Just got alerted by Paula Olsiewski & Eileen Choffnes to this paper Role of Transportation in Spread of Porcine Epidemic Diarrhea Virus Infection, United States by James Lowe, Phillip Gauger, Karen Harmon, Jianqiang Zhang, Joseph Connor, Paul Yeske, Timothy Loula, Ian Levis, Luc Dufresne, and Rodger Main. The paper is in the CDC journal “Emerging Infectious Diseases” and is freely available. I am calling this post a “pre-journal club” because I thought it might be good to post some quick thoughts and see what others thought of the paper too.
The paper reports on a study of PEDV – porcine epidemic diarrhea virus which was detected in pigs in the US in 2013. And the study did some sampling of the trailers used to transport pigs and reported some interesting results and conclusions. The abstract of the paper is as follows:
“After porcine epidemic diarrhea virus (PEDV) was detected in the United States in 2013, we tested environmental samples from trailers in which pigs had been transported. PEDV was found in 5.2% of trailers not contaminated at arrival, , suggesting that the transport process is a source of transmission if adequate hygiene measures are not implemented.”
This is an interesting and potentially important finding. And I commend the authors for getting out the results quickly and in an open / free journal.
However, I am not completely convinced of their conclusions. I am not not convinced either. But I am somewhere in between.
On first look, the one thing that makes me less than convinced is that as far as I can tell the authors only took one sample per trailer / time point. To get samples they used the following approach:
“Sample collection consisted of rubbing a phosphate-buffered saline—moistened pad (Swiffer, Procter & Gamble, Cincinnati, OH, USA) over an ≈900 cm2 area of the trailer floor, 15 cm from the rear door. “
Then these samples were assayed via real-time reverse transcription PCR to test for the presence / absence / amount of PEDV.
I like the specificity of their methods section. However, there are a variety of reasons to think that another sample collected in the same way might not produce the same results. The concern I have about this is as follows:
One of their key findings is that some trailers tested negative for PEDV before pigs were unloaded and then tested positive after the pigs were unloaded. This might mean (as they concluded) that the trailers got contaminated in association with the unloading. However, given that the frequency of positive results (i.e., detection of PEDV) in samples was pretty low jt seems plausible that the presence of PEDV in some trailers could have just been missed in the original sampling. Thus it would be nice to see some information on biological and technical replications of the sampling.
Again, the paper seems interesting to me. But it also seems, well, preliminary.
Any other thoughts would be welcome.
I wonder whether PEDv can be transmitted through the air. Do you know? Approximately half of human norovirus cases are believed to occur due to inhalation rather than ingestion. Is that a reasonably relevant model for PEDv?
The difference between fomite-based transmission in livestock and humans might be important, and the survival and reproduction might be affected by environmental conditions. I didn’t see much in the way of a description of environmental factors in the article. Of course I don’t know whether and how much they matter, but I start with an assumption that they do matter.
Sample location on the floor of a building makes a lot of difference in the results of assays for dust or particle-borne agents-especially when looking for things that are tracked in on occupants’ shoes. Samples collected close to entry doors have the most material that is tracked in from the outside, of course.
By collecting close to the rear of the truck, presumably they were more likely to pick up positive samples after the animals exited than before, as the article says.
Does transmission occur in the air? What is the source of the viruses found on the floor of the truck? What is the incubation period once the virus is inhaled or ingested? Is it from feces (presumably) but could it also be from stepping in the feces of others. And how much of this transfer might have occurred versus other transfer mechanisms?
Jonathan is right: sample-to-sample variation can be important. If these swab samples for the PEDv vary anything like air samples for fungi, it might be important here too. Experience with air sampling for fungi has shown that the air sampling in the same location and with the same instruments can return results based on culture-dependent methods with low levels for three days running and on the fourth day the numbers are off the charts. This occurred in a study done after health complaints rose at the Library of Congress back in the late 1980s. There was no explanation for this variation.
I did some work in an allegedly mold-contaminated house that had negative findings for culture-dependent mold counts in September (end of dry season) and was off the charts (>50,000 cfu/m^3) in March (end of wet season). Also, we did “aggressive sampling” while the Sept results were done quiescently. I used the same technician and lab in March that had done the work in September. So, air sampling methods, even though standardized, can still produce different results on different days or under different conditions. I suspect that some of this type of variation occurs for swab sampling as well, “no matter how standardized.” Thus, as Jonathan indicates, multiple samples are always a reasonable first order QA/QC measure.
Early investigations of new threats are appropriately at the “screening” level to begin to identify patterns. These patterns help develop the design of the next study. What is regrettable is that more variables were not characterized, or, at least, not reported in the article.
Microbes don’t exist in isolation from the environment. An interesting article in the current issue of PLoS Biology (The Ecology of Collective Behavior) nicely highlights the dynamic and interactive nature of the occurrence and evolution of microbial (and other) populations. Check it out: doi/10.1371/journal.pbio.1001805.
