Elevated rates of horizontal gene transfer in the industrialized human microbiome.

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.

Temperature-driven heterochrony as a main evolutionary response to climate changes in conodonts.

Can we predict the evolutionary response of organisms to climate changes? The direction of greatest intraspecific phenotypic variance is thought to correspond to an 'evolutionary line of least resistance', i.e. a taxon's phenotype is expected to evolve along that general direction, if not constrained otherwise. In particular, heterochrony, whereby the timing or rate of developmental processes are modified, has often been invoked to describe evolutionary trajectories and it may be advantageous to organisms when rapid adaptation is critical. Yet, to date, little is known empirically as to which covariation patterns, whether static allometry, as measured in adult forms only, or ontogenetic allometry, the basis for heterochrony, may be prevalent in what circumstances. Here, we quantify the morphology of segminiplanate conodont elements during two distinct time intervals separated by more than 130 Myr: the Devonian-Carboniferous boundary and the Carnian-Norian boundary (Late Triassic). We evidence that the corresponding species share similar patterns of intraspecific static allometry. Yet, during both crises, conodont evolution was decoupled from this common evolutionary line of least resistance. Instead, it followed heterochrony-like trajectories that furthermore appear as driven by ocean temperature. This may have implications for our interpretation of conodonts' and past marine ecosystems' response to environmental perturbations.

Exploring diet shifts and ecology in modern sharks using calcium isotopes and trace metal records of their teeth.

Sharks occupy all living environments of the marine realm as well as some freshwater systems. They display varied and flexible feeding behaviours, but understanding their diet remains challenging due to their elusive ecology and the invasiveness of stomach content analyses in regard of their threatened status. As a potential alternative, we discuss the variability in δ44/42 Ca values recorded in the tooth enamel of size-graded individuals belonging to three species of large sharks with distinct diets (Isurus oxyrinchus, Hexanchus griseus and Carcharodon carcharias). The preliminary results highlight shifts in diet linked to ontogeny (I. oxyrinchus and H. griseus) and spatial distribution (C. carcharias) characterizing feeding behaviour in these species at individual and population level. These outcomes agree with the results of traditional stomach analyses supporting that nontraditional stable isotopes thus represent new perspectives for the study of modern and extinct shark ecology. In addition, for the first time, the Sr/Ca elemental ratios measured in H. griseus reflect sexual differences that could be interpreted in terms of spatial segregation or physiological heterogeneities.

Imidacloprid Decreases Honey Bee Survival Rates but Does Not Affect the Gut Microbiome.

Accumulating evidence suggests that pesticides have played a role in the increased rate of honey bee colony loss. One of the most commonly used pesticides in the United States is the neonicotinoid imidacloprid. Although the primary mode of action of imidacloprid is on the insect nervous system, it has also been shown to cause changes in insects' digestive physiology and alter the microbiota of Drosophila melanogaster larvae. The honey bee gut microbiome plays a major role in bee health. Although many studies have shown that imidacloprid affects honey bee behavior, its impact on the microbiome has not been fully elucidated. Here, we investigated the impact of imidacloprid on the gut microbiome composition, survivorship, and susceptibility to pathogens of honey bees. Consistent with other studies, we show that imidacloprid exposure results in an elevated mortality of honey bees in the hive and increases the susceptibility to infection by pathogens. However, we did not find evidence that imidacloprid affects the gut bacterial community of honey bees. Our in vitro experiments demonstrated that honey bee gut bacteria can grow in the presence of imidacloprid, and we found some evidence that imidacloprid can be metabolized in the bee gut environment. However, none of the individual bee gut bacterial species tested could metabolize imidacloprid, suggesting that the observed metabolism of imidacloprid within in vitro bee gut cultures is not caused by the gut bacteria. Overall, our results indicate that imidacloprid causes increased mortality in honey bees, but this mortality does not appear to be linked to the microbiome.IMPORTANCE Growing evidence suggests that the extensive use of pesticides has played a large role in the increased rate of honey bee colony loss. Despite extensive research on the effects of imidacloprid on honey bees, it is still unknown whether it impacts the community structure of the gut microbiome. Here, we investigated the impact of imidacloprid on the gut microbiome composition, survivorship, and susceptibility to pathogens of honey bees. We found that the exposure to imidacloprid resulted in an elevated mortality of honey bees and increased the susceptibility to infection by opportunistic pathogens. However, we did not find evidence that imidacloprid affects the gut microbiome of honey bees. We found some evidence that imidacloprid can be metabolized in the bee gut environment in vitro, but because it is quickly eliminated from the bee, it is unlikely that this metabolism occurs in nature. Thus, imidacloprid causes increased mortality in honey bees, but this does not appear to be linked to the microbiome.

