Reinfection rate and disease severity of the BA.5 Omicron SARS-CoV-2 lineage compared to previously circulating variants of concern in the Canary Islands (Spain).

ABSTRACTThe emergence of the Omicron SARS-CoV-2 variant of concern has changed the COVID-19 scenario as this variant is characterized by high transmissibility and immune evasion ability. To evaluate the impact of this variant on the Canary Islands (Spain) population, we determined the reinfection rates and disease severity associated with the Omicron sublineages and the previously circulating variants of concern. We performed a retrospective observational study on 21,745 SARS-CoV-2 viral genomes collected from December 2020 to July 2022 in the Canary Islands (Spain). We compared the reinfection rates between lineages using pairwise proportion and Fisher's exact tests. To assess disease severity, we studied the association of Alpha, Delta, BA.1, BA.2, BA.5, and other risk factors on 28-day hospital mortality using logistic regression and Cox proportional hazard models. We observed 127 bona fide reinfection cases throughout the study period. We found that BA.5 had the highest reinfection rate compared to other lineages (vs. Delta p = 2.89 × 10-25; vs. BA.1 p = 5.17 × 10-11; vs. BA.2 p = 0.002). Among the 1,094 hospitalized patients, multivariate logistic regression showed that Alpha (Odds Ratio [OR] = 0.45, 95% Confidence Interval [CI] = 0.23-0.87, p = 0.02), BA.2 (OR = 0.38, 95% CI = 0.22-0.63, p = 1.91 × 10-4), and BA.5 (OR = 0.30, 95% CI = 0.16-0.55, p = 1.05 × 10-4) had lower 28-day hospital mortality compared to Delta. These results were confirmed by using Cox proportional hazard models. Omicron lineages, and in particular BA.5, were associated with higher reinfection rates and lower disease severity (28-day hospital mortality) than previously circulating variants of concern.

Bioinformatic approaches to draft the viral genome sequence of Canary Islands cases related to the multicountry mpox virus 2022-outbreak.

On July 23, 2022, monkeypox disease (mpox) was declared a Public Emergency of International Concern (PHEIC) by the World Health Organization (WHO) due to a multicountry outbreak. In Europe, several cases of mpox virus (MPXV) infection related to this outbreak were detected in the Canary Islands (Spain). Here we describe the combination of viral DNA sequencing and bioinformatic approaches, including methods for de novo genome assembly and short- and long-read technologies, used to reconstruct the first MPXV genome isolated in the Canary Islands on the 31st of May 2022 from a male adult patient with mild symptoms. The same sequencing and bioinformatic approaches were then validated with three other positive cases of MPXV infection from the same mpox outbreak. We obtained the best results using a reference-based approach with short reads, evidencing 46-79 nucleotide variants against viral sequences from the 2018-2019 mpox outbreak and placing the viral sequences in the new B.1 sublineage of clade IIb of the MPXV classification. This study of MPXV demonstrates the potential of metagenomics sequencing for rapid and precise pathogen identification.

Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.

Tracing the trajectories of SARS-CoV-2 variants of concern between December 2020 and September 2021 in the Canary Islands (Spain).

Several variants of concern (VOCs) explain most of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic waves in Europe. We aimed to dissect the spread of the SARS-CoV-2 VOCs in the Canary Islands (Spain) between December 2020 and September 2021 at a micro-geographical level. We sequenced the viral genome of 8,224 respiratory samples collected in the archipelago. We observed that Alpha (B.1.1.7) and Delta (B.1.617.2 and sublineages) were ubiquitously present in the islands, while Beta (B.1.351) and Gamma (P.1/P.1.1) had a heterogeneous distribution and were responsible for fewer and more controlled outbreaks. This work represents the largest effort for viral genomic surveillance in the Canary Islands so far, helping the public health bodies in decision-making throughout the pandemic.

Increasing SARS-CoV-2 RT-qPCR testing capacity by sample pooling.

OBJECTIVES: Limited testing capacity has characterized the ongoing coronavirus disease 2019 (COVID-19) pandemic in Spain, hampering timely control of outbreaks and opportunities to reduce the escalation of community transmission. This study investigated the potential to use sample pooling, followed by one-step retrotranscription and real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) to increase testing capacity for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). METHODS: Various pool sizes (five, 10 and 15 samples) were evaluated prior to RNA extraction followed by standard RT-qPCR for the diagnosis of COVID-19. The pool size achieving reproducible results with individual sample testing was subsequently used to assess nasopharyngeal samples in a tertiary hospital in August 2020. RESULTS: A pool size of five samples had higher sensitivity compared with pool sizes of 10 and 15 samples, showing a mean cycle threshold (Ct) shift of 3.5 [standard deviation (SD) 2.2] between the pooled test and positive samples in the pool. Next, a pool size of five was used to test a total of 895 pools (4475 prospective samples) using two different RT-qPCR kits. The Real Accurate Quadruplex corona-plus PCR Kit (PathoFinder) reported the lowest mean Ct shift [2.2 (SD 2.4)] between the pool and individual samples. This strategy enables detection of individual positive samples in positive pools with Ct of 16.7-39.4. CONCLUSIONS: Grouping samples into pools of five for RT-qPCR resulted in an increase in SARS-CoV-2 testing capacity with minimal loss of sensitivity compared with testing each sample individually.