This really raises more questions to me than it answers.
So 5.2% of the trailers tested positive! but what about the pigs before they were put in there? On top of that, pigs going into a trailer are going to inevitably track in some of their environment.
So is this contamination coming from dirt/mud tracked in maybe with higher level of virus particles, or is it coming from infected pigs themselves?
On top of that the area they are testing is really small for a trailer, and pigs moving in and out will certainly move things around. So is it possible those extra were already contaminated? They certainly didn’t do enough testing to completely erase this idea from my mind.
Assuming that’s not the case, it still leaves the question, were only 5.2% of the shipments contaminated (pigs or their environments) and all their transports were contaminated? Were 100% positive and only 5.2% contaminated as a result? Or do those 5.2% only perhaps represent shipments of pigs where there was a really heavy infection?
As I said, it just leaves a lot of questions in my mind I wish they would have addressed.
Lots of questions are good. And I for one am glad they published the paper even with it leaving many things unanswered. I think for emerging infectious diseases we need more rapid data and idea sharing … and they are to be commended for that. Again, not sure I agree with many of their conclusions but still happy they put this out there.
True, I think it raises a potentially important means of transmitting the virus, not to mention the importance of speed and data sharing in this (and data sharing in all science). And this May point people towards addressing many of those questions I raise, if not this lab, where they otherwise may have not thought of it.
I’d like to see a follow up though, certainly. Especially because I’d imagine the danger of this as a method of transmission is going to depend on both this particular virus itself (shedding amount, etc. infection rate, and all that), plus the environments of the farms themselves.
So in the end I think they’ve succeeded, in that they’ve left me wanting more.
I will send a note to the authors — see if they can comment on what they are doing next
As the lead author (the blog post is wrong as the authors are James Lowe, Phillip Gauger, Karen Harmon, Jianqiang Zhang, Joseph Connor, Paul Yeske, Timothy Loula, Ian Levis, Luc Dufresne, and Rodger Main) I fully appreciate that these results are preliminary. Please remember that these data were collected within 60 days of the first reported case of PEDV in the US so we were working on a very tight timeline with little knowledge of the sensitivity of our methods or approach. We know that transport of livestock and the trucks that carry them are a primary route of transmission for other important diseases (there is a large body of literature on PRRSV in pigs and YEARS of observational evidence for TGE and Swine dysentery). What we wanted to prove to the people that manage farms and harvest plants is that how they used and managed live haul transport was important to the spread of this new disease. The industry has these results by early july of 2013 and had made changes using them. The important thing was that we could take a truck that was NOT contaminated at arrival and contaminate it at the harvest plant – i.e. any truck that had been to a plant could be contaminated. The relative rate was not important but the fact that it could happen allowed producers to shift management strategies. In this case not all all trucks were washed and disinfected but it allowed producers to concentrate washing on the trucks that were the greatest risk of propagating disease (i.e. trucks that went back to breeding herds).
As for the sensitivity of the protocol. We now have a vastly improved PCR as it has been optimized over the last 9 months to greatly improve performance. We don’t know what that would mean for this study but know we missed some contaminated trailers. In addition we know that our sampling method was not that sensitive. It takes a highly concentrated sample to be detected with this method (we are in the process of completing that work and publishing those results now). So we know that a positive sample means something but a negative sample is not very informative (the false negative rate is high).
Would we do anything different next time? Likely no – this was “boots on the ground” epidemiology project in the face of an outbreak of a novel disease. As scientists we like precision but in the face of a crisis being directionally correct is more important than being perfect. We needed data to make decisions. As veterinarians we are asked to be managers of disease. I learned a long time ago that great managers don’t make better decisions they just make more of them. These kinds of studies help us do that.
The biggest win from this paper was a rapid response by a coalition of the industry. The authors of this paper are clinicians and consultants to over 50% of the swine raised in the USA.
As for what we are doing next… nothing on transport the industry has “settled” that question. Trucks are risky and there are strategies we can use to control that risk. We are working on managing farms that are infected which has proven to be a bigger challenge than we thought. Lots of work to do understanding where the virus hides on farms and how the immune system responds.
I have fixed the author information. In the previous version of the post I had written that I was “alerted to a paper by Paula Olsiewski and Eileen Choffnes” and what I meant was that these two people told me about the paper, not that they wrote the paper.
Oh – and thanks so much for quickly responding
That’s understandable, since I don’t work with industry groups I wouldn’t have considered something like that (saying it’s settled, move on), but i can understand the rush. Though to the industry then I would say the idea to consider it settled does seem perhaps a bit short-cited. But, what are you going to do I suppose.
*short sighted… My spelling stinks.
id like to se defininate research showing rather the blood collected from piglets to create blood meal used for protein in weaner meals and some piglets pellets can carry PEDV. And if it can be passed onto the piglets consuming the end product of Warner meal/pellets. This seems to be a significant source of contamination/infection for some farms.