Photodemethylation of Methylmercury in Eastern Canadian Arctic Thaw Pond and Lake Ecosystems.

Permafrost thaw ponds of the warming Eastern Canadian Arctic are major landscape constituents and often display high levels of methylmercury (MeHg). We examined photodegradation potentials in high-dissolved organic matter (DOC) thaw ponds on Bylot Island (BYL) and a low-DOC oligotrophic lake on Cornwallis Island (Char Lake). In BYL, the ambient MeHg photodemethylation (PD) rate over 48 h of solar exposure was 6.1 × 10(-3) m(2) E(-1), and the rate in MeHg amended samples was 9.3 × 10(-3) m(2) E(-1). In contrast, in low-DOC Char Lake, PD was only observed in the first 12 h, which suggests that PD may not be an important loss process in polar desert lakes. Thioglycolic acid addition slowed PD, while glutathione and chlorides did not impact northern PD rates. During an ecosystem-wide experiment conducted in a covered BYL pond, there was neither net MeHg increase in the dark nor loss attributable to PD following re-exposure to sunlight. We propose that high-DOC Arctic thaw ponds are more prone to MeHg PD than nearby oligotrophic lakes, likely through photoproduction of reactive species rather than via thiol complexation. However, at the ecosystem level, these ponds, which are widespread through the Arctic, remain likely sources of MeHg for neighboring systems.

High Methylmercury in Arctic and Subarctic Ponds is Related to Nutrient Levels in the Warming Eastern Canadian Arctic.

Permafrost thaw ponds are ubiquitous in the eastern Canadian Arctic, yet little information exists on their potential as sources of methylmercury (MeHg) to freshwaters. They are microbially active and conducive to methylation of inorganic mercury, and are also affected by Arctic warming. This multiyear study investigated thaw ponds in a discontinuous permafrost region in the Subarctic taiga (Kuujjuarapik-Whapmagoostui, QC) and a continuous permafrost region in the Arctic tundra (Bylot Island, NU). MeHg concentrations in thaw ponds were well above levels measured in most freshwater ecosystems in the Canadian Arctic (>0.1 ng L(-1)). On Bylot, ice-wedge trough ponds showed significantly higher MeHg (0.3-2.2 ng L(-1)) than polygonal ponds (0.1-0.3 ng L(-1)) or lakes (<0.1 ng L(-1)). High MeHg was measured in the bottom waters of Subarctic thaw ponds near Kuujjuarapik (0.1-3.1 ng L(-1)). High water MeHg concentrations in thaw ponds were strongly correlated with variables associated with high inputs of organic matter (DOC, a320, Fe), nutrients (TP, TN), and microbial activity (dissolved CO2 and CH4). Thawing permafrost due to Arctic warming will continue to release nutrients and organic carbon into these systems and increase ponding in some regions, likely stimulating higher water concentrations of MeHg. Greater hydrological connectivity from permafrost thawing may potentially increase transport of MeHg from thaw ponds to neighboring aquatic ecosystems.

Unsuspected functional disparity in Devonian fishes revealed by tooth morphometrics?

