PONE-D-23-24651Quantitative assessment of the risk of release of foot-and-mouth disease virus via production of bull semen in the USAPLOS ONE

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1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No

Reviewer #2: Yes

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Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: Quantitative assessment of the risk of release of foot-and-mouth disease virus via production of bull semen in the USA

Anne Meyer, Jay Weiker, Rory Meyer

This is an interesting modelling study on use of laboratory tests to mitigate the risk of release of FMDV via a bull stud. I would suggest to include the main mitigation methods in the title. The title should tell the story (tell them what you going to tell them). It is quite difficult to understand the methodology the text could be more precise. For the laboratory tests the authors should use laboratory jargon (antigen and genome testing are different) and veterinary jargon (lockdown is a human medicine control measure not a veterinary). The compartmental model is a deterministic model and therefore 100% of the animals will become infected. In a stochastic model every individual has a probability of becoming infected and sometimes infection fails. A stochastic model resembles much better what is happening in the field where antibodies against non-structural proteins are often only present in a proportion of the animals whereas they were all present during the outbreak. Still the deterministic model is probably sufficient for the purpose, but it would be good to mention the limitations.

I think the estimate of the sensitivity of clinical inspection is too high, I would use a slightly lower estimate and a wider confidence interval. It would be interesting to see if it would end up in the top 5 of variables that have the highest influence on the outcome.

There are more papers on quantifying transmission, especially performed for the use in models, it would be good to use them (I think I listed all that involved transmission in non-vaccinated cattle).

Comments:

Abstract:

Generatio spotanea is not happening. So, infection should start somewhere, this is not mentioned in the abstract. The abstract is vague, be precise, be concise.

Introduction:

Line 39: Lockdown was used during the corona epidemic but does not cover "movement stand-still" which is normally used in veterinary medicine. A lockdown during coronal included the shut-down of opera, music festivals etcetera, but cows do not attend opera. People were allowed to move during a lockdown, even fly to foreign countries. During a "movement stand-still" livestock is kept on the farm.

Line 51 - 53: I would find the risk of causing a new outbreak more interesting than the risk of releasing FMD virus.

Materials and methods:

Line 67: The US context, is not specific. Barnsize, number of barns per facility etc. is more specific, e.g. a table with the relevant information would be nice.

Line 69: What is a teaser on a bull stud? In other farming systems these are castrated male animals, but I assume there are no castrated bulls on a bull stud.

Line 72: For individual housing see: Bouma, A., Dekker, A., de Jong, M. C. M. 2004. No foot-and-mouth disease virus transmission between individually housed calves. Vet. Microbiol. 98(1); 29-36.

Line 76: You mean 8 daily 'direct' contacts. The number of indirect contacts must be much higher, especially if you would include airborne transmission.

Line 77 - 78: You should also include: Cottral, G. E., Gailiunas, P., Cox, B. F. 1968. Foot-and-mouth disease virus in semen of bulls and its transmission by artificial insemination. Arch. Gesamte Virusforsch. 23(4); 362-377. And Sharma, G. K., Subramaniam, S., De, A., Das, B., Dash, B. B., Sanyal, A., Misra, A. K., Pattnaik, B. 2012. Detection of foot-and-mouth disease virus in semen of infected cattle bulls. Indian J. Anim. Sci. 82(12); 1472-1476. There is not a lot of data on excretion of FMDV in semen but ignoring >50% of the published papers is strange. Later you mention both papers.

Line 89: Tmax? It is a bit strange to assume that all bull become immune. In epidemiology it is assumed that an infection enters a state in which the effective reproduction number Re = 1 = R0 x (1 - recovered fraction). So, the recovered fraction will be 1 - 1/R0. For R0 = 4, then the recovered fraction will be 0.75. Estimates of R0 in endemic settings are 1.2 - 1.6, but in a bull stud it might be higher. In within pen transmission studies R0 was over 10, but many between pen transmission studies show low R0 values.

