Performance of amplicon and capture based next-generation sequencing approaches for the epidemiological surveillance of Omicron SARS-CoV-2 and other variants of concern.

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.

The Modification of the Illumina® CovidSeq™ Workflow for RSV Genomic Surveillance: The Genetic Variability of RSV during the 2022-2023 Season in Northwest Spain.

There is growing interest in the molecular surveillance of the Respiratory Syncytial Virus and the monitorization of emerging mutations that could impair the efficacy of antiviral prophylaxis and treatments. A simple, scalable protocol for viral nucleic acid enrichment could improve the surveillance of RSV. We developed a protocol for RSV-A and B amplification based on the Illumina CovidSeq workflow using an RSV primer panel. A total of 135 viral genomes were sequenced from nasopharyngeal samples through the optimization steps of this panel, while an additional 15 samples were used to test the final version. Full coverage of the G gene and over 95% of the coverage of the F gene, the target of the available RSV antivirals or monoclonal antibodies, were obtained. The F:K68N mutation, associated with decreased nirsevimab activity, was detected in our facility. Additionally, phylogenetic analysis showed several sublineages in the 2022-2023 influenza season in Europe. Our protocol allows for a simple and scalable simultaneous amplification of the RSV-A and B whole genome, increasing the yield of RSV sequencing and reducing costs. Its application would allow the world to be ready for the detection of arising mutations in relation to the widespread use of nirsevimab for RSV prevention.

Proof of concept of the potential of a machine learning algorithm to extract new information from conventional SARS-CoV-2 rRT-PCR results.

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.

Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletion.

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.

In vivo monitoring of Lactiplantibacillus plantarum in the nasal and vaginal mucosa using infrared fluorescence.

Lactic acid bacteria (LAB) of the genus Lactiplantibacillus have been explored as potential mucosal vaccine vectors due to their ability to elicit an immune response against expressed foreign antigens and to their safety. However, tools for monitoring LAB distribution and persistence at the mucosal surfaces are needed. Here, we characterize Lactiplantibacillus plantarum bacteria expressing the infrared fluorescent protein IRFP713 for exploring their in vivo distribution in the mucosa and potential use as a mucosal vaccine vector. This bacterial species is commonly used as a vaginal probiotic and was recently found to have a niche in the human nose. Three different fluorescent L. plantarum strains were obtained using the nisin-inducible pNZRK-IRFP713 plasmid which contains the nisRK genes, showing stable and constitutive expression of IRFP713 in vitro. One of these strains was further monitored in BALB/c mice using near-infrared fluorescence, indicating successful colonization of the nasal and vaginal mucosae for up to 72 h. This study thus provides a tool for the in vivo spatiotemporal monitoring of lactiplantibacilli, allowing non-invasive bacterial detection in these mucosal sites. KEY POINTS: • Stable and constitutive expression of the IRFP713 protein was obtained in different L. plantarum strains. • IRFP713+ L. plantarum 3.12.1 was monitored in vivo using near-infrared fluorescence. • Residence times observed after intranasal and vaginal inoculation were 24-72 h.

Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.

A detailed understanding of how and when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help infer who infected whom. However, the effectiveness of the genomic approach in this context depends on both (high enough) mutation and (low enough) transmission rates. Today, the level of resolution that we can obtain when describing SARS-CoV-2 outbreaks using just genomic information alone remains unclear. In order to answer this question, we sequenced forty-nine SARS-CoV-2 patient samples from ten local clusters in NW Spain for which partial epidemiological information was available and inferred transmission history using genomic variants. Importantly, we obtained high-quality genomic data, sequencing each sample twice and using unique barcodes to exclude cross-sample contamination. Phylogenetic and cluster analyses showed that consensus genomes were generally sufficient to discriminate among independent transmission clusters. However, levels of intrahost variation were low, which prevented in most cases the unambiguous identification of direct transmission events. After filtering out recurrent variants across clusters, the genomic data were generally compatible with the epidemiological information but did not support specific transmission events over possible alternatives. We estimated the effective transmission bottleneck size to be one to two viral particles for sample pairs whose donor-recipient relationship was likely. Our analyses suggest that intrahost genomic variation in SARS-CoV-2 might be generally limited and that homoplasy and recurrent errors complicate identifying shared intrahost variants. Reliable reconstruction of direct SARS-CoV-2 transmission based solely on genomic data seems hindered by a slow mutation rate, potential convergent events, and technical artifacts. Detailed contact tracing seems essential in most cases to study SARS-CoV-2 transmission at high resolution.