The shape of features involved in key biological functions, such as teeth in nutrition, can provide insights into ecological processes even in ancient time, by linking the occupation of the morphological space (disparity) to the occupation of the ecological space. Investigating disparity in radiating groups may provide insights into the ecological diversification underlying evolution of morphological diversity. Actinopterygian fishes initiated their radiation in the Devonian, a period characterized by the diversification of marine ecosystem. Although a former morpho-functional analysis of jaw shape concluded to conservative and poorly diversified morphologies in this early part of their history, fish tooth disparity evidenced here an unsuspected diversity of possible functional significance in the pivotal period of the Late Devonian (Famennian). All teeth being caniniforms, some were stocky and robust, in agreement with expectations for active generalist predators. More surprisingly, elongated teeth also occurred at the beginning of Famennian. Their needle-like shape challenges morpho-functional interpretations by making them fragile in response to bending or torsion. The occurrence of both types of fish teeth during the beginning of the Famennian points to a discrete but real increase in disparity, thus testifying a first burst of feeding specialization despite overall conservative jaw morphology. The disappearance of these needle-like teeth in the Late Famennian might have been related to a relay in dental diversity with abundant co-occurring groups, namely conodonts and chondrichthyans (sharks).

Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes.

Giant viruses (GVs) are key players in ecosystem functioning, biogeochemistry, and eukaryotic genome evolution. GV diversity and abundance in aquatic systems can exceed that of prokaryotes, but their diversity and ecology in lakes, especially polar ones, remain poorly understood. We conducted a comprehensive survey and meta-analysis of GV diversity across 20 lakes, spanning polar to temperate regions, combining our extensive lake metagenome database from the Canadian Arctic and subarctic with publicly available datasets. Leveraging a novel GV genome identification tool, we identified 3304 GV metagenome-assembled genomes, revealing lakes as untapped GV reservoirs. Phylogenomic analysis highlighted their dispersion across all Nucleocytoviricota orders. Strong GV population endemism emerged between lakes from similar regions and biomes (Antarctic and Arctic), but a polar/temperate barrier in lacustrine GV populations and differences in their gene content could be observed. Our study establishes a robust genomic reference for future investigations into lacustrine GV ecology in fast changing polar environments.

Motivation to participate and attrition factors in a COVID-19 biobank: A qualitative study.

BACKGROUND: The Biobanque québécoise de la COVID-19 (Quebec Biobank for COVID-19, or BQC19) is a provincial initiative that aims to manage the longitudinal collection, storage, and sharing of biological samples and clinical data related to COVID-19. During the study, BQC19 investigators reported a high loss-to-follow-up rate. The current study aimed to explore motivational and attrition factors from the perspective of BQC19 participants and health care and research professionals. METHODS: This was an inductive exploratory qualitative study. Using a theoretical sampling approach, a sample of BQC19 participants and professionals were invited to participate via semi-structured interviews. Topics included motivations to participate; participants' fears, doubts, and barriers to participation; and professionals' experiences with biobanking during the COVID-19 pandemic. RESULTS: Interviews were conducted with BQC19 participants (n = 23) and professionals (n = 17) from 8 clinical data collection sites. Motivations included the contribution to science and society in crisis, self-worth, and interactions with medical professionals. Reasons for attrition included logistical barriers, negative attitudes about public health measures or genomic studies, fear of clinical settings, and a desire to move on from COVID-19. Motivations and barriers seemed to evolve over time and with COVID-19 trends and surges. Certain situations were associated with attrition, such as when patients experienced indirect verbal consent during hospitalization. Barriers related to human and material resources and containment/prevention measures limited the ability of research teams to recruit and retain participants, especially in the ever-evolving context of crisis. CONCLUSION: The pandemic setting impacted participation and attrition, either by influencing participants' motivations and barriers or by affecting research teams' ability to recruit and retain participants. Longitudinal and/or biobanking studies in a public health crisis setting should consider these factors to limit attrition.

