Draft Genome Sequence of the New Pathogen for Bivalve Larvae \u3cem\u3eVibrio bivalvicida\u3c/em\u3e

Vibrio bivalvicida is a novel pathogen of bivalve larvae responsible for recent vibriosis outbreaks affecting shellfish hatcheries. Here, we announce the draft genome sequence of V. bivalvicida 605 and describe potential virulence factors

Making waves : wastewater-based epidemiology for COVID-19 - approaches and challenges for surveillance and prediction

The presence of SARS-CoV-2 in the feces of infected patients and wastewater has drawn attention, not only to the possibility of fecal-oral transmission but also to the use of wastewater as an epidemiological tool. The COVID-19 pandemic has highlighted problems in evaluating the epidemiological scope of the disease using classical surveillance approaches, due to a lack of diagnostic capacity, and their application to only a small proportion of the population. As in previous pandemics, statistics, particularly the proportion of the population infected, are believed to be widely underestimated. Furthermore, analysis of only clinical samples cannot predict outbreaks in a timely manner or easily capture asymptomatic carriers. Threfore, community-scale surveillance, including wastewater-based epidemiology, can bridge the broader community and the clinic, becoming a valuable indirect epidemiological prediction tool for SARS-CoV-2 and other pandemic viruses. This article summarizes current knowledge and discusses the critical factors for implementing wastewater-based epidemiology of COVID-19

Identification of emerging hazards in mussels by the Galician Emerging Food Safety Risks Network (RISEGAL). A first approach

Emerging risk identification is a priority for the European Food Safety Authority (EFSA). The goal of the Galician Emerging Food Safety Risks Network (RISEGAL) is the identification of emerging risks in foods produced and commercialized in Galicia (northwest Spain) in order to propose prevention plans and mitigation strategies. In this work, RISEGAL applied a systematic approach for the identification of emerging food safety risks potentially affecting bivalve shellfish. First, a comprehensive review of scientific databases was carried out to identify hazards most quoted as emerging in bivalves in the period 2016–2018. Then, identified hazards were semiquantitatively assessed by a panel of food safety experts, who scored them accordingly with the five evaluation criteria proposed by EFSA: novelty, soundness, imminence, scale, and severity. Scores determined that perfluorinated compounds, antimicrobial resistance, Vibrio parahaemolyticus, hepatitis E virus (HEV), and antimicrobial residues are the emerging hazards that are considered most imminent and severe and that could cause safety problems of the highest scale in the bivalve value chain by the majority of the experts consulted (75%). Finally, in a preliminary way, an exploratory study carried out in the Galician Rías highlighted the presence of HEV in mussels cultivated in class B production areas.info:eu-repo/semantics/publishedVersio

World Society for Virology first international conference: Tackling global virus epidemics

This communication summarizes the presentations given at the 1st international conference of the World Society for Virology (WSV) held virtually during 16–18 June 2021, under the theme of tackling global viral epidemics. The purpose of this biennial meeting is to foster international collaborations and address important viral epidemics in different hosts. The first day included two sessions exclusively on SARS-CoV-2 and COVID-19. The other two days included one plenary and three parallel sessions each. Last not least, 16 sessions covered 140 on-demand submitted talks. In total, 270 scientists from 49 countries attended the meeting, including 40 invited keynote speakers.Peer reviewe

Detection and quantification of Sapovirus in bivalve molluscs from Galicia (NW Spain).

Sapovirus (SaV), etiologic agent of human gastroenteritis, is a RNA virus from the Caliciviridae family, mostly detected in Asia. It has been classified by the U.S. Environmental Protection Agency as an emergent human pathogen with risk for public health in aquatic environments. Bivalves, due to their filtrating feeding, concentrate viral particles presented in seawater, and it has been demonstrated that the bioaccumulated viruses can resist depuration treatments to which bivalves are submitted. In addition, the traditional way of bivalve consumption increases the probability of infection, making them a high risk food [1]. The main objective of this work was to detect and quantify SaV in bivalves from Galicia, Northwestern Spain. A total of 168 samples, including mussels (Mytilus galloprovincialis), clams (Venerupis philippinarum and V. decussata) and cockles (Cerastoderma edule) were obtained during a period of 18 months from two Galician Rías (Ría of Ares-Betanzos and Ría of Vigo, respectively at North and South of the region). Samples consisted into 10 or 20 individuals, which were dissected under aseptic conditions to obtain their digestive tissue. The viral RNA was extracted using Nucleospin RNA Virus Kit (Macherey-Nagel; Dürem, Germany). Subsequently, viral detection and quantification by real time RT-PCR was performed using Platinum Quantitative RT-PCR Thermoscript One-Step System Kit (Invitrogen, Saint Aubin, France), according to the recently developed standard method ISO/TS 15216:2013. Primers SaV124F and SaV124R, and probe SaV124TP designed to amplify human genogroups I, II and IV were used [2]. Both through viral RNA extraction and viral detection and quantification, internal controls were used to avoid false positive or negative results, and the possible presence of inhibitors. SaV was detected in 30 of the 168 samples (17,85%). There was no significant difference between the two Rías in terms of detections, although it was observed a seasonality increment of positive samples from November 2011 until April 2012 in both Rías due to the rainy season and the decrease of seawater temperature. Total quantification ranged between 103 and 105 copies of viral RNA/g of digestive tissue (c/g), being mussels the specie with lower main quantification (3,1 x 104 c/g) and clams the species with higher medium rates (2,0 x 105 c/g). This represents the first study out of Japan in which human Sapovirus was detected and quantified into human food intended for consumption

