas mas não existe nenhuma relação entre estas e os níveis e gramíneas.Conclusões: O nível de pólen de gramíneas parece aumentar a probabilidade de sobreconsultas por rinite alérgica, nos cuidados primários de saúde. Não existe evidência de que os níveis de pólen de gramíneas aumentem o número de consultas, por asma, nos cuidados primários de saúde.

Objetivo. Conocer el impacto de los niveles de polen de gramíneas en la utilización de las consultas de atención primaria por episodios de rinitis alérgica y asma en Santiago de Compostela durante un año. Método. Se realizó un estudio ecológico descriptivo. Se comparó la variable dicotómica “sobreconsulta” (semanas con un número de consultas mayor al esperado) con los niveles de polen. Además, se correlacionaron los episodios de asma o rinitis alérgica con los recuentos de polen, los contaminantes atmosféricos y las condiciones atmosféricas. Las variables que mostraron asociación se analizaron mediante regresión logística. Resultados. Las sobreconsultas por rinitis alérgica se asocian significativamente con los niveles altos de gramíneas. Existe fuerte asociación directa del número de episodios de rinitis alérgica con el recuento de polen y con los niveles de ozono. Los niveles de polen influyen significativamente en la existencia de sobreconsultas pero no existe relación entre estas y los niveles de ozono. Existe un número significativamente mayor de consultas por asma cuando los niveles de polen de gramíneas son altos. Se observa fuerte asociación directa de los episodios de asma con el polen y con los niveles de ozono. Estos influyen significativamente en la existencia de sobreconsultas pero no existe relación entre estas y los niveles de gramíneas. Conclusiones. El nivel de polen de gramíneas parece aumentar la probabilidad de sobreconsultas en atención primaria por rinitis alérgica. No existe evidencia de que los niveles de polen de gramíneas aumenten el número de consultas en atención primaria por asma.

Objetivo. Conocer el impacto de los niveles de polen de gramíneas en la utilización de las consultas de atención primaria por episodios de rinitis alérgica y asma en Santiago de Compostela durante un año. Método. Se realizó un estudio ecológico descriptivo. Se comparó la variable dicotómica “sobreconsulta” (semanas con un número de consultas mayor al esperado) con los niveles de polen. Además, se correlacionaron los episodios de asma o rinitis alérgica con los recuentos de polen, los contaminantes atmosféricos y las condiciones atmosféricas. Las variables que mostraron asociación se analizaron mediante regresión logística. Resultados. Las sobreconsultas por rinitis alérgica se asocian significativamente con los niveles altos de gramíneas. Existe fuerte asociación directa del número de episodios de rinitis alérgica con el recuento de polen y con los niveles de ozono. Los niveles de polen influyen significativamente en la existencia de sobreconsultas pero no existe relación entre estas y los niveles de ozono. Existe un número significativamente mayor de consultas por asma cuando los niveles de polen de gramíneas son altos. Se observa fuerte asociación directa de los episodios de asma con el polen y con los niveles de ozono. Estos influyen significativamente en la existencia de sobreconsultas pero no existe relación entre estas y los niveles de gramíneas. Conclusiones. El nivel de polen de gramíneas parece aumentar la probabilidad de sobreconsultas en atención primaria por rinitis alérgica. No existe evidencia de que los niveles de polen de gramíneas aumenten el número de consultas en atención primaria por asma.

BackgroundThe development of new large-scale saliva pooling detection strategies can significantly enhance testing capacity and frequency for asymptomatic individuals, which is crucial for containing SARS-CoV-2. ObjectiveThis study aims to implement and scale-up a SARS-CoV-2 screening method using pooled saliva samples to control the virus in critical areas and assess its effectiveness in detecting asymptomatic infections. MethodsBetween August 2020 and February 2022, our laboratory received a total of 928,357 samples. Participants collected at least 1 mL of saliva using a self-sampling kit and registered their samples via a smartphone app. All samples were directly processed using AutoMate 2550 for preanalytical steps and then transferred to Microlab STAR, managed with the HAMILTON Pooling software for pooling. The standard pool preset size was 20 samples but was adjusted to 5 when the prevalence exceeded 2% in any group. Real-time polymerase chain reaction (RT-PCR) was conducted using the Allplex SARS-CoV-2 Assay until July 2021, followed by the Allplex SARS-CoV-2 FluA/FluB/RSV assay for the remainder of the study period. ResultsOf the 928,357 samples received, 887,926 (95.64%) were fully processed into 56,126 pools. Of these pools, 4863 tested positive, detecting 5720 asymptomatic infections. This allowed for a comprehensive analysis of pooling’s impact on RT-PCR sensitivity and false-negative rate (FNR), including data on positive samples per pool (PPP). We defined Ctref as the minimum cycle threshold (Ct) of each data set from a sample or pool and compared these Ctref results from pooled samples with those of the individual tests (ΔCtP). We then examined their deviation from the expected offset due to dilution [ΔΔCtP = ΔCtP – log2]. In this work, the ΔCtP and ΔΔCtP were 2.23 versus 3.33 and –0.89 versus 0.23, respectively, comparing global results with results for pools with 1 positive sample per pool. Therefore, depending on the number of genes used in the test and the size of the pool, we can evaluate the FNR and effective sensitivity (1 – FNR) of the test configuration. In our scenario, with a maximum of 20 samples per pool and 3 target genes, statistical observations indicated an effective sensitivity exceeding 99%. From an economic perspective, the focus is on pooling efficiency, measured by the effective number of persons that can be tested with 1 test, referred to as persons per test (PPT). In this study, the global PPT was 8.66, reflecting savings of over 20 million euros (US $22 million) based on our reagent prices. ConclusionsOur results demonstrate that, as expected, pooling reduces the sensitivity of RT-PCR. However, with the appropriate pool size and the use of multiple target genes, effective sensitivity can remain above 99%. Saliva pooling may be a valuable tool for screening and surveillance in asymptomatic individuals and can aid in controlling SARS-CoV-2 transmission. Further studies are needed to assess the effectiveness of these strategies for SARS-CoV-2 and their application to other microorganisms or biomarkers detected by PCR.