Arctic bacterial diversity and connectivity in the coastal margin of the Last Ice Area.

Arctic climate change is leading to sea-ice attrition in the Last Ice Area along the northern coast of Canada and Greenland, but less attention has been given to the associated land-based ecosystems. Here we evaluated bacterial community structure in a hydrologically coupled cryo-ecosystem in the region: Thores Glacier, proglacial Thores Lake, and its outlet to the sea. Deep amplicon sequencing revealed that Polaromonas was ubiquitous, but differed genetically among diverse niches. Surface glacier-ice was dominated by Cyanobacteria, while the perennially ice-capped, well-mixed water column of Thores Lake had a unique assemblage of Chloroflexi, Actinobacteriota, and Planctomycetota. Species richness increased downstream, but glacier microbes were little detected in the lake, suggesting strong taxonomic sorting. Ongoing climate change and the retreat of Thores Glacier would lead to complete drainage and loss of the lake microbial ecosystem, indicating the extreme vulnerability of diverse cryohabitats and unique microbiomes in the Last Ice coastal margin.

A Tale of Two Seasons: Distinct Seasonal Viral Communities in a Thermokarst Lake.

Thermokarst lakes are important features of subarctic landscapes and are a substantial source of greenhouse gases, although the extent of gas produced varies seasonally. Microbial communities are responsible for the production of methane and CO2 but the "top down" forces that influence microbial dynamics (i.e., grazers and viruses) and how they vary temporally within these lakes are still poorly understood. The aim of this study was to examine viral diversity over time to elucidate the seasonal structure of the viral communities in thermokarst lakes. We produced virus-enriched metagenomes from a subarctic peatland thermokarst lake in the summer and winter over three years. The vast majority of vOTUs assigned to viral families belonged to Caudovirales (Caudoviricetes), notably the morphological groups myovirus, siphovirus and podovirus. We identified two distinct communities: a dynamic, seasonal community in the oxygenated surface layer during the summer and a stable community found in the anoxic water layer at the bottom of the lake in summer and throughout much of the water column in winter. Comparison with other permafrost and northern lake metagenomes highlighted the distinct composition of viral communities in this permafrost thaw lake ecosystem.

Adapting Transportation Planning e-Tools to Older Adults' Needs: Scoping Review.

BACKGROUND: Aging is often accompanied by a decrease in physical and sensory capacities and financial resources, which makes travel and the use of public transport a big challenge for older adults. These mobility limitations may prevent them from going out for groceries, medical appointments, or entertainment, which increases the risk of social isolation. A key element in helping older adults to maintain healthy aging and social engagement is to foster autonomy, freedom, and active mobility. A transportation planning e-tool can provide older adults with information about transport and trip options. There are many transportation planning e-tools, but little is known about whether and how their characteristics and functionalities address older adults' needs and preferences. OBJECTIVE: This study aims to map existing transportation e-tools and identify gaps to be filled in order to match their functionalities with older adults' needs and preferences. METHODS: A scoping review of existing transportation planning e-tools was conducted based on the approach developed by Arksey and O'Malley. A search in the scientific literature (Academic Search Complete, MEDLINE, CINAHL, SocINDEX, and ERIC) as well as gray literature (TRID Database, Google Scholar, Proquest, Google Play, etc) was conducted in June 2020 and updated 3 times; in September 2021, December 2021, and May 2022. After the studies were selected, a comparative analysis was performed by 2 evaluators; an occupational therapy student and a computer science student. These e-tools were analyzed with respect to some characteristics (eg, tool's development status, target customers, and geographic coverage) as well as 10 functionalities (time autonomy, walkability, crowd avoidance, incline avoidance, weather consideration, dark avoidance, winter obstacles avoidance, amenities inclusion, taxi driver's information, and support affordance) that we defined based on older adults' needs and preferences (mainly Canadians). These needs were identified from a literature review and confirmed by workshops (focus groups). RESULTS: The scientific and gray literature search yielded 463 sources, and 42 transportation e-tools were included. None of the e-tools reviewed addresses all 10 functionalities. More specifically, functionalities such as dark avoidance and support affordance were not addressed by any of the included e-tools. CONCLUSIONS: Most of the e-tools currently available to plan trips do not address older adults' needs and preferences. The results of this scoping review helped fill this gap by identifying functionalities to include in transportation planning e-tools designed to promote active aging. The findings of this study highlight the need to use a multicriteria optimization algorithm to address older adults' mobility needs and preferences. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.2196/33894.

Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection.

(1) Background: Individuals with COVID-19 display different forms of disease severity and the upper respiratory tract microbiome has been suggested to play a crucial role in the development of its symptoms. (2) Methods: The present study analyzed the microbial profiles of the oral cavity and oropharynx of 182 COVID-19 patients compared to 75 unaffected individuals. The samples were obtained from gargle screening samples. 16S rRNA amplicon sequencing was applied to analyze the samples. (3) Results: The present study shows that SARS-CoV-2 infection induced significant differences in bacterial community assemblages, with Prevotella and Veillonella as biomarkers for positive-tested people and Streptococcus and Actinomyces for negative-tested people. It also suggests a state of dysbiosis on the part of the infected individuals due to significant differences in the bacterial community in favor of a microbiome richer in opportunistic pathogens. (4) Conclusions: SARS-CoV-2 infection induces dysbiosis in the upper respiratory tract. The identification of these opportunistic pathogenic biomarkers could be a new screening and prevention tool for people with prior dysbiosis.

Local Habitat Filtering Shapes Microbial Community Structure in Four Closely Spaced Lakes in the High Arctic.

Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is lacking for many ecosystems. The aim of this study was to characterize and compare the microbial communities of four closely spaced lakes in Stuckberry Valley (northern Ellesmere Island, Canadian Arctic Archipelago), in the coastal margin zone of the Last Ice Area, that differed in their physicochemical, morphological and catchment characteristics. We performed high-throughput amplicon sequencing of the V4 16S rRNA gene to provide inter- and intra-lake comparisons. Two deep (>25 m) and mostly oxygenated lakes showed highly similar community assemblages that were distinct from those of two shallower lakes (<10 m) with anoxic bottom waters. Proteobacteria, Verrucomicrobia, and Planctomycetes were the major phyla present in the four water bodies. One deep lake contained elevated proportions of Cyanobacteria and Thaumarchaeota that distinguished it from the others, while the shallow lakes had abundant communities of predatory bacteria, as well as microbes in their bottom waters that contribute to sulfur and methane cycles. Despite their proximity, our data suggest that local habitat filtering is the primary determinant of microbial diversity in these systems. This study provides the first detailed examination of the microbial assemblages of the Stuckberry lakes system, resulting in new insights into the microbial ecology of the High Arctic.

Physical Activity Interventions in Rehabilitation Programs for Outpatients With Mild Traumatic Brain Injury.

Introduction: There is limited scientific evidence about the optimal content and parameters of physical activity (PA) interventions for rehabilitation outpatients with persisting symptoms of a mild traumatic brain injury (mTBI). Clinicians have thus had to develop services based on their expertise, feasibility and patient needs. Objectives: This study aimed to document PA interventions delivered in specialized programs of a Canadian province offering outpatient rehabilitation services for individuals with persisting symptoms of mTBI to inform clinical intervention development and future research. Materials and methods: Cross-sectional study using an online survey containing 32 multiple choice and short open-ended questions to be answered by program administrators, with their clinical team's input. Content analysis and descriptive statistics were used. Results: Data from 94% of rehabilitation sites (n = 17) revealed that PA interventions are delivered to children (n = 4), adults (n = 15) and older adults (n = 5) with mTBI symptoms lasting ≥1 month to ≥1 year post injury. PA interventions aim to increase participation (n = 14), improve body functions (n = 9), manage persisting mTBI symptoms (n = 5) and improve self-management skills (n = 5) and knowledge (n = 4). Interventions include individual (n = 15) or group-based (n = 12) format, home-programs (n = 7), and teaching/education (n = 6). Most PA interventions include aerobic and resistance exercises. PA dosage parameters vary greatly. Conclusion: Clinical experts use multimodal interventions for rehabilitation program users that target improvement in body functions, participation and symptoms. The results can inform the development, enhancement and evaluation of PA interventions. Studies evaluating the effectiveness of these interventions for this clientele are warranted.

