pnas_dataset.csv

The dataset is acquired via the VIRRION platform designed for label-free capture and enrichment of viruses. It consists of Raman spectra of three groups of RNA viruses, including human respiratory viruses (influenza A H1N1 and H3N2, influenza B, rhinovirus, respiratory syncytial virus (RSV)), avian respiratory viruses (influenza A H5N2 and H7N2, infectious bronchitis virus (IBV), reovirus), and human enteroviruses (Coxsackievirus B type 1 and 3 (CVB1, CVB3), enteroviruses EV70 and EV71). Avian influenza virus (AIV) was propagated in specific-pathogen-free (SPF) embryonating chicken eggs (ECE) via allantoic cavity route inoculation at 9-11 days of age. The inoculated ECEs were incubated in a 37°C egg incubator for 3d (or 72 h) and then were removed/chilled at 4 °C for a minimum of 4 h or overnight. Allantoic fluid (AF) containing the virus was harvested from each egg using a sterile technique (a 3 mL sterile syringe with a 25G×5/8” needle). The harvested AF was clarified by centrifugation at 8000-1000 rpm for 10 min. Virus titer was determined in embryo infectious doses 50% (EID50) titers by the Reed-Muench method. Briefly, the EID50 test was conducted in ECE. The propagated fresh stock H5N2 AIV was prepared in 10-fold serial dilutions from 10-1 through 10-9. Each dilution was inoculated into 5 eggs, 0.1 mL per egg. The inoculated eggs were incubated at 37 °C for 72 hours. The eggs were candled daily to remove dead eggs to chill them at 4 °C refrigerator. After 72 hours of incubation, allantoic fluid was harvested from each egg. H1N1, H3N2, FluB, Rhinovirus, and RSV were prepared in Madin-Darby canine kidney-London (MDCK-London) cell culture. MDCK-London cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum and 1% penicillin-streptomycin, and incubated at 37°C in a humidified CO2 incubator. Enteroviruses (CVB1, CVB3, EV70, EV71, or PV2) were propagated using HEK 293 cell lines. The VIRRION platform constructed with nitrogen-doped carbon nanotube arrays and gold (Au) nanoparticles was used as SERS substrate for collecting Raman spectra from virus samples. A 100 μL sample of each virus was directly dropped (drop-cast) onto the VIRRION Au-CNT substrate and air-dried at room temperature for 10 hrs prior to Raman measurements. Raman data acquisition was recorded using a Horiba-LabRAM HR Evolution system with a 785nm diode laser line. The laser power on the sample was ca. 3.6 mW, focused through a 100× objective. The 600 gr/mm grating was used with a spectral range from 500 cm-1 to 2000 cm-1. The typical acquisition time was 30 s. <br>