从应对不明原因性传染病疫情的角度来看，新病原体应该包括：1.在某个国家或地区第一次出现的病原体；2.发生了变异、毒力增强，使用现有的技术和方法无法准确诊断或鉴定的病原体；3.在世界范围内，第一次出现的病原体。建议建设新病原学，开展基础理论研究，通过和临床医学、生物信息学、生态学、流行病学等学科交融，建立发现新病原、判断新病原与疾病的关联度以及危害预警等的技术和理论体系。新病原学的主要目标是提高发现新病原、研究新病原、预防和控制新病原的能力,包括建立病原体检测技术储备，准确鉴定在我国第一次出现的病原体；建立病原体分子分型网络 发现发生变异的病原体；建立能够及时发现在世界范围第一次出现的病原体的技术和理论。

New pathogens have truly emerged with the globalization of travel and trade, changes in demographics and land use, susceptibility to opportunistic organisms associated with immunosuppression, and climate change. The so-called new pathogens can be divided into three categories, the pathogen identified first time in a region or a country, the mutated pathogens with increased virulence and/or infectivity which could not be correctly identified by current methods, and the pathogen emerged for the first time worldwide. The new pathogen in term of a subject should include the basic research, development of technology and strategies to establish the technology and scientific system to define a causal relationship between agent and disease, to understand how it causes disease and to assess the potential threat to public. The subject of new pathogen should interact with many disciplines such as genomics, epidemiology, clinical medicine, computational biology, ecology, animal sciences and others. The new molecular technologies such as microbial microarrays and unbiased high throughput sequencing have enabled efficient microbial surveillance and discovery. The aim of new pathogen study is to improve our ability and capacity to identify, to study, to control the new pathogens with public health significance. With development and progress of theory and methodology, we should be able to correctly identify the pathogen emerged for first time in China, to correctly and timely identify the mutated pathogen with significant public health significance, and to timely find the pathogen emerged for first time in the world.