Developing a One-Stop Platform Transportation Planning Service to Help Older Adults Move Around in Their Community Where, When, and How They Wish: Protocol for a Living Lab Study.

BACKGROUND:  Multiple mobility-related challenges frequently appear with aging. As a result, many older adults have difficulty getting around, to go, for example, to doctors' appointments or leisure activities. Although various means of transportation are currently available, older adults do not necessarily use them, partly because they do not know which ones are adapted to their needs and preferences. To foster older adults' autonomy and freedom in their decision-making about transportation, it is crucial to help them make informed decisions about the means that suit them best. OBJECTIVE: Our aim is to develop Mobilainés, a one-stop platform transportation planning service combining different transport modes and services to help older adults move around in their community where, when, and how they wish. More specifically, we aim to (1) define older adults' mobility needs and preferences in order to conceptualize a one-stop platform; (2) cocreate a prototype of the one-stop platform; and (3) test the prototype with users in a real-life context. METHODS: This ongoing study uses a "Living Lab" co-design approach. This approach differs from traditional research on aging by facilitating intersectoral knowledge sharing and innovative solutions by and with older adults themselves. A steering committee of 8 stakeholders from the public, scientific, and private sectors, as well as older citizens, will meet quarterly throughout the study. The design comprises three phases, each with several iterative subphases. Phase 1 is exploration: through co-design workshops and literature reviews, members of the intersectoral committee will define older adults' mobility needs and preferences to support the conceptualization of the one-stop platform. Phase 2 is experimentation: 4 personas will be produced that reflect the different needs and preferences of typical older adult end users of the platform; for development of a prototype, scenarios and mockups (static designs of the web application) will be created through co-design sessions with older adults (N=12) embodying these personas. Phase 3 is evaluation: we will test the usability of the prototype and document changes in mobility, such as the ability to move around satisfactorily and to participate in meaningful activities, by and with older adults (N=30) who use the prototype. The steering committee will identify ways to support the adoption, implementation, and scaling up of Mobilainés to ensure its sustainability. Qualitative and quantitative data will be triangulated according to each subphase objective. RESULTS:  The first phase began in September 2019. The study is scheduled for completion by mid-2023. CONCLUSIONS:  This innovative transportation planning service will merge existing transportation options in one place. By meeting a wide variety of older adults' needs and preferences, Mobilainés will help them feel comfortable and safe when moving around, which should increase their participation in meaningful activities and reduce the risk of social isolation. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/33894.

Morphometric variance, evolutionary constraints and their change through time in Late Devonian Palmatolepis conodonts.

Phenotypic variation is the raw material of evolution. Standing variation can facilitate response to selection along "lines of least evolutionary resistance", but selection itself might alter the structure of the variance. Shape was quantified using 2D geometric morphometrics in Palmatolepis conodonts through the Late Devonian period. Patterns of variance were characterized along the record by the variance-covariance matrix (P-matrix) and its first axis (Pmax). The Late Frasnian was marked by environmental oscillations culminating with the Frasnian/Famennian mass extinction. A shape response was associated with these fluctuations, together with a deflection of the Pmax and the P-matrix. Thereafter, along the Famennian, Palmatolepis mean shape shifted from broad elements with a large platform to slender elements devoid of platform. This shift in shape was associated with a reorientation of Pmax and the P-matrix, due to profound changes in the functioning of the elements selecting for new types of variants. Both cases provide empirical evidences that moving adaptive optimum can reorient phenotypic variation, boosting response to environmental changes. On such time scales, the question seems thus not to be whether the P-matrix is stable, but how it is varying in response to changes in selection regimes and shifts in adaptive optimum.

