ABSTRACT
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info , a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Genomics , Disease Outbreaks , MutationABSTRACT
Despite great efforts have been made worldwide, the coronavirus disease 19 (COVID-19) still has not a definitive cure, although the availability of different vaccines are slowing down the transmission and severity. It has been shown that surfactin, a cyclic lipopeptide produced by Bacillus subtilis, is a molecule able to counteract both SARS-CoV-1, MERS-CoV and HCoV-229E coronaviruses. In this study the potential antiviral activity of surfactin against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was tested in vitro in a cellular model of infection. Our results show that 2 h treatment with surfactin is able to reduce SARS-CoV-2 infectivity on Vero E6 cells both at 24 h and after 7 days from viral inoculation, probably impairing the viral membrane integrity. Moreover, surfactin, at the concentrations used in our experimental settings, is not cytotoxic. We suggest surfactin as a new potential molecule against SARS-CoV-2, to be employed at least as a disinfectant.
ABSTRACT
The timely release of SARS-CoV-2 first genomic sequences allowed the identification of the etiologic agent and development of diagnostic protocols. Genomic sequencing was a crucial step in generating data for driving laboratory response and detections of SARS-CoV-2 since the start of the COVID-19 pandemic. Because of all the progression and achievements that timely release of genetic sequence data represents in the public health response, the Pan American Health Organization (PAHO) in collaboration with countries' public health laboratories, started implementation of a network for strengthening the Latin America and Caribbean (LAC) region on timely generation of SARS-CoV-2 genomic data. Here we describe the implementation of the COVID-19 Genomic Surveillance Regional Network in the Americas region during the beginning of the pandemic. The establishment of this network has strengthened laboratory response capacity at the country level, as well as facilitated timely release of SARS-CoV-2 genomic information to be used to complement the multiple response strategies for COVID-19 pandemic mitigation. As genomic epidemiology is useful for guiding public health decisions on outbreak and response, we also analysed the first SARS-CoV-2 genomic sequence data from countries of the Latin America and Caribbean Region.
Subject(s)
PandemicsABSTRACT
The immune system is a complex architecture of a collective and coordinated network regulated by various pathways to thermodynamically maintain immune homeostasis. The gut microbiota plays a pivotal role that offers significant stimuli (i.e., gut-brain, gut-lung, and gut-liver axis) for both innate and adaptive immunity, mediating immune and metabolic homeostasis. An intricate correlation between changes in the gut microbiota (dysbiosis) and common diseases/disorders have been attributed to the invasion of pathogens, constant use of antibiotics, and hypercytokinemia—a hallmark of immune homeostasis imbalance. These factors contribute to the severity of inflammatory diseases such as cardiovascular diseases, neurological disorders, and of late the coronavirus disease, Covid-19. Probiotics (Lactobacillus spp. and Bifidobacterium spp.) have been considered as alternative and/or adjuvant therapeutic in restoring the balance of gut microbiota for maintaining immune homeostasis and integrity. The probiotics catalyze dietary fibers and proteins to generate short-chain fatty acids and tryptophan to promote antiinflammatory cytokines, reduce epithelium permeability, reinforcing immunity in the gut mucosa, and regulating the systemic immune response. Herein, we review our overarching understanding of current applications of probiotics in amelioration of gut microbiome, and the improvement of gut barrier function and maintaining immune homeostasis. We also highlight clinical trials on probiotics with reported results for the treatment of inflammatory diseases. Additionally, the looming global Covid-19 pandemic makes it prudent to highlight the role of probiotics in both the innate and adaptive human immune responses, especially amid the Covid-19 vaccination paradigm.