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[Background] The involvement of SARS-CoV-2 antibodies in mediating immunopathogenetic events in COVID-19 patients has been suggested. By using several experimental approaches, we investigated the potential association between SARS-CoV-2 IgGs recognizing the spike (S) protein receptor-binding domain (RBD), neutralizing antibodies (NtAb) targeting S, and COVID-19 severity., [Patients and methods] This unicenter, retrospective, observational study included 51 hospitalized patients (24 at the intensive care unit; ICU). A total of 93 sera from these patients collected at different time points from the onset of symptoms were analyzed. SARS-CoV-2 RBD IgGs were quantitated by ELISA and NtAb50 titers were measured in a GFP reporterbased pseudotyped virus platform. Demographic and clinical data, complete blood counts, as well as serum levels of ferritin, Dimer-D, C reactive protein (CRP), lactose dehydrogenase (LDH), and interleukin-6 (IL-6) were retrieved from clinical charts., [Results] The overall correlation between levels of both antibody measurements was good (Rho = 0.82; P = 0 < 0.001). SARS-CoV-2 RBD IgG and NtAb50 levels in sera collected up to day 30 after the onset of symptoms were comparable between ICU and non-ICU patients (P=>0.1). Four ICU patients died; two of these achieved NtAb50 titers ≥1/160 while the other two exhibited a 1/80 titer. Very weak (Rho=>0.0–<0.2) or weak (Rho=>0.2–<0.4) correlations were observed between anti-RBD IgGs, NtAb50, and serum levels pro-inflammatory biomarkers., [Conclusions] The data presented herein do not support an association between SARS-CoV-2 RBD IgG or NtAb50 levels and COVID-19 severity.

Background: The involvement of SARS-CoV-2 antibodies in mediating immunopathogenetic events in COVID-19 patients has been suggested. By using several experimental approaches, we investigated the potential association between SARS-CoV-2 IgGs recognizing the spike (S) protein receptor-binding domain (RBD), neutralizing antibodies (NtAb) targeting S, and COVID-19 severity. Patients and Methods: This unicenter, retrospective, observational study included 51 hospitalized patients (24 at the intensive care unit; ICU). A total of 93 sera from these patients collected at different time points from the onset of symptoms were analyzed. SARS-CoV-2 RBD IgGs were quantitated by ELISA and NtAb50 titers were measured in a GFP reporter-based pseudotyped virus platform. Demographic and clinical data, complete blood counts, as well as serum levels of ferritin, Dimer-D, C reactive protein (CRP), lactose dehydrogenase (LDH), and interleukin-6 (IL-6) were retrieved from clinical charts. Results: The overall correlation between levels of both antibody measurements was good (Rho=0.79; P=0<0.001). SARS-CoV-2 RBD IgG and NtAb50 levels in sera collected up to day 30 after the onset of symptoms were comparable between ICU and non-ICU patients (P=>0.1). The percentage of patients who exhibited high NtAb50 titers (≥160) was similar (P=0.20) in ICU (79%) and non-ICU (60%) patients. Four ICU patients died; two of these achieved NtAb50 titers ≥1/160 while the other two exhibited a 1/80 titer. Very weak (Rho=>0.0-<0.2) or weak (Rho=>0.2-<0.4) correlations were observed between anti-RBD IgGs, NtAb50, and serum levels pro-inflammatory biomarkers. Conclusions: The data presented herein do not support an association between SARS-CoV-2 RBD IgG or NtAb50 levels and COVID-19 severity