Line 107 - 108: What do you mean with antigen assay. Do you mean a complement fixation test or ELISA to detect viral antigen in the sample? (antigen is the protein that is immunogenic and can be detected by ELISA or complement fixation test; virus is capable of infecting cells and can be detected by virus isolation; genome can be tested by RT-PCR). In figure 1 you mention PCR test (which is incorrect as it an RNA virus so you would perform an RT-PCR test), so you do not do antigen detection, but genome detection.

Line 110: A batch contains 200 - 800 straws (estimate from an interview in a newspaper, I do not know if this is accurate, but the author should know and mention this), I assume that even if 1 straw is removed you consider the batch released. Or are the collection facility and the distribution facility 2 separate entities?

Line 124: It is a valid assumption that an AI centre would have a high biosecurity status, but in the 1997 CSF outbreak in the Netherlands an AI centre became infected and transmitted CSF to many farms. The moment they knew CSF was present they quickly removed some old boars for slaughter, but due to the haste biosecurity was breached……. The personal that were responsible for the boars helped them on the truck that moved them to the slaughterhouse, but after entering the truck they entered the AI facility through the same door as was used to remove the boars. So, they did not use the showering facility to enter the place as they did every morning……… Is the probability really low?

S1: Trying to understand I did the calculation 143/28779 = 0.004968901 (neither for the other models). This does not match the numbers in the table. Are the numbers correct? I'm missing the number of replicates in each model, as I understand that you used the outcomes of different runs for the empirical distribution of H.

Line 133: What is the value of tmax? When I use P1 x 365 / H = 0.00034 x 365 / 0.0024 = 51.7 days (the unit is nowhere defined, I assume it is days). I see this is mentioned in the results.

Line 135: In most experimental studies 10 000 bovine ID50 is injected into the tongue, then 100% clinical disease is seen. But in studies with other routes of infection, clinical disease might be absent (see e.g. Sutmoller, P., Olascoaga, R. C. 2002. Unapparent foot and mouth disease infection (sub-clinical infections and carriers): implications for control. Rev. Sci. Tech. 21(3); 519-529). What is the sensitivity of the model for this assumption of 100% clinical disease (compare e.g. with 80%).

Line 152: The sensitivity of clinical detection might be biased. The persons responsible for clinical detection did the estimation. The estimate for the 2006 UK outbreak was much lower. Cattle in the field were observed over the fence, clinical disease was missed. It would be good to do a sensitivity analysis on this parameter (e.g. 50% sensitive)

Line 164: "intense scrutiny" is this true? When the bull is not used for collecting semen it is only fed, and not inspected on a daily basis.

Line 176: I searched Wikipedia for Beta PERT distribution but could not find it. Do you mean a normal PERT distribution?

Line 215 - 225 and elsewhere: Replace PCR by RT-PCR

Line 227: Be specific. "Are all bulls negative for FMD genome at the next routine blood test?"

Line 237: What is meant by "The use of either an antigen or an antibody test was considered"? Be precise.

Line 248: You refer to Brocchi et al. who validated ELISA tests to detect antibodies against non-structural proteins. That is a good choice, but you should mention that in line 241 "Antibody ELISA to detect antibodies against non-structural proteins". In non-vaccinated cattle the sensitivity of a good NS ELISA is high but increases with the time after infection. In the Brocchi paper all 5 sera collected 7-14 dpi in non-vaccinated cattle were positive.

Line 249: replace "Antigen assay on serum" by "Genome detection in serum".

Line 256: sensitivity of the RT-PCR is high when compared to virus isolation. But the probability of scoring a positive sample in a bull that is infected is important. This is also high in non-vaccinated cattle. But referring to sensitivity is not that relevant if virus isolation is the gold standard.

Line 289: How many false positive results are expected? 3 every 100 samples? Be precise.

Line 290 and elsewhere: Replace "antigen" by "genome" or "RT-PCR"

Line 298 - 306: Do I understand correctly that clinical detection is less important than RT-PCR, this is probably due to the limited SD that is given to clinical detection. In the sensitivity analysis only 1 SD difference is tested.

