Norway rats (Rattus norvegicus) are globally distributed and concentrate in urban environments, where they live and feed in closer proximity to human populations than most other mammals. Despite the potential role of rats as reservoirs of zoonotic diseases, the microbial diversity present in urban rat populations remains unexplored. In this study, we used targeted molecular assays to detect known bacterial, viral, and protozoan human pathogens and unbiased high-throughput sequencing to identify novel viruses related to agents of human disease in commensal Norway rats in New York City. We found that these rats are infected with bacterial pathogens known to cause acute or mild gastroenteritis in people, including atypical enteropathogenic Escherichia coli, Clostridium difficile, and Salmonella enterica, as well as infectious agents that have been associated with undifferentiated febrile illnesses, including Bartonella spp., Streptobacillus moniliformis, Leptospira interrogans, and Seoul hantavirus. We also identified a wide range of known and novel viruses from groups that contain important human pathogens, including sapoviruses, cardioviruses, kobuviruses, parechoviruses, rotaviruses, and hepaciviruses. The two novel hepaciviruses discovered in this study replicate in the liver of Norway rats and may have utility in establishing a small animal model of human hepatitis C virus infection. The results of this study demonstrate the diversity of microbes carried by commensal rodent species and highlight the need for improved pathogen surveillance and disease monitoring in urban environments.

The microbiome of wild Mus musculus (house mouse), a globally distributed invasive pest that resides in close contact with humans in urban centers, is largely unexplored. Here, we report analysis of the fecal virome of house mice in residential buildings in New York City, NY. Mice were collected at seven sites in Manhattan, Queens, Brooklyn, and the Bronx over a period of 1 year. Unbiased high-throughput sequencing of feces revealed 36 viruses from 18 families and 21 genera, including at least 6 novel viruses and 3 novel genera. A representative screen of 15 viruses by PCR confirmed the presence of 13 of these viruses in liver. We identified an uneven distribution of diversity, with several viruses being associated with specific locations. Higher mouse weight was associated with an increase in the number of viruses detected per mouse, after adjusting for site, sex, and length. We found neither genetic footprints to known human viral pathogens nor antibodies to lymphocytic choriomeningitis virus.

We report the case of a COVID-19-positive 6-week-old who presented with fever, cough, and 2 brief 10-15 seconds episodes of upward gaze and bilateral leg stiffening. CaseA 6-week-old term male infant presented for evaluation after 1 day of cough, fever, and brief episodes of sustained upward gaze associated with bilateral leg stiffening. The initial episode occurred after a diaper change. There was no shaking, breathing change, or pallor during this episode. There was no association with feeding. The infant had 2 siblings with cough and fever at the time of presentation, both diagnosed with streptococcal pharyngitis. On arrival to the emergency department, vital signs were notable for fever of 38.4°C and mild hypertension (114/57). Examination was notable for a mottled appearance and bilateral overlapping of the fourth and fifth toes. The anterior fontanel was soft and nonbulging, and neurologic examination was unremarkable. However, the patient had a witnessed episode of sustained upward gaze associated with bilateral leg stiffening and decreased responsiveness lasting 10 seconds with subsequent return to baseline and no hypoxia or vital signs change.The patient was born at 39 weeks via uncomplicated normal spontaneous vaginal delivery, weighing 3.91 kg. Family history was notable for simple febrile seizures in a developmentally normal sibling. There was no family history of epilepsy.Laboratory data were notable for leukopenia of 5.07 ×10 3 white blood cells (wbcs)/μL (normal 8.14-14.99 × 10 3 ) with a normal differential and elevated procalcitonin of 0.21 ng/mL (normal <0.08 ng/mL). Electrolytes were normal. Respiratory pathogen PCR panel was positive for rhinovirus/enterovirus. SARS-CoV-2 Real-Time Reverse Transcriptase (rRT)-PCR was positive. A chest radiograph was not performed. A lumbar puncture had an unremarkable CSF