The aim of the present study was to perform the molecular epidemiology of rotaviruses and noroviruses detected in sewage samples from a large wastewater facility from the city of Valencia, Spain. A total of 46 sewage samples were collected over a one-year period (September 2016 to September 2017). Norovirus and rotavirus were detected and quantified by RT-qPCR, genotyped by semi-nested RT-PCR and further characterized by sequencing and phylogenetic analyses. Noroviruses and rotaviruses were widely distributed in sewage samples (69.6% for norovirus GI, 76.0% norovirus GII, and 71.7% rotaviruses) and viral loads varied from 4.33 to 5.75 log PCRU/L for norovirus GI, 4.69 to 6.95 log PCRU/L for norovirus GII, and 4.08 to 6.92 log PCRU/L for rotavirus. Overall, 87.5% (28/32) of GI noroviruses could not be genotyped, 6.25% (2/32) of the samples contained GI.2 genotype, and another 6.25% (2/32) were positive for GI.4 genotype. The most common genotype of GII noroviruses was GII.2 (40%, 14/35), followed by GII.6 (8.6%, 3/35) and GII.17 (5.7%, 2/35) while the remaining GII strains could not be typed (45.7%, 16/35). Rotavirus VP4 genotype P[8] was the only one found in 19 out of 33 rotavirus-positive samples (57.7%). G2 was the most prevalent rotavirus VP7 genotype (15.2%, 5/33) followed by G3, G9, and G12, with two positive samples for each genotype (6.1%, 2/33). In one sample both G1 and G2 genotypes were detected simultaneously (3%). The results presented here show that the surveillance of noroviruses and rotaviruses in sewage is useful for the study of their transmission in the population and their molecular epidemiology.

Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.

The host microbiota has emerged a third player in interactions between hosts and viral pathogens. This opens new possibilities to use different tools to modulate the intestinal microbial composition, aimed at reducing the risk of or treating viral enteric infections.

Rotavirus (RV) and norovirus (NoV) are the major etiological agents of viral acute gastroenteritis worldwide. Host genetic factors, the histo-blood group antigens (HBGA), are associated with RV and NoV susceptibility and recent findings additionally point to HBGA as a factor modulating the intestinal microbial composition. In vitro and in vivo experiments in animal models established that the microbiota enhances RV and NoV infection, uncovering a triangular interplay between RV and NoV, host glycobiology, and the intestinal microbiota that ultimately influences viral infectivity. Studies on the microbiota composition in individuals displaying different RV and NoV susceptibilities allowed the identification of potential bacterial biomarkers, although mechanistic data on the virus–host–microbiota relation are still needed. The identification of the bacterial and HBGA interactions that are exploited by RV and NoV would place the intestinal microbiota as a new target for alternative therapies aimed at preventing and treating viral gastroenteritis.

Aged-green tea extract (GTE) is known to reduce the infectivity of hepatitis A virus (HAV) and murine norovirus (MNV), a human norovirus surrogate, in vitro and in washing solutions. Initially, the effect of aged-GTE was evaluated on virus like particles (VLPs) of human norovirus (HuNoV) genogroup I (GI) by a porcine gastric mucine (PGM)-enzyme-linked immunosorbent assay (ELISA) and transmission electron microscopy (TEM), and on HuNoV GI suspensions by an in situ capture-RT-qPCR method, suggesting that HuNoVs are very sensitive to aged-GTE treatment at 37 °C. Moreover, the potential application of aged-GTE was evaluated using model foods and simulated gastric conditions. Then, aged-GTE samples prepared in orange juice, apple juice, horchata, and milk, respectively, were individually mixed with each virus and incubated overnight at 37 °C. Aged-GTE at 5 mg/ml in apple juice reduced MNV infectivity to undetectable levels and from 1.0 to 1.8 log in milk, horchata and orange juice. Aged-GTE at 5 mg/ml in orange juice, apple juice, horchata and milk reduced HAV infectivity by 1.2, 2.1, 1.5, and 1.7 log, respectively. Additionally, aged-GTE at 5 mg/ml in simulated intestinal fluid reduced MNV titers to undetectable levels and reduced HAV infectivity by ca. 2.0 log. The results show a potential for aged-GTE as a suitable natural option for preventive strategies for foodborne viral diseases.