Aptamer Sandwich Assay for the Detection of SARS-CoV-2 Spike Protein Antigen.

The novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged at the end of 2019, resulting in the ongoing COVID-19 pandemic. The high transmissibility of the virus and the substantial number of asymptomatic individuals have led to an exponential rise in infections worldwide, urgently requiring global containment strategies. Reverse transcription-polymerase chain reaction is the gold standard for the detection of SARS-CoV-2 infections. Antigen tests, targeting the spike (S) or nucleocapsid (N) viral proteins, are considered as complementary tools. Despite their shortcomings in terms of sensitivity and specificity, antigen tests could be deployed for the detection of potentially contagious individuals with high viral loads. In this work, we sought to develop a sandwich aptamer-based assay for the detection of the S protein of SARS-CoV-2. A detailed study on the binding properties of aptamers to the receptor-binding domain of the S protein in search of aptamer pairs forming a sandwich is presented. Screening of aptamer pairs and optimization of assay conditions led to the development of a laboratory-based sandwich assay able to detect 21 ng/mL (270 pM) of the protein with negligible cross-reactivity with the other known human coronaviruses. The detection of 375 pg of the protein in viral transport medium demonstrates the compatibility of the assay with clinical specimens. Finally, successful detection of the S antigen in nasopharyngeal swab samples collected from suspected patients further establishes the suitability of the assay for screening purposes as a complementary tool to assist in the control of the pandemic.

Clínica diferencial en niños infectados por SARS-CoV-2, trazabilidad de contactos y rentabilidad de pruebas diagnósticas: estudio observacional transversal / Differential clinic in children infected by SARS-CoV-2, traceability of contacts and cost-effectiveness of diagnostic tests: Cross-sectional observational study

INTRODUCCIÓN: Ante la posible coexistencia de la infección por el virus SARS-CoV-2 con otras infecciones estacionales, se pretende identificar síntomas diferenciales. Se ha estudiado el papel de los niños en el contagio intrafamiliar y la sensibilidad de la reacción en cadena de la polimerasa con transcriptasa inversa (RT-PCR) en un área con baja transmisión comunitaria. MATERIAL Y MÉTODOS: Estudio observacional transversal. Pacientes entre 0-15 años estudiados por técnica RT-PCR por sospecha clínica de infección por virus SARS-CoV-2 en los meses de marzo-mayo del 2020. Encuesta sobre síntomas y contactos. Determinación de anticuerpos anti-SARS-CoV-2 al menos 21 días después del test RT- PCR. RESULTADOS: Se incluyó a 126 pacientes, 33 con infección confirmada y edad media 8,4 años (IC del 95%, 6,8-10,0) superior a los no infectados. La fiebre fue el síntoma más común y con mayor sensibilidad. Las diferencias encontradas fueron una mayor frecuencia de anosmia (p = 0,029) y cefalea (p = 0,009) entre los niños infectados con una especificidad del 96,7 y el 81,5% respectivamente. No hubo diferencias en la duración de los síntomas. Un 81,8% de los infectados fue probablemente contagiado en el núcleo familiar, en un 85,2% por un progenitor que trabajaba fuera del hogar. La sensibilidad de RT-PCR fue 70,9% y su valor predictivo negativo 91,1%. CONCLUSIONES: El cuadro clínico es inespecífico y los síntomas más específicos difíciles de detectar en niños más pequeños. Los niños tuvieron un papel reducido en la transmisión intrafamiliar. La sensibilidad de la RT-PCR podría estar relacionada con una menor contagiosidad infantil tras una semana de infección

INTRODUCTION: Given the possible coexistence of infection by the SARS-CoV-2 with other seasonal infections, the aim is to identify differential symptoms. I know has studied the role of children in intrafamily contagion and the sensitivity of reverse transcriptase polymerase chain reaction (RT-PCR) in an area with low community transmission. MATERIAL AND METHODS: Cross-sectional observational study. Patients between 0-15 years studied by RT-PCR technique due to clinical suspicion of infection by SARS-CoV-2 virus in the months of March-May 2020. Survey on symptoms and contacts. Determination of Anti-SARS-CoV-2 antibodies at least 21 days after the RT-PCR test. RESULTS: 126 patients were included, 33 with confirmed infection and age mean 8.4 years (95% CI 6.8-10,5) higher than not infected. Fever was the most common and with greater sensitivity. The differences found were a greater frequency of anosmia (P = 0.029) and headache (P = .009) among children infected with a specificity of 96.7% and 81.5% respectively. There were no differences in the duration of the symptoms. 81.8% of those infected were probably infected in the nucleus 85.2% by a parent who worked outside the home. The sensitivity of RT-PCR was 70.9% and its negative predictive value 91.1%. CONCLUSIONS: The clinical picture is nonspecific and the symptoms more specific difficult to detect in younger children. Children had a reduced role in the intrafamily transmission. The sensitivity of RT-PCR could be related to a less contagiousness in children after one week of infection