Line 313: Replace "Serological surveillance" by "Laboratory testing of sera" (serological surveillance refers to evaluation of antibodies and is not used for RT-PCR testing).

Line 350 - 353: Perhaps the author should evaluate the following papers it gives information on relation between transmission rate in calves that are separated (Bouma et al. 2004) and calves that mix freely (Orsel et al. 2005):

Bouma, A., Dekker, A., de Jong, M. C. M. 2004. No foot-and-mouth disease virus transmission between individually housed calves. Vet. Microbiol. 98(1); 29-36.

Orsel, K., Dekker, A., Bouma, A., Stegeman, J. A., de Jong, M. C. M. 2005. Vaccination against foot and mouth disease reduces virus transmission in groups of calves. Vaccine 23(41); 4887-4894.

For the risk of transmission by the environment by indirect contact (not airborne as Bouma et al. showed that calves in the same room did not transmit FMDV).

Bravo de Rueda, C., de Jong, M. C., Eble, P. L., Dekker, A. 2015. Quantification of transmission of foot-and-mouth disease virus caused by an environment contaminated with secretions and excretions from infected calves. Vet. Res. 46; 43.

Colenutt, C., Brown, E., Nelson, N., Paton, D. J., Eblé, P., Dekker, A., Gonzales, J. L., Gubbins, S. 2020. Quantifying the Transmission of Foot-and-Mouth Disease Virus in Cattle via a Contaminated Environment. mBio 11(4); e00381-20.

Quantification of the transmission rate in the incubation period was studied by:

Graves, J. H., McVicar, J. W., Sutmoller, P., Trautman, R. 1971. Contact Transmission of Foot-and-Mouth Disease from Infected to Susceptible Cattle. J. Infect. Dis. 123(4); 386-391.Orsel, K., Bouma, A., Dekker, A., Stegeman, J. A., de Jong, M. C. M. 2009. Foot and mouth disease virus transmission during the incubation period of the disease in piglets, lambs, calves, and dairy cows. Prev. Vet. Med. 88(2); 158-163.

Charleston, B., Bankowski, B. M., Gubbins, S., Chase-Topping, M. E., Schley, D., Howey, R., Barnett, P. V., Gibson, D., Juleff, N. D., Woolhouse, M. E. 2011. Relationship between clinical signs and transmission of an infectious disease and the implications for control. Science 332(6030); 726-9.

Reviewer #2: Quantitative assessment of the risk of release of foot-and-mouth disease virus via production of bull semen in the USA

Aim: The present manuscript presents a quantitative assessment of the risk of release of FMD virus from some of the largest bull studs in the US via contaminated frozen bovine semen.

https://doi.org/10.3390/ani11061697 : this paper will help you in introduction and discussion

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Reviewer #1: No

Reviewer #2: No

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Laboratory testing and on-site storage are successful at mitigating the risk of release of foot-and-mouth disease virus via production of bull semen in the USA

PONE-D-23-24651R1

Dear Dr. Meyer,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Reviewers' comments:

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Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: All requested comments have been corrected so the manuscript is ready to be Accept

Thousands of frozen bovine semen doses are produced daily in the US for domestic

use. An incursion of foot-and-mouth disease (FMD) in the country would pose strong

challenges to the movements of animals and animal products between premises.

Secure supply plans require an estimation of the risk associated with target

commodities and the effectiveness of mitigation measures. This study presents the

results of a quantitative assessment of the risk of release of FMD virus from five of the

largest commercial bull studs in the US via contaminated frozen processed semen.

The methodology from a previous study was adapted to better fit the US production

system and includes more recent data. Two models were combined, a deterministic

compartmental model of FMD transmission and a stochastic risk assessment model.

The compartmental model simulated an FMD outbreak within a collection facility

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Reviewer #2: Yes: Ahmed N F Neamat-Allah

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