Data from: Seasonal dynamics and co-occurrence patterns of honey bee pathogens revealed by high-throughput RT-qPCR analysis

The health of the honey bee Apis mellifera is challenged by introduced parasites that interact with its inherent pathogens and cause elevated rates of colony losses. To elucidate co-occurrence, population dynamics and synergistic interactions of honey bee pathogens, we established an array of diagnostic assays for a high-throughput qPCR platform. Assuming that interaction of pathogens requires co-occurrence within the same individual, single worker bees were analyzed instead of collective samples. Eleven viruses, four parasites and three pathogenic bacteria were quantified in more than one thousand single bees sampled from sixteen disease-free apiaries in Southwest Germany. The most abundant viruses were Black Queen Cell Virus (84%), Lake Sinai Virus 1 (42%), and Deformed Wing Virus B (35%). Forager bees from asymptomatic colonies were infected with two different viruses in average, and simultaneous infection with four to six viruses was common (14%). Also the intestinal parasites Nosema ceranae (96%) and Crithidia mellificae/Lotmaria passim (52%) occurred very frequently. These results indicate that low-level infections in honey bees are more common than previously assumed. All viruses showed seasonal variation, while N. ceranae did not. The foulbrood bacteria Paenibacillus larvae and Melissococcus plutonius were regionally distributed. Spearman's correlations and multiple regression analysis indicated possible synergistic interactions between the common pathogens, particularly for Black Queen Cell Virus. Beyond its suitability for further studies on honey bees, this targeted approach may be, due to its precision, capacity and flexibility, a viable alternative to more expensive, sequencing-based approaches in non-model systems.西方蜜蜂（Apis mellifera）的健康受到外来寄生虫的威胁，这些寄生虫与其体内固有病原体相互作用，导致蜂群死亡率升高。为阐明蜜蜂病原体的共现情况、种群动态及协同互作机制，我们针对高通量qPCR平台搭建了一套诊断检测体系。我们假设病原体之间的互作需要在同一宿主体内共存，因此选择对单个工蜂进行分析，而非集体混合样本。我们从德国西南部16个无病蜂场采集了千余只工蜂，并对其中的11种病毒、4种寄生虫及3种致病菌完成了定量检测。丰度最高的病毒为黑蜂王台病毒（Black Queen Cell Virus，检出率84%）、湖西奈病毒1型（Lake Sinai Virus 1，42%）及残翅病毒B型（Deformed Wing Virus B，35%）。来自无症状蜂群的采集蜂平均会感染2种不同病毒，同时感染4至6种病毒的情况十分普遍（占比14%）。肠道寄生虫东方蜜蜂微孢子虫（Nosema ceranae，检出率96%）与蜜蜂短膜虫/洛特莫尔虫（Crithidia mellificae/Lotmaria passim，检出率52%）的检出频率同样极高。上述结果表明，蜜蜂体内的低水平感染比此前预想的更为常见。所有病毒均呈现季节动态变化，而东方蜜蜂微孢子虫则无此类波动。引发幼虫腐臭病的致病菌幼虫芽孢杆菌（Paenibacillus larvae）与蜂房球菌（Melissococcus plutonius）呈区域分布特征。斯皮尔曼秩相关分析及多元回归分析显示，常见病原体间存在潜在协同互作，尤以黑蜂王台病毒最为显著。该靶向检测方法除适用于蜜蜂相关的后续研究外，凭借其精准性、检测通量与灵活性，可作为非模式生物研究中替代昂贵测序技术的可行方案。