Differential clinic in children infected by SARS-CoV-2, traceability of contacts and cost-effectiveness of diagnostic tests: Cross-sectional observational study.

INTRODUCTION: Given the possible coexistence of infection by the SARS-CoV-2 with other seasonal infections, the aim is to identify differential symptoms. The role of children in intrafamily contagion and the sensitivity of reverse transcriptase polymerase chain reaction (RT-PCR) in an area with low community transmission has been studied. MATERIAL AND METHODS: Cross-sectional observational study. Patients between 0-15 years studied by RT-PCR technique due to clinical suspicion of infection by SARS-CoV-2 virus in the months of March-May 2020. Survey on symptoms and contacts. Determination of Anti-SARS-CoV-2 antibodies at least 21 days after the RT-PCR test. RESULTS: 126 patients were included, 33 with confirmed infection and age mean 8.4 years (95% CI 6.8-10.5) higher than not infected. Fever was the most common and with greater sensitivity. The differences found were a greater frequency of anosmia (P = .029) and headache (P = .009) among children infected with a specificity of 96.7% and 81.5% respectively. There were no differences in the duration of the symptoms. 81.8% of those infected were probably infected in the nucleus 85.2% by a parent who worked outside the home. The sensitivity of RT-PCR was 70.9% and its negative predictive value 91.1%. CONCLUSIONS: The clinical picture is nonspecific and the symptoms more specific difficult to detect in younger children. Children had a reduced role in the intrafamily transmission. The sensitivity of RT-PCR could be related to a less contagiousness in children after one week of infection.

INTRODUCCIÓN: Ante la posible coexistencia de la infección por el virus SARS-CoV-2 con otras infecciones estacionales, se pretende identificar síntomas diferenciales. Se ha estudiado el papel de los niños en el contagio intrafamiliar y la sensibilidad de la reacción en cadena de la polimerasa con transcriptasa inversa (RT-PCR) en un área con baja transmisión comunitaria. MATERIAL Y MÉTODOS: Estudio observacional transversal. Pacientes entre 0-15 años estudiados por técnica RT-PCR por sospecha clínica de infección por virus SARS-CoV-2 en los meses de marzo-mayo del 2020. Encuesta sobre síntomas y contactos. Determinación de anticuerpos anti-SARS-CoV-2 al menos 21 días después del test RT- PCR. RESULTADOS: Se incluyó a 126 pacientes, 33 con infección confirmada y edad media 8,4 años (IC del 95%, 6,8-10,0) superior a los no infectados. La fiebre fue el síntoma más común y con mayor sensibilidad. Las diferencias encontradas fueron una mayor frecuencia de anosmia (p = 0,029) y cefalea (p = 0,009) entre los niños infectados con una especificidad del 96,7 y el 81,5% respectivamente. No hubo diferencias en la duración de los síntomas.Un 81,8% de los infectados fue probablemente contagiado en el núcleo familiar, en un 85,2% por un progenitor que trabajaba fuera del hogar. La sensibilidad de RT-PCR fue 70,9% y su valor predictivo negativo 91,1%. CONCLUSIONES: El cuadro clínico es inespecífico y los síntomas más específicos difíciles de detectar en niños más pequeños. Los niños tuvieron un papel reducido en la transmisión intrafamiliar. La sensibilidad de la RT-PCR podría estar relacionada con una menor contagiosidad infantil tras una semana de infección.

[Differential clinic in children infected by SARS-CoV-2, traceability of contacts and cost-effectiveness of diagnostic tests: Cross-sectional observational study]. / Clínica diferencial en niños infectados por SARS-CoV-2, trazabilidad de contactos y rentabilidad de pruebas diagnósticas: estudio observacional transversal.

