The emergence of SARS-CoV-2 variants has prompted the need for near real-time genomic surveillance to inform public health interventions. In response to this need, the global scientific community, through unprecedented effort, has sequenced over 7 million genomes as of December 2021. The 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 can be used to track 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 data pipelines that enable the scalable ingestion and standardization of heterogeneous data on SARS-CoV-2 variants, the server infrastructure that enables the dissemination of the processed data, and the client-side applications that provide intuitive visualizations of the underlying data.

/pdf/outbreak-info-genomic-reports-scalable-and-dynamic-1eqf8yff.pdf

Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations

https://doi.org/10.1016/j.jiph.2022.11.024

Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies

Objectives: Region X of the protein A gene (spa) was sequenced from methicillin-resistant Staphylococcus aureus (MRSA) isolates originating from animals, humans and the environment at veterinary hospitals in the UK and Ireland. MRSA transmission between animals and veterinary staff was assessed on the basis of spa typing, PFGE and epidemiological data. Methods: MRSA isolates from dogs (n = 27), horses (n = 9), cats (n = 6), staff (n = 22) and environmental surfaces (n = 3) were analysed by PFGE and spa typing. Known contacts between human and animal MRSA carriers were ascertained from the veterinary hospitals. Results: All feline, most canine (96%) and human (82%) isolates showed PFGE profiles that were either indistinguishable (subtype A1) or closely related (subtypes A2–A10) to that of the epidemic clone EMRSA-15 (CC22), whereas most equine isolates (88%) were related to CC8 (types C, D, E and G). spa polymorphism enabled discrimination among MRSA strains assigned to the same PFGE type. Fifteen spa types clustering into two distinct groups were detected, with t032 being the most prevalent (48%). The spa and PFGE types of MRSA isolated from seven staff members were the same as those of strains isolated from infected animals attended by the staff. Conclusions: Irrespective of geographical origin, MRSA isolated from equine and small animal hospitals generally clustered into two distinct clonal complexes, CC8 and CC22, respectively. The combined use of spa and PFGE typing allowed better discrimination than each method used individually, and provided useful information on MRSA transmission between animal and human individuals.

spa typing of methicillin-resistant Staphylococcus aureus isolated from domestic animals and veterinary staff in the UK and Ireland

Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control. In this Review, the authors describe how phylogenetic and phylodynamic methods provide insight into viral evolution, focusing on the SARS-CoV-2 pandemic. The approaches reveal routes and timings of transmission events, and they can assess the effectiveness of various intervention measures aimed at controlling the virus. 

/pdf/phylogenetic-and-phylodynamic-approaches-to-understanding-245r1fim.pdf

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

The purpose of this retrospective study was to evaluate the use of partial parenteral nutrition (PPN) in dogs and cats. The medical records of all dogs and cats receiving PPN between 1994 and 1999 were reviewed to determine signalment, reasons for use of PPN, duration of PPN administration, duration of hospitalization, complications, and mortality. Complications were classified as metabolic, mechanical, or septic. One hundred twenty-seven animals (80 dogs and 47 cats) were included in the study, accounting for 443 patient days of PPN. The most common underlying diseases were pancreatitis (n = 41), gastrointestinal disease (n = 33), and hepatic disease (n = 23). Median time of hospitalization before initiation of PPN was 2.8 days (range, 0.2-10.7 days). Median duration of PPN administration was 3.0 days (range, 0.3-8.8 days). Median duration of hospitalization was 7 days (range, 2-20 days). In the 127 animals receiving PPN, 72 complications occurred. These included metabolic (n = 43), mechanical (n = 25), and septic (n = 4) complications. The most common metabolic complication was hyperglycemia (n = 19), followed by lipemia (n = 17) and hyperbilirubinemia (n = 6). Most complications were mild and did not require discontinuation of PPN. Ninety-three (73.2%) of the 127 patients were discharged. All 4 animals with septic complications were discharged from the hospital. The presence, type, and number of complications did not impact the duration of hospitalization or outcome. However, animals that received supplemental enteral nutrition survived more often than those receiving PPN exclusively. Although PPN seems to be a relatively safe method of providing nutritional support, future studies are warranted to determine its efficacy.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1939-1676.2002.tb01262.x

Retrospective evaluation of partial parenteral nutrition in dogs and cats.

Abstract Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced &gt;0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time &lt;21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity. 

/pdf/global-disparities-in-sars-cov-2-genomic-surveillance-ddmrk5g2.pdf

Global disparities in SARS-CoV-2 genomic surveillance

Handle everyday research tasks with reliable, citation-backed results

Your personal Research Agent to handle research tasks with citation-backed results

Popular Tasks used by Researchers

How can I help with your research?

Meet SciSpace

Get more enhanced response by uploading the PDFs you want me to reference.

No relevant PDFs in your library

SciSpace is the AI research assistant for academics. Run systematic literature reviews on 280M+ papers, and write papers with cited sources. Trusted by 1M+ students, PhDs & researchers.

SciSpace | AI for Research

Analyze PDFs

Code & Manuscripts

Funding & Grants

Literature & Patents

Medical & Clinical Data

Systematic Review

Visualize & Present

Web & Data

Build a Google Scholar-like website for your research.

Build a website

Create charts and images for your research

Create a Chart

Write a paper for submission to a journal

Draft a manuscript

Patent Search

Design eye-catching scientific posters in minutes.

Scientific Poster Generation

Systematic Literature Review

One task is running at the moment. Your messages will be shown right after.

Drag and drop or click here to browse

Loved by <highlight>1 million+</highlight> researchers

Extract a list of specific topics and their sources from unstructured text

Topics

Compare and analyze relevant papers that matches with your search

Papers

Get insights from PDFs and bookmarked papers from your library

My library

Recent searches

Try searching for:

Catch AI-generated content in scholarly and non-scholarly content

{ai} Detector

Ai Writer

Get PDF Summaries, highlighted text explanations 

Chat with PDF

Effortlessly create in-text citations and bibliographies in APA and 2,500 other formats

Citation generator

Get explanations, summaries, and answers on academic papers

Ease up your research workflow with {scispace}'s cohort of exciting AI tools

Elevate your academic writing skills and convey your ideas the way you want

Paraphraser

Explore our range of reading and writing tools

Your file is being prepared and should be ready in a few minutes. If it's a large file, it might take a bit longer. You can close this window, and we'll email you the file when it's done.

You have reached a maximum limit of <strong>{limit}</strong> columns in the table. Remove at least <strong>1</strong> column to add or create another one.

Ben Branda

Author Tools

Chat about Author

Papers

Global disparities in SARS-CoV-2 genomic surveillance