Complete data set.

Longitudinal monitoring of 50 honey bee (Apis mellifera) colonies from one Montana-based commercial beekeeping operation was conducted over the course of one year from November 2015 to October 2016. Samples were collected at six discrete time points, including two while colonies were located in California during (i.e. March 10, 2016) and just after almond pollination (i.e., April 23, 2016). By the end of the study in October 2016, colonies were sampled between three and six times. In total, we analyzed 262 samples, of which 37 were categorized as weak, 24 as average, 197 as strong, 4 were dead at the time of sampling. Honey bee colony population size was used as a proxy for colony health by counting the number of frames more than 2/3 covered with bees (i.e. weak (5 or fewer frames), average (6–8 frames), strong (9 or more frames) covered with bees)). Pathogen diagnostics was performed by PCR (1 = positive detection, 0 = not detected, NA—not assessed or no sample) for 13 pathogens and the most prevalent viral pathogens were assessed by qPCR. Relative RNA equivalents were determined by qPCR and were natural log transformed for statistical analyses (NA = not assessed by qPCR). Samples for which there was no virus detected by PCR would be below detection by qPCR and were thus considered as 0 during statistical analyses of qPCR. Over the course of the study, 22 colonies died, only four of which were collected as dead and analyzed (October 2016). The 18 other colonies that died throughout the study are included in the table at the time period they were found dead, then ommited from the table thereafter. (XLSX)本研究于2015年11月至2016年10月的一年周期内，对美国蒙大拿州某商业养蜂场的50群西方蜜蜂（Apis mellifera）开展了纵向监测。采样共设置6个离散时间节点，其中2次采样分别于蜂群位于加利福尼亚州进行杏仁授粉期间（2016年3月10日）及授粉刚结束后（2016年4月23日）开展。截至2016年10月研究结束时，每群蜂的采样次数介于3至6次之间。本研究共分析262份样本，其中37份归类为弱群、24份为中等群、197份为强群，另有4份样本对应的蜂群在采样时已死亡。本研究以蜂群覆盖蜜蜂比例超过2/3的巢脾数量作为蜂群健康状况的替代指标：覆盖蜜蜂的巢脾数≤5个为弱群，6~8个为中等群，≥9个为强群。针对13种病原体，本研究通过聚合酶链式反应（PCR）完成病原体诊断（检测结果赋值规则：1为阳性检出，0为未检出，NA表示未评估或无有效样本）；针对检出率最高的病毒病原体，则通过实时荧光定量PCR（qPCR）进行检测。通过qPCR测定相对RNA当量值，并对其进行自然对数转换以用于统计分析（NA表示未通过qPCR评估）。经PCR未检出病毒的样本，其qPCR检测结果低于检测限，因此在qPCR的统计分析中赋值为0。研究期间共有22群蜂死亡，其中仅4群在死亡时被采样并完成分析（采样时间为2016年10月）。其余18群死亡蜂群仅在其被发现死亡的对应时间节点纳入表格，后续时间节点则将其从表格中剔除。(XLSX)