INTRODUCTION: Given the possible coexistence of infection by the SARS-CoV-2 with other seasonal infections, the aim is to identify differential symptoms. There has been studied the role of children in intrafamily contagion and the sensitivity of reverse transcriptase polymerase chain reaction (RT-PCR) in an area with low community transmission. MATERIAL AND METHODS: Cross-sectional observational study. Patients between 0-15 years studied by RT-PCR technique due to clinical suspicion of infection by SARS-CoV-2 virus in the months of March-May 2020. Survey on symptoms and contacts. Determination of Anti-SARS-CoV-2 antibodies at least 21 days after the RT-PCR test. RESULTS: 126 patients were included, 33 with confirmed infection and mean age 8.4 years (95% CI 6.8-10,5), age higher than not infected. Fever was the most common symptom and with greater sensitivity. The differences found were a greater frequency of anosmia (P=0.029) and headache (P=.009) among children infected with a specificity of 96.7% and 81.5% respectively. There were no differences in the duration of the symptoms. 81.8% of those infected were probably infected in the family nucleus, 85.2% by a parent who worked outside the home. The sensitivity of RT-PCR was 70.9% and its negative predictive value 91.1%. CONCLUSIONS: The clinical picture is nonspecific and the more specific symptoms difficult to detect in younger children. Children had a reduced role in the intrafamily transmission. The sensitivity of RT-PCR could be related to a less contagiousness in children after one week of infection.

Pooling for SARS-CoV-2 control in care institutions.

BACKGROUND: Workers and residents in Care Homes are considered at special risk for the acquisition of SARS-CoV-2 infection, due to the infectivity and high mortality rate in the case of residents, compared to other containment areas. The role of presymptomatic people in transmission has been shown to be important and the early detection of these people is critical for the control of new outbreaks. Pooling strategies have proven to preserve SARS-CoV-2 testing resources. The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people. METHODS: A total of 25,386 Nasopharyngeal swab samples from the total of the residents and workers at Care Homes in Galicia (March to May 2020) were individually tested using RT-PCR. Prevalence and quantification cycle (Cq) value distribution of positives was calculated. Besides, 26 pools of 20 samples and 14 pools of 5 samples were tested using RT-PCR as well (1 positive/pool). Pooling proof of concept was performed in two populations with 1.7 and 2% prevalence. RESULTS: Distribution of SARS-CoV-2 infection at Care Homes was uneven (0-60%). As the virus circulation global rate was low in our area (3.32%), the number of people at risk of acquiring the infection continues to be very high. In this work, we have successfully demonstrated that pooling of different groups of samples at low prevalence clusters, can be done with a small average delay on Cq values (5 and 2.85 cycles for pools of 20 and 5 samples, respectively). CONCLUSIONS: A new screening system with guaranteed protection is required for small clusters, previously covered with individual testing. Our proposal for Care Homes, once prevalence zero is achieved, would include successive rounds of testing using a pooling solution for transmission control preserving testing resources. Scale-up of this method may be of utility to confront larger clusters to avoid the viral circulation and keeping them operative.

Identificación bacteriana directamente del hemocultivo mediante una técnica rápida de espectrometría de masas Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight / Bacterial identification from blood cultures by a rapid Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight mass spectrometry technique

Introducción La espectrometría de masas Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight (MALDI-TOF) es una técnica rápida y fiable de identificación bacteriana. Métodos Se evalúa un método para identificación directa del hemocultivo fácil, rápido de realizar y de bajo coste. Resultados El porcentaje de identificaciones con (..) (AU)

Introduction Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight (MALDI-TOF) Mass Spectrometry is rapid and accurate for the bacterial identification. Methods We have evaluated a less laborious and less time consuming method for microorganism identification directly from positive blood cultures. Results When we considered the scores (..) (AU)

[Bacterial identification from blood cultures by a rapid Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight mass spectrometry technique]. / Identificación bacteriana directamente del hemocultivo mediante una técnica rápida de espectrometría de masas Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight.

INTRODUCTION: Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight (MALDI-TOF) Mass Spectrometry is rapid and accurate for the bacterial identification. METHODS: We have evaluated a less laborious and less time consuming method for microorganism identification directly from positive blood cultures. RESULTS: When we considered the scores ≥1.7 and ≥1.4 for acceptable identification of species and genus, the percentage of identification was 77.5% and 93.9%, respectively. CONCLUSIONS: This method is reliable, rapid and cost-effective for implementation in routine use in clinical microbiology laboratories.