How ASF Spreads
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Before the SARS-CoV-2 virus emerged in China in late 2019, one of the infectious disease threats we spent a good deal of time on was African Swine Fever - which, while not affecting humans directly - causes huge economic losses and growing food insecurity around the world.
After smoldering in Eastern Europe and Russia for a decade, ASF arrived in China in the summer of 2018, and quickly spread across that nation killing a much as half of their pig population.
ASF is often spread - at least locally - via infected pigs and wild boars, but the virus can live for weeks or even months in infected food products, and exported pork products are believed to be a major cause of the international spread of African Swine Fever.
In 2018 the FAO described how easily ASF can cross borders, and even oceans.
A robust virus with a long lifeDespite being caused by a relatively stable double-stranded DNA virus in the Asfarviridae family, ASF remains very difficult to control. Only recently has an experimental vaccine been shown to be effective in limited trials (see Vaccine targets African swine fever), and it is not yet commercially available.
The ASF virus is very hardy and can survive long periods in very cold and very hot weather, and even in dried or cured pork products. The strain detected in China is similar to one that infected pigs in eastern Russia in 2017 but, so far, and while the investigations continue, the China Animal Health and Epidemiology Center has found no conclusive evidence of this latest outbreak's source or linkages.
"The movement of pig products can spread diseases quickly and, as in this case of African Swine Fever, it's likely that the movement of such products, rather than live pigs, has caused the spread of the virus to other parts of China," explained Juan Lubroth, FAO's Chief Veterinarian.
Just over a year ago, in DEFRA: Preliminary Assessment Of ASF Outbreak In the Americas (Dominican Republic), we looked at the first detection of African Swine Fever in the Americas in nearly 40 years. It has since spread to neighboring Haiti.
Although North American swine herds remains free of ASF, it continues to have new opportunities to enter our backyard (see USDA's A qualitative assessment of the likelihood of ASF virus entry to the United States. March 2019).
While a vaccine may be on the way, a new preprint - published yesterday in BioRxiv - reports on a sudden, and unexpected, spate of variant detections in Europe. Changes that could have an, as yet, unknown impact on the future course of the disease.
First the abstract, and a brief excerpt, then I'll return with a postscript.
African swine fever virus – variants on the rise
Jan Hendrik Forth, Sten Calvelage, Melina Fischer, Jan Hellert, Julia Sehl-Ewert, Hanna Roszyk, Paul Deutschmann, Adam Reichold, Martin Lange, Hans-Hermann Thulke, Carola Sauter-Louis, Dirk Höper, Svitlana Mandyhra, Maryna Sapachova, Martin Beer, Sandra Blome
doi: https://doi.org/10.1101/2022.09.07.506908
This article is a preprint and has not been certified by peer review [what does this mean?].Preview PDF
Abstract
African swine fever virus (ASFV), a large and complex DNA-virus circulating between soft ticks and indigenous suids in sub-Saharan Africa, has made its way into swine populations from Europe to Asia. This virus, causing a severe haemorrhagic disease (African swine fever) with very high lethality rates in wild boar and domestic pigs, has demonstrated a remarkably high genetic stability for over 10 years.Consequently, analyses into virus evolution and molecular epidemiology often struggled to provide the genetic basis to trace outbreaks while few resources have been dedicated to genomic surveillance on whole-genome level.During its recent incursion into Germany in 2020, ASFV has unexpectedly diverged into five clearly distinguishable linages with at least ten different variants characterized by high-impact mutations never identified before.Noticeably, all new variants share a frameshift mutation in the 3' end of the DNA polymerase PolX gene O174L, suggesting a causative role as possible mutator gene. Although epidemiological modelling supported the influence of increased mutation rates, it remains unknown how fast virus evolution might progress under these circumstances.Moreover, a tailored Sanger sequencing approach allowed us, for the first time, to trace variants with genomic epidemiology to regional clusters. In conclusion, our findings suggest that this new factor has the potential to dramatically influence the course of the ASFV pandemic with unknown outcome. Therefore, our work highlights the importance of genomic surveillance of ASFV on whole-genome level, the need for high-quality sequences and calls for a closer monitoring of future phenotypic changes of ASFV.
(SNIP)
Conclusion
In conclusion, we report here the emergence of distinct ASFV variants that point to a higher sequence variability of ASFV in strains observed at the German-Polish border. We identified a frameshift mutation in the O174L gene/ PolX that affects the 5’ binding pocket of the enzyme as plausible cause.The resulting ASFV variants allow, on the upside, for the first time a meaningful genomic ASFV epidemiology. On the downside, the accelerated occurrence of viral variants has the potential to result in ASFV variants with novel features which might in the future dramatically influence the course of the ASFV epizootic with unknown outcome.
While we worry first and foremost about diseases that can directly infect, sicken, or even kill humans, agricultural diseases like ASF, FMD, Rift Valley Fever, Anthrax, and avian flu (among others) are also capable of having a huge impact on society.
Food insecurity - whether due to the cost or the unavailability of food - can bring on severe economic, and societal challenges. In extreme cases, it can even destabilize regions (see Iran: Bird Flu, Food Insecurity & Civil Unrest).
The importation of non-native agricultural disease threats is of constant concern, and can have devastating economic impacts. In 2001 the UK experienced an outbreak of FMD that cost them as much as 18 billion (USD).
The USDA prepares for this threat with FAD PReP, which stands for Foreign Animal Disease Preparedness and Response Plan. FAD PReP is designed to deal with a variety of imported animal diseases, including:
- Avian influenza
- Foot-and-Mouth Disease
- Classical Swine Fever
- Newcastle Disease
- African Swine Fever
As a result, the cost of eggs has doubled over the past 6 months, while the coast of chicken has soared (see chart below). Further price increases are possible if - as feared - we get another wave of bird flu this fall.
For most people in the United States the impact of the avian flu enzootic has been limited to increased pain at the checkout aisle, but should AI worsen - or worse, be joined by another severe epizootic - the situation could grow substantially more dire.
And in countries with fewer resources, or that are already experiencing food insecurity, the impacts could be devastating.
In a world with 8 billion hungry mouths to feed, anything that threatens the supply of affordable meat protein must be regarded as a serious threat. Which is why, when we start seeing growing diversity among ASF variants, it is worthy of our attention.
