An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3

Abstract

Human parechovirus types 1-16 (HPeV1-16) are positive strand RNA viruses in the family Picornaviridae. We investigated a 2015 outbreak of HPeV3 causing illness in infants in Victoria, Australia. Virus genome was extracted from clinical material and isolates and sequenced using a combination of next generation and Sanger sequencing. The HPeV3 outbreak genome was 98.7% similar to the HPeV3 Yamagata 2011 lineage for the region encoding the structural proteins up to nucleotide position 3115, but downstream of that the genome varied from known HPeV sequences with a similarity of 85% or less. Analysis indicated that recombination had occurred, may have involved multiple types of HPeV and that the recombination event/s occurred between March 2012 and November 2013. However the origin of the genome downstream of the recombination site is unknown. Overall, the capsid of this virus is highly conserved, but recombination provided a different non-structural protein coding region that may convey an evolutionary advantage. The indication that the capsid encoding region is highly conserved at the amino acid level may be helpful in directing energy towards the development of a preventive vaccine for expecting mothers or antibody treatment of young infants with severe disease.

Figure 1. Sequence similarity between Geelong’s outbreak parechovirus and related parechovirus sequences.

SimPlot analysis was used to calculate and plot the degree of similarity between the Geelong outbreak parechovirus and a panel of parechovirus strain sequences obtained from NCBI. The key to the panel of strain sequences are as follows: AB759206, AB759207, AB759199, AB759204 HPEV3 (Yamagata 2011 lineage – only include coding regions); AB759189, AB7591 HPeV3 (Yamagata 2008 lineage - only include coding regions); GQ183030, GQ183032, GQ183027 HPeV3; GQ183018, GQ183020 HPEV1; KJ659490 HPeV3; KT726985 HPeV1; AJ889918 HPeV3; FJ840477 HPeV1; and DQ315670 HPeV4. Based on information from AB759206 (HPeV3Yamagata 2011 lineage52), the structural/capsid coding region is from nucleotide 701–3013 and the non-structural protein coding region from 3014–7231.

Figure 2. Bootscan analysis of Geelong’s outbreak parechovirus with selected parechovirus sequences.

Bootscan analysis was used to calculate the percentage of the permutated tree to which the selected parechovirus sequences cluster to the Geelong outbreak parechovirus sequence. The key to the selected parechovirus sequences is as follows: AB759204 HPeV3 (Yamagata 2011 lineage - only coding region); GQ183018, GQ183020, KT726985 HPeV1; and DQ315670 HPeV4. Based on information from AB759206 (HPeV3Yamagata 2011 lineage52), the structural/capsid coding region is from nucleotide 701–3013 and the non-structural protein coding region from 3014–7231.