["Dys" disorders in health care training]. / Les troubles "dys" dans la formation des professionnels de santé.

"Dys" disorders must be taken into account by trained teams in order for the people concerned to be able to undertake their training of choice. Learning is not easy, but neither is it impossible. With adapted support and a detailed analysis of the needs and tools required, it is possible to envisage working in the health care sector.

The outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A review of the current global status.

There is currently an ongoing worldwide pandemic of a novel virus belonging to the family of Coronaviruses (CoVs) which are large, enveloped, plus-stranded RNA viruses. Coronaviruses belong to the order of Nidovirales, family of Coronavirinae and are divided into four genera: alphacoronavirus, betacoronavirus, gammacoronavirus and deltacoronavirus. CoVs cause diseases in a wide variety of birds and mammals and have been found in humans since 1960. To date, seven human CoVs were identified including the alpha-CoVs HCoVs-NL63 and HCoVs-229E and the beta-CoVs HCoVs-OC43, HCoVs-HKU1, the severe acute respiratory syndrome-CoV (SARS-CoV), the Middle East respiratory syndrome-CoV (MERS-CoV) and the novel virus that first appeared in December 2019 in Wuhan, China, and rapidly spread to 213 countries as of the writing this paper. It was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the international committee on taxonomy of viruses (ICTV) and the disease's name is COVID-19 for coronavirus disease 2019. SARS-CoV-2 is very contagious and is capable of spreading from human to human. Infection routes include droplet and contact, and aerosol transmission is currently under investigation. It is associated with a respiratory illness that may cause severe pneumonia and acute respiratory distress syndrome (ARDS). SARS-CoV-2 became an emergency of international concern. As of July 12, 2020, the virus has been responsible for 12,698,995 confirmed cases and 564,924 deaths worldwide and the number is still increasing. Up until now, no specific treatment has yet been proven effective against SARS-CoV-2. Since the beginning of this outbreak, several interesting papers on SARS-CoV-2 and COVID-19 have been published to report on the phylogenetic evolution, epidemiology, pathogenesis, transmission as well as clinical characteristics of COVID-19 and possible treatments agents. This paper is a systematic review of the available literature on SARS-CoV-2. It was performed in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) and aims to help readers access the latest knowledge surrounding this new infectious disease and to provide a reference for future studies.

Extreme Viral Partitioning in a Marine-Derived High Arctic Lake.

High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of marine origin on the far northern coast of Ellesmere Island, in the Canadian High Arctic. We collected triplicate samples for double-stranded DNA (dsDNA) viromics from five depths that encompassed the major features of the lake, as determined by limnological profiling of the water column. Viral abundance and virus-to-prokaryote ratios were highest at greater depths, while bacterial and cyanobacterial counts were greatest in the surface waters. The viral communities from each zone of the lake defined by salinity, temperature, and dissolved oxygen concentrations were markedly distinct, suggesting that there was little exchange of viral types among lake strata. Ten viral assembled genomes were obtained from our libraries, and these also segregated with depth. This well-defined structure of viral communities was consistent with that of potential hosts. Viruses from the monimolimnion, a deep layer of ancient Arctic Ocean seawater, were more diverse and relatively abundant, with few similarities to available viral sequences. The Lake A viral communities also differed from published records from the Arctic Ocean and meromictic Ace Lake in Antarctica. This first characterization of viral diversity from this sentinel environment underscores the microbial richness and complexity of an ecosystem type that is increasingly exposed to major perturbations in the fast-changing Arctic.IMPORTANCE The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.