Unexpected picornavirus diversity in a single diarrhoeic chicken

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Complete genome analysis of avian picornaviruses representing up to six genera

Text by Ákos Boros

In this project our aim was to gain detailed insight into the enteric picornavirus diversity of a single diarrheic chicken introduced recently to a novel location. During the course of our investigation the complete genomes of nearly all picornaviruses found in the studied cloacal sample were determined, characterized and phylogenetically analysed. Using a combination of viral metagenomic and RT-PCR techniques, a total of eight unique picornaviruses were identified which belonged to genera Megrivirus, Sicinivirus, Gallivirus, Tremovirus, Avisivirus, “Orivirus” (two potential genotypes) and an unassigned novel picornavirus (chicken phacovirus 1) (see the figure below). The phacoviruses were also detected in multiple chicken enteric samples from the USA, suggesting a worldwide distribution of these viruses among chicken flocks. The megrivirus-related sequences could not be confirmed by RT-PCR, and one picornavirus called orivirus A1 (genus “Orivirus”) was described earlier by our research group.


The initial idea for this project was conceived during a visit to my grandfather’s old, established, small “back yard” farm with stalls where chickens and other domestic animals are held in close contact with each other. The stalls have an open top and a concrete floor and are cleaned irregularly only with water wash. According to our hypothesis these conditions could be ideal for maintaining diverse virus populations in the environment and in the resident animals, and could facilitate viral transmission to newly introduced animals. In April, 2013 approximately ten healthy, 4-week-old chickens were introduced to the farm. A few days later one chicken showed signs of diarrhoea. The study sample was taken from this diseased chicken during the acute phase of diarrhoea.


Unexpectedly, the viral metagenomic analysis revealed the presence of all of the currently known chicken picornaviruses, plus a novel virus (chicken phacovirus 1) in a single cloacal sample (see the figure below). More surprising was the simultaneous presence of two genotypes of orivirus (A1 and A2), which indicated that the picornavirus diversity of the studied animal was not restricted to the presence of individual picornavirus genera, but included multiple genotypes of the same virus (i.e. orivirus A1 and A2). Co-infections with high numbers of different picornaviruses in a single animal could promote and facilitate potential recombination events. The presence of nearly identical, short, repeated RNA sequence motifs called “Unit A” sequences in the 3’ UTR of phylogenetically distant picornaviruses of genera Avisivirus, Orivirus and Megrivirus could also suggest the horizontal transfer (through recombination?) of certain genomic regions.


Figure image

Figure legend

Neighbor joining phylogenetic tree of the representative members of family Picornaviridae based on the amino acid sequences of 3D polymerese. The position of the five avian picornavirus clusters located on the main picornavirus lineages (coloured lines) are highlighted in grey. The original hosts of the avian picornaviruses are marked with thumbnail pictures. The phylogenetic position of the study viruses are indicated with black circles. Note that: the Pf-CHK1/PhV is the first known chicken picornavirus with complete genome which belongs to the avian sapelovirus cluster.


Introducing the author


Ákos Boros is a biologist at the Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary


About the research

A diarrheic chicken simultaneously co-infected with multiple picornaviruses: Complete genome analysis of avian picornaviruses representing up to six genera

Ákos Boros, Péter Pankovics, Ádám Adonyi, Hajnalka Fenyvesi, J. Michael Day, Tung Gia Phanc, Eric Delwart, Gábor Reuter

Virology, Volume 489, February 2016, Pages 63–74