Efficient Direct and Limited Environmental Transmission of SARS-CoV-2 Lineage B.1.22 in Domestic Cats

ABSTRACT The susceptibility of domestic cats to infection with SARS-CoV-2 has been demonstrated by several experimental studies and field observations. We performed an extensive study to further characterize the transmission of SARS-CoV-2 between cats, through both direct and indirect contact. To that end, we estimated the transmission rate parameter and the decay parameter for infectivity in the environment. Using four groups of pair-transmission experiment, all donor (inoculated) cats became infected, shed virus, and seroconverted, while three out of four direct contact cats got infected, shed virus, and two of those seroconverted. One out of eight cats exposed to a SARS-CoV-2-contaminated environment became infected but did not seroconvert. Statistical analysis of the transmission data gives a reproduction number R0 of 2.18 (95% CI = 0.92 to 4.08), a transmission rate parameter β of 0.23 day−1 (95% CI = 0.06 to 0.54), and a virus decay rate parameter μ of 2.73 day−1 (95% CI = 0.77 to 15.82). These data indicate that transmission between cats is efficient and can be sustained (R0 > 1), however, the infectiousness of a contaminated environment decays rapidly (mean duration of infectiousness 1/2.73 days). Despite this, infections of cats via exposure to a SARS-CoV-2-contaminated environment cannot be discounted if cats are exposed shortly after contamination. IMPORTANCE This article provides additional insight into the risk of infection that could arise from cats infected with SARS-CoV-2 by using epidemiological models to determine transmission parameters. Considering that transmission parameters are not always provided in the literature describing transmission experiments in animals, we demonstrate that mathematical analysis of experimental data is crucial to estimate the likelihood of transmission. This article is also relevant to animal health professionals and authorities involved in risk assessments for zoonotic spill-overs of SARS-CoV-2. Last but not least, the mathematical models to calculate transmission parameters are applicable to analyze the experimental transmission of other pathogens between animals.

Gerhards et al. have performed experimental studies to evaluate both direct contact and environmental transmission via fomites of SARS-CoV-2 in cats. They found direct contact transmission occurred to 3/4 contacts with limited evidence of environmental transmission to a single cat. The animals were sampled repeated and both qRT-PCR and seroconversion were used as evidence of infection. As a final component of the manuscript, the author's utilize their experimental data to estimate the R0, decay rate parameter.
Major Comments: 1. The authors have extensively used qRT-PCR to assess viral infection. They have used both E gene PCR which indicates the presence of the virus and sub genomic PCR as a surrogate for viral replication. When using qRT-PCR to assess viral replication the data is convincing when viral RNA is detected over multiple time points and the levels of RNA peak and then decline. This would be consistent with a productive infection if replicating virus was assayed. The interpretation of E and sgPCR becomes challenging when there is detection at a single time point. This is observed in the Group 1 indirect contact. This animal also did not seroconvert. Therefore, the conclusion of limited transmission is based upon a single data point. It is possible that an infected animal could have shed mucus containing infected cells and that the indirect contact animal sampled this infected material. Thus, I would recommend that all the indirect contact samples be cultured to ensure replicating virus can be recovered. In the event infectious virus cannot be recovered the authors will need to explain two possible interpretations of their findings: one in which the sample is positive and one in which the sample is virus negative.
Minor Comments: 1. Results section page 4. The experimental designed outlined in this section is very difficult to understand. Understanding this section required re-reading both the results, methods section, and figure legend multiple times. This section should be revised for clarity to clearly explain the experimental design and should also clearly indicate the number of animals and replicates. 2. In the section on clinical signs and pathology, the authors need to indicate if they expected pathology on day 23. If so, then please provide a rationale and/or reference. If not, please indicate pathology would not be expected at day 23. Staff Comments:

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Response to reviewers
Reviewer comments: Reviewer #1 (Comments for the Author): In this study, the authors studied the direct and indirect transmission of SARS-CoV-2 by fomites. The transmission by direct contact was efficient, while indirect transmission by a contaminated environment was substantively less efficient. In general, the study has been adequately designed and the materials and methods sustained the results and discussion. We could isolate infectious virus from lungs and trachea up until DPI 4, and from the nasal conchae until DPI 7. Considering that the first swabs were taken on DPI 8 in the current study, we think that our study designs has missed the window to take samples for virus isolations. This limitation of our study design is also described the discussion section.
We added a sentence in the results section clarifying this comment:

Viral RNA load in swabs and organs
Oral and rectal swabs were taken frequently, while nasal and oropharyngeal swabs were only sampled on a few time points (D0, D8, D15 and D23). Swabs were analyzed by both total E-gene PCR according to (14), and by subgenomic PCR (sgPCR) according to (15). No virus isolations were attempted, because many swab samples had high Ct values (> 30) from which virus can only occasionally be isolated (16, 17).