Prevalence of Calicivirus and Hepatitis A virus in bivalve molluscs from Galicia

From a virological standpoint, shellfish safety continues to be a sanitary challenge. Bivalves are one of the most common vehicles of viral illness and the adoption of viral standards into European Union legislation is being considered. In this study, a 18-months survey were conducted in ten harvesting areas from two estuaries in Galicia (NW of Spain), the most important bivalve production area in Europe. Hepatitis A virus (HAV) and human norovirus (NoV), including genogroups I (GI) and II (GII) were quantified by reverse transcription-real time PCR (RT-qPCR), according to the recently developed standard method ISO/TS 15216:2013. Four bivalve species were studied, including wild and cultured mussels (Mytilus galloprovincialis), clams (Venerupis philippinarum and V. decussata) and cockles (Cerastoderma edule). Overall, 54.8% of the analysed samples were contaminated by at least one of the studied viruses, being detected the simultaneous presence of two or three viruses in 11.3% of the samples. NoV GI was the most prevalent virus (32.1%) followed by NoV GII (25.6%) and HAV (9.5%). The results showed the presence of viral contamination throughout the year in both areas and all species of molluscs. However, diverse patterns of prevalence and seasonality were observed among different viruses. HAV was detected only between March and June 2012. NoV GI was detected intermittently throughout the study period, with significant peaks in the spring and summer of 2011. NoV GII showed a clear seasonality to during the cold months by 2011; however, a significant peak was detected in the spring of 2012

Detection and quantification of Hepatitis A and E vírus in wastewater from Tunisia <br />

Enteric viruses contaminating the environment represent a danger for public health. They are present quite frequently in wastewater and transmitted to humans by the fecal-oral route. The aim of our study was to detect hepatitis A and E viruses (HAV and HEV) in wastewater samples collected from 6 different Tunisian sewage treatment plants during thirteen months. A total of 325 samples were analyzed by real time reverse transcriptase-polymerase chain reaction (RT-qPCR). Results showed the presence of HAV contamination in 36% of the samples. Msaken (58.9%) and SidiBouzid (51.85%) regions showed the highest contamination, followed by Ouerdanine (35.2%), Kasserine (38.9%), Sbitla (23.6%) and El Jem (7.7%) regions. Contamination with HEV was significantly lower (4.9%), being detected HEV positive samples in SidiBouzid (9.25%), El Jem (5.76%), Kasserine (3.7%), Ouerdanine (3.7%), Sbitla (3.63%) and Msaken (3.6%) regions. On the another hand, our research found that, in entry points, 54% of wastewater samples were contaminated with HAV, whereas, in exit points a percentage of 17.9% was found. HAV values were also analyzed by plant showing percentages of positive samples in entry points between 15.38% and 85.18%, while in exit points values ranged from 3.57% to 57.14%. HAV was detected in exit points of all plants except El Jem region. Concerning HEV, the average percentage of contaminated wastewater at entry was 6.75% which was reduced until 3.1% at exit. By plant, HEV positive samples were detected only in three plants, Kasserine, El Jem and Sidi Bouzid at rates of 3.7% 3.84% and 11.11%, respectively. These results support previous findings on the stability of enteric viruses in wastewater and the inefficiency of the procedures employed in the sewage treatment plants. On the other hand, molecular procedures proved to be very sensitive to detect viral genomes in this type of samples. In conclusion, wastewater treatments employed in Tunisian plants can reduce the number of viral particles of hepatitis A and E but do not remove all of them, which constitute a potential risk for human health