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been and remains one of the major challenges modern society has faced thus far. Over the past few months, large amounts of information have been collected that are only now beginning to be assimilated. In the present work, the existence of residual information in the massive numbers of rRT-PCRs that tested positive out of the almost half a million tests that were performed during the pandemic is investigated. This residual information is believed to be highly related to a pattern in the number of cycles that are necessary to detect positive samples as such. Thus, a database of more than 20,000 positive samples was collected, and two supervised classification algorithms (a support vector machine and a neural network) were trained to temporally locate each sample based solely and exclusively on the number of cycles determined in the rRT-PCR of each individual. Overall, this study suggests that there is valuable residual information in the rRT-PCR positive samples that can be used to identify patterns in the development of the SARS-CoV-2 pandemic. The successful application of supervised classification algorithms to detect these patterns demonstrates the potential of machine learning techniques to aid in understanding the spread of the virus and its variants.

To control the SARS-CoV-2 pandemic, healthcare systems have focused on ramping up their capacity for epidemiological surveillance through viral whole genome sequencing. In this paper, we tested the performance of two protocols of SARS-CoV-2 nucleic acid enrichment, an amplicon enrichment using different versions of the ARTIC primer panel and a hybrid-capture method using KAPA RNA Hypercap. We focused on the challenge of the Omicron variant sequencing, the advantages of automated library preparation and the influence of the bioinformatic analysis in the final consensus sequence. All 94 samples were sequenced using Illumina iSeq 100 and analysed with two bioinformatic pipelines: a custom-made pipeline and an Illumina-owned pipeline. We were unsuccessful in sequencing six samples using the capture enrichment due to low reads. On the other hand, amplicon dropout and mispriming caused the loss of mutation G21987A and the erroneous addition of mutation T15521A respectively using amplicon enrichment. Overall, we found high sequence agreement regardless of method of enrichment, bioinformatic pipeline or the use of automation for library preparation in eight different SARS-CoV-2 variants. Automation and the use of a simple app for bioinformatic analysis can simplify the genotyping process, making it available for more diagnostic facilities and increasing global vigilance.

Abstract Background: SARS-CoV-2 variant tracking is key to the genomic surveillance of the COVID-19 pandemic. While next-generation sequencing (NGS) is commonly used for variant determination, it is expensive and time-consuming. Variant-specific PCR (vsPCR) is a faster, cheaper method that detects specific mutations that are considered variant-defining. These tests usually rely on specific amplification when a mutation is present or a specific melting temperature peak after amplification. Case presentation: A discrepant result between vsPCR and NGS was found in seventeen SARS-CoV-2 samples from Galicia, Spain. A cluster of BA.1 Omicron SARS-CoV-2 variant showed a BA.2-like melting temperature pattern due to a point mutation (C21772T) downstream the deletion of the spike amino acids 69/70. As the 69/70 deletion is widely used for differentiation between BA.1 and BA.2 by vsPCR, C21772T can cause BA.1 samples to be misinterpreted as BA.2. Over a thousand BA.1 sequences in the EpiCoV database contain this mutation. Conclusions: To our knowledge, this is the first case of a point mutation causing a vsPCR algorithm to misclassify BA.1 samples as BA.2. This is an example of how mutations in the probe target area of vsPCR tests based on melting curve analysis can lead to variant misclassification. NGS confirmation of vsPCR results is relevant for the accuracy of the epidemiological surveillance. In order to overcome the possible impact of novel mutations, diagnostic tools must be constantly updated.