(…)
And we also added a sentence in the discussion section: (…) Although our study contributes to an improved understanding of SARS-CoV-2 transmission amongst cats by providing a detailed estimation of both the transmission rate parameter and the decay rate parameter, there are limitations that need to be considered. For instance, we did not follow a potential transmission chain from an inoculated cat to a direct contact then to another direct contact cat, which would be a sensitive measure for infectiousness of the infected direct contact cats. Next, our follow-up time was limited to 17 days for the environmentally exposed cats, which may have been too short for cats exposed to lower amounts of SARS-CoV-2 to develop antibodies compared to an inoculated cat. Furthermore, a sparse sampling under anesthesia was performed on purpose, however, samples collected from the nose and oropharynx were the most sensitive samples and we may have missed viral shedding of cats. This is particularly true for samples taken shortly after exposure, which usually have the highest viral loads and highest chance to retrieve an infectious virus. In our study, no samples suitable for virus isolation were obtained. (…) * It will be valuable to include more details on the M&M of environmental sampling, since it is the main focus of the study. I.e. In my understanding, the authors wiped a tissue over the surfaces to collect the sample. Were the samples collect in the same spot over the duration of the experiment?
Response of authors: The samples were all collected on different spots each day, except of the litter box. We specified this in the methods section: Animal inoculation and samplings (…) Electrostatic dust cloths were used to sample the environment daily from D0 to 23. There were five different sample locations: floor (random area of 10x10cm; a different spot was sampled every day), wall (random area of 1x1m; a different spot was sampled every day), litter box (non-porous plastic, rim of one litter box was wiped; the same rim of the same litter box was sampled every day), feeding tray (stainless steel, one feeding tray out of two was wiped before feed was added per group every day), toy (cotton and non-porous plastic; another randomly selected toy was wiped every day. (…) * Were the cages cleaned daily? Sandboxes?
Response of authors: The pens were not cleaned after cats X.1 were inoculated to not interfere with environmental contamination. Faeces and urine were removed from the litter boxes each day.
We added this to the methods section: Animal housing and experimental design (…) In every animal unit, pen A and B were separated by more than 30cm distance and a plastic separator to prevent droplet transmission between the pens. To avoid transmission by personnel, animal technicians first entered Pen B before approaching Pen A until D6, and from D7 onwards Pen A first, and Pen B second. The inoculated cats (i.e. X.1) were handled last. No exchange of equipment took place between pens. The pens were not cleaned from D0 until the end of the study, except for the daily removal of feces and urine from litter boxes. The average temperature throughout the study was 20.4°C in Group 1 (range 19.9 -21.1), 19. Response of authors: In the materials and methods section, we added the texture of plastic. For stainless steel, floor and walls as well as for cotton, a distinction between porous and non-porous is not common.

