Virus Discovery and Characterization using Next-Generation Sequencing

Abstract

Infectious diseases can be caused by a wide variety of pathogens, including viruses, bacteria, protozoa, fungi, helminths and prions. For numerous known pathogens, the disease incidence has increased over the last few decades. In addition, several previously unknown pathogens have recently been discovered, adding up to the impact of infectious diseases in humans and animals. The term “emerging infectious diseases” has been coined to describe infectious diseases caused by newly discovered pathogens and by known pathogens that have recently become more widespread. Much emerging infectious disease research focuses on the importance of the interplay between humans, animals, and the environment in relation to health and disease. Because of industrialization, globalization, urbanization, deforestation, extensive commercialization of agriculture, and various other factors, the incidence of exposure of both animal and human populations to pathogens has increased. This results in increased risks of a wide range of zoonotic diseases, i.e. diseases that can be passed from animals to humans. Animals are known to represent the origin of up to 75% of the emerging infectious diseases in humans. Examples of such zoonoses are the human immunodeficiency virus (HIV) and Ebola virus that were transmitted from non-human primates, and Lyme disease that is transmitted from animals by ticks. On many occasions, humans are infected through an intermediate animal host rather than the original “reservoir” species. Hendra virus, Nipah virus, and SARS coronavirus (SARS-CoV) are pathogens that originate from bats, but infected humans through horses, pigs, and palm civets, respectively. The rate of contact between a pathogen reservoir and a novel host species is an important factor for successful interspecies transmission. Unfortunately, due to the changes described above, these contact rates have increase. From 1980 onwards, the number of infectious outbreaks in both humans and animals have increased. Nearly 40 infectious diseases in humans have been identified that were unknown a few decades ago. In addition, many known infectious diseases that were thought to be under control have recently re-emerged. According to the WHO, “ It would be extremely naïve and complacent to assume that there will be no other disease like AIDS, Ebola, or SARS, sooner or later”. In response to these words, several international initiatives were launched to counteract this threat, including a European consortium that leads the framework 7 program “EMPERIE”. Many of the recent outbreaks of infectious disease in humans and animals were caused by RNA-viruses, as summarized in figure 1. RNA viruses are among the most variable and taxonomically diverse pathogens, with a wide variety of host species.