Identificación y sensibilidad rápida de cocos grampositivos en hemocultivos BacT/ALERT mediante inoculación directa en el sistema Vitek 2 / Rapid identification and susceptibility testing of Gram-positive cocci in BacT/ALERT blood cultures by direct inoculation into the Vitek 2 system

Introducción: La información precoz del resultado del hemocultivo al clínico permite mejorar el pronóstico y reducir la mortalidad del paciente con sepsis. Para contribuir a ello, se realizó un estudio para la identificación y sensibilidad de cultivos de sangre por inoculación directa en el sistema Vitek 2. Material y Métodos: Se estudiaron los hemocultivos de 57 pacientes con bacteriemias monomicrobianas por cocos grampositivos. Se añadió saponina al líquido de botellas del sistema BacT/ALERT® 3D antes de la inoculación en los paneles del sistema Vitek 2. Las muestras fueron examinadas asimismo por el método estándar, consistente en la realización de las pruebas a partir del crecimiento en placa de los hemocultivos positivos. Resultados: La comparación de los resultados obtenidos entre el método estándar y el método directo reveló una concordancia en la identificación del 82% y en la sensibilidad del 97% del total de antibióticos analizados. La tasa de errores muy graves fue tan solo del 0,5%, de errores graves del 0,5% y de errores menores del 2% en comparación con el método estándar. Conclusión: Estos datos sugieren que la adición de saponina al líquido de las botellas del sistema BacT/ALERT® 3D antes de la inoculación en los paneles Vitek 2 conduce a una identificación y estudio de sensibilidad rápido y fiable de cocos grampositivos en muestras de sangre. Comparando con el método estándar, el método directo anticiparía en un día la obtención de resultados(AU)

Introduction: To provide the clinician with early information about blood culture results allows a better prognosis and a reduced mortality rate of the patient with sepsis. In order to contribute to this aim, we performed a study for the identification and susceptibility profiling of positive blood cultures by direct inoculation into the automated Vitek 2 system. Materials and Methods: Blood cultures of 57 patients with monomicrobial bacteriaemia due to gram-positive cocci were evaluated. Addition of saponin to the fluid from blood culture bottles was performed prior to the inoculation of Vitek 2 system cards. The same samples were also examined with the standard method starting from agar plate grown subcultures. Results: Comparison between the results obtained with the standard method and the direct method revealed that 82% of the samples were correctly identified and that 97% of the isolates showed a concordant antimicrobial susceptibility profile for all drugs tested. Compared to the standard method, the very major error rate of the direct method was just 0.5%, the major error rate was 0.5%, and the minor error rate was 2%. Conclusion: These data suggest that addition of saponin to the fluid from blood culture bottles of the BacT/ALERT® 3D before inoculation of the appropriate Vitek 2 cards leads to the rapid and reliable identification and susceptibility profiling of gram-positive cocci in blood samples. Compared to the standard method, the direct method would reduce turnaround time by at least 24 hours (AU)

Simultaneous PCR detection of ica cluster and methicillin and mupirocin resistance genes in catheter-isolated Staphylococcus.

Recent data show that more than 50% of catheter-associated bloodstream infections are caused by staphylococci. Staphylococcal infections produced by intercellular-adhesion cluster (ica) carriers can be even more problematic due to the presence of methicillin and mupirocin resistance genes. In the present study, a multiplex PCR protocol that allows the simultaneous identification of staphylococci and detection of both the ica and methicillin and/or mupirocin resistance genes was developed. Furthermore, the method allows differential detection of the ica locus from Staphylococcus aureus and Staphylococcus epidermidis.

Simultaneous PCR detection of ica cluster and methicillin and mupirocin resistance genes in catheter-isolated Staphylococcus / Detección simultánea del cluster ica y de los genes de resistencia a meticilina y mupiricina en Staphylococcus aislados de catéteres

Recent data show that more than 50% of catheter-associated bloodstream infections are caused by staphylococci. Staphylococcal infections produced by intercellular-adhesion cluster (ica) carriers can be even more problematic due to the presence of methicillin and mupirocin resistance genes. In the present study, a multiplex PCR protocol that allows the simultaneous identification of staphylococci and detection of both the ica and methicillin and/or mupirocin resistance genes was developed. Furthermore, the method allows differential detection of the ica locus from Staphylococcus aureus and Staphylococcus epidermidis (AU)

Estudios recientes han demostrado que más del 50 por ciento de las septicemias asociadas al uso de catéteres están causadas por estafilococos. Las infecciones estafilococales producidas por cepas portadoras del operón de adhesión intercelular (ica) pueden agravarse por la presencia de genes de resistencia a la meticilina y/o a la mupirocina. Hemos desarrollado un protocolo de PCR múltiple que permite, simultáneamente, identificar estafilococos y detectar la presencia de ica y de los genes de resistencia a la meticilina y/o a la mupirocina. Además, dicho método permite la detección diferencial del locus ica de Staphylococcus aureus y/o S. epidermidis (AU)