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>

本数据集通过专为无标记捕获与富集病毒设计的VIRRION平台获取。该数据集包含三组RNA病毒（RNA virus）的拉曼光谱（Raman spectra），分别为人类呼吸道病毒：甲型流感病毒H1N1（influenza A H1N1）、H3N2（influenza A H3N2）、乙型流感病毒（influenza B）、鼻病毒（rhinovirus）、呼吸道合胞病毒（respiratory syncytial virus, RSV）；禽类呼吸道病毒：甲型流感病毒H5N2（influenza A H5N2）、H7N2（influenza A H7N2）、传染性支气管炎病毒（infectious bronchitis virus, IBV）、呼肠孤病毒（reovirus）；以及人类肠道病毒：柯萨奇病毒B型1型（Coxsackievirus B type 1, CVB1）、3型（Coxsackievirus B type 3, CVB3）、肠道病毒EV70（enterovirus EV70）、EV71（enterovirus EV71）。
禽流感病毒（avian influenza virus, AIV）通过尿囊腔接种途径，在9~11日龄的无特定病原体（specific-pathogen-free, SPF）受精鸡胚（embryonating chicken eggs, ECE）中增殖。接种后的受精鸡胚置于37℃卵孵箱中培养3天（即72小时），随后取出并置于4℃冰箱冷藏至少4小时或过夜。采用无菌操作（使用3mL无菌注射器搭配25G×5/8号针头）从每枚鸡胚中收集含病毒的尿囊液（allantoic fluid, AF）。收集得到的尿囊液经8000~1000 rpm离心10分钟以澄清。采用Reed-Muench法测定病毒的50%鸡胚感染量（embryo infectious doses 50%, EID50）效价。具体而言，EID50检测在受精鸡胚中开展：将增殖得到的新鲜H5N2型禽流感病毒原液进行10倍系列稀释，稀释梯度为10^-1至10^-9；每个稀释梯度接种5枚鸡胚，每枚接种0.1mL。接种后的鸡胚置于37℃培养72小时，每日通过照蛋检出死胚并将其置于4℃冰箱冷藏。培养72小时后，从每枚鸡胚中收集尿囊液。
H1N1、H3N2、乙型流感病毒、鼻病毒及呼吸道合胞病毒在Madin-Darby犬肾-伦敦株（Madin-Darby canine kidney-London, MDCK-London）细胞中培养制备。Madin-Darby犬肾-伦敦株细胞在含10%胎牛血清与1%青霉素-链霉素的达尔伯克改良伊格尔培养基（Dulbecco's modified Eagle's medium, DMEM；Invitrogen, Carlsbad, CA）中培养，培养条件为37℃、湿润二氧化碳培养箱。肠道病毒（CVB1、CVB3、EV70、EV71及PV2）采用HEK 293细胞系进行增殖。
本研究采用以氮掺杂碳纳米管阵列与金（gold, Au）纳米颗粒构建的VIRRION平台作为表面增强拉曼散射（surface-enhanced Raman scattering, SERS）基底，用于采集病毒样本的拉曼光谱。将每份100μL的病毒样本直接滴加（滴涂法，drop-cast）至VIRRION Au-CNT基底上，于室温下风干10小时后再开展拉曼检测。拉曼数据采集采用Horiba-LabRAM HR Evolution拉曼光谱仪，激发光源为785nm二极管激光器；样本处的激光功率约为3.6mW，通过100倍物镜聚焦；采用600线/毫米的光栅，光谱采集范围为500 cm^-1至2000 cm^-1；单次采集时长通常为30秒。