Aim: To improve the efficacy of intercalating dyes to distinguishing between infectious and inactivated hepatitis A virus (HAV) in food. Methods and Results: Different intercalating dyes were evaluated for the discrimination between infectious and thermally inactivated HAV suspensions combining with the RT‐qPCR proposed in the ISO 15216. Among them, PMAxx was the best dye in removing the RT‐qPCR signal from inactivated HAV. Applied to lettuce and spinach, PMAxx–Triton pretreatment resulted in complete removal of the RT‐qPCR signal from inactivated HAV. Likewise, this study demonstrates that this pretreatment is suitable for the discrimination of inactivated HAV in shellfish without further sample dilution. In mussels and oysters, the developed viability RT‐qPCR method reduced the signal of inactivated HAV between 1·7 and 2·2 logs at high inoculation level, and signal was completely removed at low inoculation level. Conclusions: This study showed that the use of PMAxx is an important improvement to assess HAV infectivity by RT‐qPCR. It was shown that PMAxx–Triton pretreatment is suitable for the analysis of infectious HAV in complex food samples such as vegetables and shellfish. Significance and Impact of the Study: The PMAxx–Triton pretreatment can be easily incorporated to the ISO norm for infectious virus detection.

Host genetic factors, such as histo-blood group antigens (HBGAs), are associated with susceptibility to norovirus (NoV) and rotavirus (RV) infections. Recent advances point to the gut microbiome as a key player necessary for a viral pathogen to cause infection. In vitro NoV attachment to host cells and resulting infections have been linked to interactions with certain bacterial types in the gut microbiota. We investigated the relationship between host genotype, gut microbiota, and viral infections. Saliva and fecal samples from 35 adult volunteers were analysed for secretor status genotype, the gut microbiota composition by 16S rRNA gene sequencing, and salivary IgA titers to NoV and RV. Higher levels of IgA against NoV and RV were related to secretor-positive status. No significant differences were found between the FUT2 genotype groups, although the multivariate analysis showed a significant impact of host genotype on specific viral susceptibilities in the microbiome composition. A specific link was found between the abundance of certain bacterial groups, such as Faecalibacterium and Ruminococcus spp., and lower IgA titers against NoV and RV. As a conclusion, we can state that there is a link between host genetics, gut microbiota, and susceptibility to viral infections in humans.