Analysis of the scallop microbiota by means of 16S rRNA gene pyrosequencing

Bivalve molluscs, due to its filter-feeding mechanism, have an abundant associated bacterial microbiota composed of a large number of species of different genera. The knowledge about the composition of the microbiota associated with bivalve molluscs is based, mostly, on techniques of cultivation of microorganisms, but also on DGGE methods. However, it is estimated that less than 1% of the bacteria are culturable with current methods, which lead to an underestimation of the microbial diversity. On the other hand, DGGE methodology has a limited resolution due to the low number of DNA fragments obtained as representative of a microbial community. The introduction of new molecular approaches allowed the improvement of the knowledge about bacterial communities present in a sample [1]. In recent years, new molecular techniques known as Next Generation Sequencing (NGS) have been developed, based on high- throughput sequencing [2]. In this study, we present the analysis of the microbiota associated to reared scallop gonads before and after spawning by pyrosequencing of the 16S rRNA gene. After the DNA extraction of the samples, amplification was performed using a set of degenerate primers with low stringency conditions. Pyrosequencing of samples was carried out using the sequencer 454 GLX Titanium Plus (Roche). The data obtained was further subjected to bioinformatics analysis using Galaxy and UCHIME program and the Ribosomal Database Project. Rarefaction curves were obtained, the composition of the bacterial community was analysed after the taxonomic assignment, and the total composition of the bacterial communities of the samples were compared using the principal coordinates analysis (PCoA) by FastUnifrac tool [3]. Pyrosequencing of the samples resulted in a total of 18520 sequences (3000 per sample, approximately) with an average length of 325 bp (base pairs). The taxonomic assignment of sequences allowed the identification to the genus level, being observed a large bacterial diversity with over 110 genera. The most prevalent genera in the samples were Hydrotalea, Acinetobacter, Delftia, Sediminibacter and Pseudomonas, among others. Differences in the microbial communities were observed among the samples, and the PCoA analysis allowed their separation by means on their gender and if they proceed from sampling before or after the spawning. Nevertheless, the rarefaction curves obtained for each sample failed to reach a saturation phase, indicating that more sequencing effort would be necessary

<i>Sinobacterium norvegicum</i> sp . nov., a new species isolated from scallop (<i>Pecten maximus</i>).

The family Oceanospirillaceae (Garrity et al., 2005) includes 18 genera, 11 of which were described in the last 10 years (Arahal et al., 2007). Members of this family are motile and exclusive from aquatic environments. As part of a study on the microbiota associated to Great scallop (Pecten maximus) and its rearing system performed in a hatchery in Bergen (Norway), seven strains: 3CM4T(= CECT 8267T; = CAIM 1884T) 3CH4, 2CH8, 2SH3, 1CH5, 1CH6 and 1SH4 (= CECT 8268; = CAIM 1885) were isolated from broodstock gonads. These strains are aerobic, oxidase and catalase positive and they do not grow in TCBS. Isolates form small (less than 1 mm) pale brown pigmentated colonies on marine agar. They are halophiles and their temperature range for growth is 4 to 20ºC. Cells are Gram-negative, non-motile long rods, measuring 0.2-0.4 μm in diameter and 5-20 μm in length. With oxidative metabolism, the isolates do not ferment carbohydrates. The results of analysis of DNA-DNA hybridization confirmed that these isolates constitute a new and differentiated cluster within the genus Sinobacterium. The predominant fatty acids were C16: 0, C16: 1 ω7c/C16: 1 ω6c and C18: 1 ω7c. The G + C content of the new isolates is 52.2 ± 1 mol%. Based on phenotypic and phylogenetic characteristics, the seven isolates represent a new species for which the name Sinobacterium norvegicum sp. nov. is proposed, with strain 3CM4T (= CECT 8267T = CAIM 1884T) as the type strain

The pan-genome of Splendidus clade species in the family Vibrionaceae : Insights into evolution, adaptation, and pathogenicity

The Splendidus clade is the largest clade in Vibrionaceae, and its members are often related to mortality of marine animals with huge economic losses. The molecular bases of their pathogenicity and virulence, however, remain largely unknown. In particular, the complete genome sequences of the Splendidus clade species are rarely registered, which is one of the obstacles to predict core and/or unique genes responsible for their adaptation and pathogenicity, and to perform a fine scale meta-transcriptome during bacterial infection to their hosts. In this study, we obtained the complete genomes of all type strains in the Splendidus clade and revealed that (1) different genome sizes (4.4-5.9 Mb) with V. lentus the biggest and most of them had several big plasmids, likely because of the different features on mobilome elements; (2) the Splendidus clade consists of 19 species except V. cortegadensis, and 3 sub-clades (SC) were defined with the 15 most closely related members as SC1; (3) different carbohydrate degradation preferences may be the result of environmental adaptation; and (4) a broad prediction of virulence factors (VFs) revealed core and species unique VF genes