Knockout of the ORF8 protein has repeatedly spread through the global viral population during SARS-CoV-2 evolution. Here we use both regional and global pathogen sequencing to explore the selection pressures underlying its loss. In Washington State, we identified transmission clusters with ORF8 knockout throughout SARS-CoV-2 evolution, not just on novel, high fitness viral backbones. Indeed, ORF8 is truncated more frequently and knockouts circulate for longer than for any other gene. Using a global phylogeny, we find evidence of positive selection to explain this phenomenon: nonsense mutations resulting in shortened protein products occur more frequently and are associated with faster clade growth rates than synonymous mutations in ORF8. Loss of ORF8 is also associated with reduced clinical severity, highlighting the diverse clinical impacts of SARS-CoV-2 evolution.

Exotic invasive plants alter the structure and function of native ecosystems and may influence the distribution and abundance of arthropod disease vectors by modifying habitat quality. This study investigated how invasive plants alter the ecology of Culex pipiens, an important vector of West Nile virus (WNV) in northeastern and midwestern regions of the United States. Field and laboratory experiments were conducted to test the hypothesis that three native leaf species (Rubus allegheniensis, blackberry; Sambucus canadensis, elderberry; and Amelanchier laevis, serviceberry), and three exotic invasive leaf species (Lonicera maackii, Amur honeysuckle; Elaeagnus umbellata, autumn olive; and Rosa multiflora, multiflora rose) alter Cx. pipiens oviposition site selection, emergence rates, development time, and adult body size. The relative abundance of seven bacterial phyla in infusions of the six leaf species also was determined using quantitative real-time polymerase chain reaction to test the hypothesis that variation in emergence, development, and oviposition site selection is correlated to differences in the diversity and abundance of bacteria associated with different leaf species, important determinants of nutrient quality and availability for mosquito larvae. Leaf detritus from invasive honeysuckle and autumn olive yielded significantly higher adult emergence rates compared to detritus from the remaining leaf species and honeysuckle alleviated the negative effects of intraspecific competition on adult emergence. Conversely, leaves of native blackberry acted as an ecological trap, generating high oviposition but low emergence rates. Variation in bacterial flora associated with different leaf species may explain this asymmetrical production of mosquitoes: emergence rates and oviposition rates were positively correlated to bacterial abundance and diversity, respectively. We conclude that the displacement of native understory plant species by certain invasive shrubs may increase production of Cx. pipiens with potential negative repercussions for human and wildlife health. These findings may be relevant to mosquito control and invasive plant management practices in the geographic range of Cx. pipiens. Further, our discovery of a previously unknown ecological trap for an important vector of WNV has the potential to lead to novel alternatives to conventional insecticides in mosquito control by exploiting the apparent “attract-kill” properties of this native plant species.

Background: Management of acute, uncomplicated cystitis in outpatients benefits from knowledge of drug resistance patterns in the population. However, antibiograms are often not available for the outpatient setting, and the role of host factors such as sex and age in assessing the likelihood of resistance are not well understood. We investigated whether antibiotic resistance patterns of outpatient urinary Escherichia coli isolates vary by age group and sex in a large database of antibiotic susceptibility test (AST) results from Washington State. Methods: We retrospectively analyzed AST data for outpatient urinary E. coli isolates in Washington State tested at a clinical reference laboratory from 2013 to 2017. In logistic regression models stratified by sex, we tested the associations of antibiotic resistance with patient age. Results: We found females >50 years had greater odds than females younger than 19 for resistance to amoxicillin-clavulanate (odds ratio [OR], 1.43; 95% confidence interval [CI], 1.22–1.69), ciprofloxacin (OR, 3.04; 95% CI, 2.48–3.74), ceftriaxone (OR, 2.58; 95% CI, 1.77–3.92), and gentamicin (OR, 1.62; 95% CI, 1.27–2.08) (all P < .001). Compared to males younger than 19, males >50 years had greater odds of resistance to ciprofloxacin (OR, 2.59; 95% CI, 1.18–5.69) and lower odds of resistance to amoxicillin-clavulanate (OR, 0.56; 95% CI, .34–.96) (all P < .05). Conclusions: These findings demonstrate that age and sex are associated with variability in antibiotic resistance patterns in the outpatient setting. Availability of outpatient antibiotic resistance data based on sex and age may be useful to inform empiric prescribing for outpatient UTIs and to support antibiotic stewardship efforts.

Patterns of antibiotic resistance in E. coli urinary isolates can vary between outpatient specialties. The use of clinical data to create practice and specialty-specific antibiograms in outpatient settings may improve antibiotic stewardship.

Background SARS-CoV-2 is believed to have emerged from an animal reservoir as a zoonotic pathogen. Over the course of the current pandemic, evidence has mounted that infected humans can transmit the virus to animals including household pets, however the frequency of and risk factors for this transmission remain unclear. We carried out a community-based study of pets in households with one or more confirmed SARS-CoV-2 case among the human residents, and report here on interim findings from sampling of dogs. Methods Data collection included a survey of human and animal demographic and clinical variables, features of their shared environment, and human-animal contact; blood collection from animals for serology for anti-SARS-CoV-2 antibodies; and nasopharyngeal sampling for PCR testing for SARS-CoV-2. Results Sampling consisted of 67 dogs from 46 households. Nasopharyngeal PCR testing results were available for 58 dogs, and serological testing results were available for 51. Clinical signs consistent with COVID-19 were reported in 14 dogs (23.7%, 95% CI 0.13, 0.35), and SARS-CoV-2 antibody testing using viral receptor binding domain ELISA was positive in 22 dogs (43.1%, 95% CI 0.30, 0.57). All PCR tests of nasopharyngeal swabs were negative. Survey respondents commonly reported close human-animal contact, and the majority of households were aware of and adopted measures to mitigate human-to-animal transmission of SARS-CoV-2 following diagnosis. While no statistically significant associations were detected between human-animal contact variables and either seropositivity or COVID-19 like illness in dogs, positive trends were found for sharing beds with humans and the number of SARS-CoV-2 positive humans in the corresponding household. Reported measures taken by the household to mitigate transmission showed a protective trend, and COVID-19 like illness in a dog was positively associated with seropositivity in that dog. Discussion These data indicate that human-to-animal transmission of SARS-CoV-2 in households is common, in a study population characterized by close human-animal contact. They also indicate that infected pets often manifest signs of COVID-like illness. While nasopoharyngeal sampling of dogs in this study has not to date demonstrated positive PCR results, this could be due to delays in sampling. Household members reported taking precautions to protect pets from SARS-CoV-2 infection, indicating an opportunity for further measures to reduce transmission of SARS-CoV-2 between people and animals sharing households.