Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhoea virus. MC Jarvis, H Ching Lam, Y Zhang, L Wang, RA Hesse, BM Hause, A Vlasova, Q Wang, J Zhang, MI Nelson, MP Murtaugh, and D Marthaler. Preventive Veterinary Medicine 123 (2016) 175–184. http://dx.doi.org/10.1016/j.prevetmed.2015.10.020
What are they studying?
Complete genomic sequencing was done on PEDv isolates from the 2014 outbreaks in the US, which were then compared with complete genome sequences available from GenBank (n = 126) to determine the most variable genomic areas of the virus and improve understanding of viral evolution. This analysis should help understand the impact of variation on diagnostics and vaccine development.
How is it done?
A total of 93 field isolates (from faecal, intestinal homogenate, oral fluid, feedback and environmental samples) were selected for complete genome sequencing from January to December 2014. Samples were screened for PEDv by RT-PCR. Samples for complete genome sequencing were selected based on the criteria of a high viral concentration from the RT-PCR results and geographical diversity within the US. Using the complete PEDv genome sequences from this study (n = 93) and the available PEDv sequences from GenBank (n = 126), two nucleotide and amino acid alignments were created and analysed to determine the phylogenetic relationships between American and global PEDv sequences to identify genes or regions of high diversity between strains. To understand the virus evolution and changes in the receptor binding domain (RBD), which is believed to be central in PEDv infectivity and virulence various complex tools were used for recombination analysis.
What are the results?
This article contains several revelations, namely:
- nsp2 and nsp3 were the most divergent regions between strains (part of ORF1a)
- Among the structural genes, the S gene had the highest entropy levels compared to the other structural genes and the highest evolutionary rate, reflecting a higher selection pressure.
- Recombination plays a pivotal role in the evolution of coronavirus by creating new strains with altered virulence. The Minnesota211 strain originated from a recombination event between an S-INDEL and a US pandemic strain. While recombination may occur more often during an epidemic, recombination events were demonstrated in most of the Asian strains.
What implications does this paper have?
The PED genealogy picture is more complicated than was previously thought. Results indicate changes in ORF1 and spike regions which point towards a high level of variation between isolates. Diagnostic tests aimed towards the virus' ORF1 region may yield false negatives due to high genetic variability. The more conserved C-terminal region of the structural protein of the virus may be a more suitable target.
Epidemiological studies only examining the variable S region may miss important evolutionary changes occurring in the ORF1 region. Whole virus sequencing should lead to more accurate conclusions.
Despite differences between US and Asian strains, some similarities do exist which support an Asian origin for the US pandemic strains. The origin of the European strains is less clear.
Recombination and evolution rate is high in both US and Asian strains, which which makes the development of a broadly protective vaccine a challenge.
The view from the field by Enric Marco
The recent outbreak of porcine epidemic diarrhoea (PED) that swept Asia, USA and Europe has highlighted the weaknesses of our production system. Although biosecurity measures have, in general, improved significantly, they have not been sufficient to prevent the spread of infection. But why is an infection that was already known in Europe since the late 80s hitting back so forcefully? How is it possible that biosecurity improvements have had no impact on dissemination? Why have countries that were already hit by PED in previous years suffered a new epidemic?
As we mentioned before, the infection had been regularly hitting Europe. One of the latest descriptions before the most recent outbreaks came from Italy in 2008, but the outbreak's spread was smaller, more localized and less virulent. When the infection reached the United States, it spread across the country and into Canada in a few months, and its symptoms were much more aggressive in North America when compared to those observed in Europe, causing high mortality among the affected piglets (100% in some cases). In other words, the same disease had two very distinct features: infectivity and virulence. The new molecular biology techniques have allowed the study of the genome of the DEP viruses involved in these new outbreaks, proving that, indeed, this is a different strain from the one isolated in the European outbreaks. The differences are so extreme that they not only affect the two characteristics mentioned, but also cause the vaccines developed from classical strains (in the North American market) to be unable to control the virus. This new virus may even yield false negatives results in some diagnostic tests based on some of the genome fragments that have been modified in these new strains.
Today, knowledge of the genetic differences between strains allows us to understand the reasons for the occurrence of new outbreaks, and should help us improve some issues, such as diagnosis or biosecurity. Detailed knowledge of the different strains of a particular virus, such as the DEPv, allows us to work out its movements, to study potential biosecurity failures in order to correct them in the future, and to develop diagnostic tests based on the most stable genes in order to avoid problems derived from potential viral recombinations.