[EN] Human milk contains a large number of oligosaccharides, either free or bound to proteins and lipids, and their physiological role is mostly unknown. These oligosaccharides are resistant to host gastrointestinal digestion and therefore, a significant proportion reaches the infant colon, where they can be substrates for the resident microbiota. Lacto-N-biose (LNB) and galacto-N-biose (GNB) are the core type-1 sugar structures in HMO and mucin glycoproteins, respectively. They are fermented by species of the genus Bifidobacterium, but, there is no data about their utilization by the genus Lactobacillus. There is also no information for this genus about the metabolism of N-acetyllactosamine (LacNAc), which constitutes the type-2 sugar core in HMO, and lacto-N-triose, which forms part of the structure of lacto-N-tetraose, one of the most abundant HMOs. Lactobacillus casei is a lactic acid bacteria isolated from several environmental niches such as milk, meat, and reproductive and gastrointestinal tracts of animals and humans. In addition, some strains are used as starter cultures in the dairy industry and also as probiotics. The capability of L. casei species to survive in the gastrointestinal tract would depend in part of its ability to metabolize the available carbohydrates. In this Thesis we have shown that this strain is able to grow using LNB, GBN, LacNAc, and lacto-N-triose as carbon sources, and we have characterized the corresponding metabolic pathways. L. casei contains a gene cluster, gnbREFGBCDA, involved in the metabolism of GNB, LNB and also N-acetylgalactosamine. Transcriptional analysis showed that the gnb operon is regulated by substrate-specific induction mediated by the transcriptional repressor GnbR. Upstream of the gnb operon, there are two genes, bnaG and manA, encoding a b-N-acetylglucosaminidase precursor and a mannose-6P isomerase. It has been shown that BnaG is an extracellular wall-attached enzyme and that it is involved on lacto-N-triose m, [ES] La leche humana contiene una gran cantidad de oligosacáridos, libres o unidos a lípidos y proteínas, y su función fisiológica es mayoritariamente desconocida. Estos oligosacáridos son resistentes a la digestión y una gran proporción llega al intestino del lactante, donde pueden ser substratos para la microbiota. La lacto-N-biosa (LNB) y la galacto-N-biosa (GNB) son las estructuras tipo-1 que forman el núcleo de los oligosacáridos de la leche humana (OLH) y de las glicoproteínas de la mucina, respectivamente. Los dos azúcares son fermentados por especies del género Bifidobacterium, pero no hay datos acerca de su utilización por el género Lactobacillus. Tampoco hay información para este género acerca del metabolismo de la N-acetil-lactosamina (LacNAc), que constituye la cadena de azúcar tipo-2 en los OLH, y de la lacto-N-triosa, que forma parte de la estructura de la lacto-N-tetraosa, uno de los OLH más abundantes. La capacidad de Lactobacillus casei, de prevalecer en el sistema gastrointestinal dependerá en parte de su versatilidad metabólica para utilizar los carbohidratos disponibles. En la presente Tesis Doctoral se ha demostrado que la cepa L. casei BL23 se puede cultivar en presencia de LNB, GBN, LacNAc, y lacto-N-triosa como fuentes de carbono. En el metabolismo de la LNB, GNB y también N-acetilgalactosamina (GalNAc) está implicado el operon gnbREFGBCDA. Análisis transcripcionales demostraron que el operon gnb está regulado por inducción del substrato mediada por el represor transcripcional GnbR. Por encima del operon gnb, hay dos genes bnaG y manA, que codifican para el precursor de una b-N-acetilglucosaminidasa y una manosa-6P isomerasa. Se ha demostrado que BnaG es un enzima extracelular unido a la pared celular y que está implicado en el metabolismo de la lacto-N-triosa. El enzima ManA está implicada en el metabolismo de la manosa presente en el disacárido 3'-N-acetilglucosaminil-manosa, el cual es también una fuente de carbono para L. casei BL23. Por, [CA] La llet humana conté una gran quantitat d'oligosacàrids, lliures o conjugats amb lípids o proteïnes i la seua funció fisiològica és majoritàriament desconeguda. Aquests oligosacàrids són resistents a la digestió i una gran proporció arriba a l'intestí dels lactants, on poden ser substrat per a la microbiota. La lacto-N-biosa (LNB) i la galacto-N-biosa (GNB) són les estructures tipus-1 que conformen el nucli dels oligosacàrids de la llet humana (OLH) i de les glicoproteïnes de la mucina, respectivament. Els dos sucres són fermentats per espècies del gènere Bifidobacterium, però no existeixen dades sobre l'ús pel gènere Lactobacillus. Tampoc no hi ha informació per a aquest gènere sobre el metabolisme de la N-acetil-lactosamina (LacNAc), que cosntitueix la cadena de sucre tipus-2 als OLH i de la lacto-N-triosa, que forma part de l'estructura de als OLH tipus-1 i 2. La capacitat de L. casei, una bactèria làctica aïllada de múltiples nínxols ambientals, de prevaler al sistema gastrointestinal dependrà en part de la seua versatilitat metabòlica per a utilitzar els carbohidrats disponibles. A la present tesi doctoral s'ha demostrat que la soca L. casei BL23 es pot cultivar en presència de LNB, GBN, LacNAc i lacto-N-triosa com a fonts de carboni. Al metabolisme de la LNB, GNB i també de la N-acetilgalactosamina (GalNAc) està implicat l'operó gnbREFGBCDA. Anàlisi transcripcionals demostraren que l'operó gnb està regulat per inducció del substrat mitjançant el repressor transcripcional GnbR. A sobre de l'operó gnb, hi ha dos gens bnaG i manA, que codifiquen per al precursor d'una b-N-acetilglucosaminidasa i una manosa-6P isomerasa. S'ha demostrat que BnaG és un enzim extracel·lular unit a la paret cel·lular i que està implicat en el metabolisme de la lacto-N-triosa. Aquesta és hidrolitzada per BnaG en lactosa i N-acetilglucosamina (GlcNAc). L'enzim ManA està implicada en el metabolisme de la manosa present al disacàrid 3-N-acetilglucosaminil-manosa, el qual també repres