Animal inoculation and samplings
(…) Electrostatic dust cloths were used to sample the environment daily from D0 to 23. There were five different sample locations: floor (random area of 10x10cm; a different spot was sampled every day), wall (random area of 1x1m; a different spot was sampled every day), litter box (non-porous plastic, rim of one litter box was wiped; the same rim of the same litter box was sampled every day), feeding tray (stainless steel, one feeding tray was wiped before feed was added; one out of the two feeding trays were sampled per group every day), toy (cotton and non-porous plastic; another randomly selected toy was wiped every day. (…) * About the lack of direct transmission in one group. Do you have records of cat behavior? Did the cats lick each other?
Response of authors: As described in the supplemental material 1, we recorded cat behaviour using video, and analyzed the activity in each group based on pixel changes. Compared to the other three groups, it seems that overall activity was somewhat lower in group 3. However, due to the three-dimensional animal housing, it is difficult to distinguish between real interaction and false interaction due to proximity of two cats on a two-dimensional video, when they in fact were on different levels on the z-axis. Moreover, the analysis of interactions in this study is further complicated by the fact that some interactions are not visible on video (e.g. when two cats are in the same litter box). For proper analysis of interactions, a tracker-based system would have been preferred that allows analyses in a three-dimensional environment. We therefore feel that we could only speculate about a reduced interaction in group 3, without sufficient proof supporting our speculation.
* Did the authors change the sandboxes?
Response of authors: Please see our response to the question regarding cleaning of the pens above.
* Include a paragraph on the limitations of this study, especially the absence of VI.
Response of authors: We added the absence of virus isolation to our section of limitations in the discussion: (…) Although our study contributes to an improved understanding of SARS-CoV-2 transmission amongst cats by providing a detailed estimation of both the transmission rate parameter and the decay rate parameter, there are limitations that need to be considered. For instance, we did not follow a potential transmission chain from an inoculated cat to a direct contact then to another direct contact cat, which would be a sensitive measure for infectiousness of the infected direct contact cats. Next, our follow-up time was limited to 17 days for the environmentally exposed cats, which may have been too short for cats exposed to lower amounts of SARS-CoV-2 to develop antibodies compared to an inoculated cat. Furthermore, a sparse sampling under anesthesia was performed on purpose, however, samples collected from the nose and oropharynx were the most sensitive samples and we may have missed viral shedding of cats. This is particularly true for samples taken shortly after exposure, which usually have the highest viral loads and highest chance to retrieve an infectious virus. The absence of suitable samples for virus isolation is a clear limitation of our study. Anesthesia can negatively impact the immune system (19,20), implying that frequently anesthetized animals may become more sensitive to infections compared to animals infected under natural conditions. Finally, in our analysis we assume that direct contact cats are equally infectious as the inoculated cats. This assumption cannot be tested based on virus excretion because the samples that we took more frequently without anesthesia (oral swabs and rectal swabs) were less sensitive than samples taken sparsely under anesthesia (nasal swabs and oropharyngeal swabs), which would have been more adequate to compare the shedding levels of inoculated and direct contact cats. It also cannot be tested based on transmission to contact cats as only one possibly infected cat (the indirect contact cat) was housed together with a recipient. This did not lead to infection of the recipient cat, but there was also no infection in one out of four instances of contact between inoculated cats and their recipients. Response of authors: We thank the reviewer for this comment and agree to the need for virus isolations. Please see our answer to the first question of reviewer 1 for explanation why virus isolations were not performed. Moreover, we have analyzed the data using the two different scenarios as presented in table 1 -if we use serology as a readout, the indirect contacts did not become infected as well as 2/4 direct contacts; while if we use sgPCR as a readout, 1/8 indirect contacts as well as 3/4 direct contacts are considered infected.
We added another column in table 1 'R same day' to indicate the transmission rate that occurs within one day which we hope will aid understanding the differences in the estimates: Table 1. Results for the stochastic SIR model with environmental transmission. Four different scenarios (datasets) were analyzed based on the observed infection events using either seroconversion ('sero') or sgPCR ('SG') as a test to determine which cats had become infected and analyzing only the first part of the experiment with direct exposure ('direct') or combining the data with indirect exposure ('both'). The model yielded two parameters: the transmission rate parameter β and the decay rate parameter μ. From those parameters, the shedding rate and the reproduction ratio of SARS-Cov-2 in cats were calculated, assuming an infectious period T of six days (10) The results section was changed as following: (…) For the analysis performed using the scenario represented in the datasets 'data3' we observed that the direct transmission SIR model fits the data best because the direct-contact cat -Cat 4.2 ( Figure 2) -became infected very early during exposure at the interval 1 to 2 days. However, when using the sgPCR as indicator of infection, there is an infection observed (Cat 1.3) in the indirect transmission group ('data4'). Using this scenario (data4), we get a finite estimate of the decay rate parameter. The maximum likelihood estimate (Table 1) is calculated for the transmission rate parameter β = 0.23 day -1 (95% confidence Intervals CI: 0.06 -0.54) and for decay rate parameter μ = 2.73 day -1 (0.77 -15.82), which implies an average survival time (duration of infectiousness in the environment = 1/ μ) of 8.8 (1.5 -31.2) hours. The interpretation of these estimates can be seen in Figure 4. For the direct transmission SIR model, infection only occurs during direct exposure, i.e. in the five days the direct contact animals are present. In the environmental SIR model the infection probability increases over time during the direct exposure period and it is still present when the infected animals, contaminating the environment, are removed and naïve animals are placed to indirectly expose them to the contaminated environment.
Assuming an infectious period of 6 days (10), the estimated R 0 is 2.12 (0.92 -4.08) for transmission between cats for the direct and the indirect transmission route combined. The R 0 for the direct contact transmission alone is 1.38 (0.36 -3.24). The contribution of the environment to the overall transmission is the difference between these two R 0 : 2.12 -1.38 = 0.74. In other words, around 1/3 of the overall transmission risk could be attributed to the environment. (…) And in the discussion, we added: (…) A major challenge in the analysis of transmission experiments is the definition of 'being infected'. Almost all cats (except indirect contacts in Group 3) were tested positive by E-gene PCR, indicating the presence of viral RNA in samples. These positive samples were further tested by sgPCR, which specifically quantifies the mRNA of the E-gene, generated during virus active replication. Next to the presence of viral RNA or mRNA, the third potential definition of 'being infected' is seroconversion, which may be dependent on inoculation dose and follow-up time.
Given the different results in the number of contact cats considered infected based on serology or sgPCR, we analysed transmission using either sgPCR or seroconversion as the determinant of successful infection. We explored the use of information generated from only the direct-contact experiments or both direct and indirect contact experiments. Serology as an indicator for successful transmission did not provide sufficient information for reliable quantification of the decay rate. Contrasting R 0 estimates were obtained when using data from direct-contact only (data1) and from direct and indirect contact (data2). However, when using sgPCR as an indicator for successful transmission, similar R 0 were estimated for datasets 3 and 4, which were 2.5 (95%CI: 0.97 -5.15) and 2.12 (95%CI: 0.92 -4.08), respectively (Table 1). These estimates are in agreement with those made by (10) using published data from direct transmission experiments R 0 = 3.0 (95% CI: 1.5 -5.8) or from household infections R 0 = 2.3 (95%CI: 1.1 -4.9) and provide further certainty that cat-to-cat transmission is efficient. In addition, the analysis also indicates that transmission is a result of both close contact interaction between cats and the contamination of the shared environment, with the later having a lower contribution (1/3 of the overall contribution) to the risk of transmission. (…) And in the methods section, we added:

