Contribution of newly discovered and emerging viruses to human disease

Abstract

According to the World Health Organization, over 200 infectious diseases in humans originate from animals (zoonoses), posing significant threats to human health. Zoonotic agents account for the majority of emerging and re-emerging pathogens. The human-animal interface has been recognised as an important risk factor that facilitates viruses to cross the species barrier and establish infection in humans. This indicates a need to perform surveillance of human populations who are at high risk of zoonotic infection due to their frequent contact with animals, together with the animals to which humans are exposed. The VIZIONS (Vietnam Initiative on Zoonotic Infections) has been conducted to directly respond to that need. The large virus family Picornaviridae include known emerging pathogens that have major impacts on the economies and human and animal health (e.g. foot-and-mouth disease virus, hand foot and mouth disease virus). Some enteroviruses (EVs) and parechoviruses in this family have been shown to be able to infect both humans and animals while a number of new picornaviruses (new EV variants, cosaviruses, cardioviruses, hunniviruses) with unknown pathogenicity and zoonotic potential have been discovered. This thesis, as part of VIZIONS, hopes to address the following gaps in our knowledge of such viruses in six genera (Enterovirus, Parechovirus, Cosavirus, Cardiovirus, Kobuvirus and Hunnivirus) of the family Picornaviridae: 1) The prevalence and genetic diversity of picornaviruses in studied samples 2) The epidemiology and disease association of the identified viruses 3) The overlaps (if any) of picornaviruses circulating in animals and humans 4) Possible animal sources of picornavirus infections in humans In order to do that, over 2,000 faecal samples collected from a wide range of hosts (pigs, rats, bamboo rats, shrews, bats, chickens, ducks, boars, civets, porcupines, monkeys and humans) were screened for picornaviruses by nested PCR and real-time PCR assays. Detection frequencies varied between viruses and sample origins with kobuvirus as the most commonly detected virus, followed by EV, cardiovirus and hunnivirus. Parechovirus and cosavirus were not detected. Comparison of detection frequencies of viruses infecting pigs revealed a disease (diarrhoea) association with porcine kobuvirus (PKV) but not EV infections. However, differences in PKV viral loads between diarrhoeic and non-diarrhoeic pigs were not statistically significant (p = 0.22). In addition, the PKV VP1 sequences from the two pig categories were not phylogenetically distinct. EV VP1 sequences obtained from pigs and boars showed high genetic diversity with four previously known types and nine new types (EV-G8 to -G16). Analyses of complete genome sequences of two new EV types provided evidence for inter-type recombination with a putative breakpoint in the 2A coding region. Similarly, study on samples from monkeys showed endemic infection of EV but no overlap with EV variants in humans was observed. The majority of EV detected in monkeys were novel with evidence for chimeric genomes and putative recombination breakpoints in the 2A region. New criteria for the classification of EV were additionally proposed. Characterization by sequencing of VP4/VP2 and VP1 regions or complete genomes of picornaviruses in rats and bamboo rats also showed relatively high genetic diversity. While these viruses can infect different species of rats, they were again genetically different from viruses detected in the studied human populations. In summary, studies in this thesis provide substantial new information on the prevalence, genetic diversity and disease association of picornaviruses in the studied populations. However, picornaviruses detected from animals were consistently separate from those found in humans, consistent with a relatively limited zoonotic potential of members of the virus family.