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

Recombination is a common evolutionary tool for RNA viruses, and coronaviruses are no exception. We review here the evidence for recombination in SARS-CoV-2 and reconcile nomenclature for recombinants, discuss their origin and fitness, and speculate how recombinants could make a difference in the future of the COVID-19 pandemics.

/pdf/recombination-in-coronaviruses-with-a-focus-on-sars-cov-2-1kn1h3n8.pdf

Recombination in Coronaviruses, with a Focus on SARS-CoV-2

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.

Since SARS-CoV-2 BA.5 (Omicron) emerged and spread in 2022, Omicron lineages have markedly diversified. Here we review the evolutionary trajectories and processes that underpin the emergence of these lineages, and identify the most prevalent sublineages. We discuss the potential origins of second-generation BA.2 lineages. Simple and complex recombination, antigenic drift and convergent evolution have enabled SARS-CoV-2 to accumulate mutations that alter its antigenicity. We also discuss the potential evolutionary trajectories of SARS-CoV-2 in the future. 

SARS-CoV-2 evolution in the Omicron era.

http://www.cell.com/article/S1931312822003158/pdf

Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

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Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America