Statistical analyses incorporating environmental transmission
The observed number of cases in an interval in each separated pen is the dependent variable. This dependent variable is assumed to be binomial distributed with the number of non-infected cats as the binomial total. Additionally, it is assumed that inoculated and contact infected cats are equally infectious. In this case, analysis can be done as Bernoulli trials for each recipient separately. Whether the recipient becomes infected also depends on the number of infected cats in the pen through the infectivity present in the environment. The environmental load is assumed to change deterministically according to the following differential equation: Note that ' ' is always a whole number and changes stochastically with integer jumps. Hence the different notation used for E(t) which changes continuously. Given the ' ' and ' 0' (the environmental contamination at the start of the interval), values ( ) can be calculated during each interval by solving equation (1). The value of can be fixed without loss of generality.
To further understand the contribution of a contaminated environment to transmission, the shedding rate is chosen such that ( ) = 1 for one infectious individual during one day in a clean environment. This shedding rate then depends on the decay rate as follow: For an interval ∆ , the probability to become infected for each of the recipient cats is: This model assumes shedding to the environment with constant rate parameter and decay rate parameter (inactivation of the virus) . The transmission occurs with transmission rate parameter . The parameters and can be estimated by maximum likelihood either directly by optimizing the log likelihood as we did here (Supplementary Material 2) or by Generalized Linear Models using an offset (29). The parameter can be then calculated using the estimated value of . The total contribution of both environment and direct contact to transmission from the first day of shedding of one infectious individual is then and the basic reproduction number is: where the is the infectious period. Because for the first day of exposure (donor -recipient) ( ) = 1 , the transmission rate during this day is equal to and it represents the expected transmission due to direct contact alone. The reproduction number due to direct contact alone would be = * . The apparent contribution of the environment to the total transmission is then the difference between and .
Minor Comments: 1. Results section page 4. The experimental designed outlined in this section is very difficult to understand. Understanding this section required re-reading both the results, methods section, and figure legend multiple times. This section should be revised for clarity to clearly explain the experimental design and should also clearly indicate the number of animals and replicates.
Response of authors: We acknowledge that the study design is complex, and that it can be described in the results section as well to enhance readability.
We added a brief description of the study design to the results section: The study design is explained in detail in the Methods section and summarized in Figure 1. In brief, a total of 16 cats were divided into four replicate groups (group 1, 2, 3 and 4) consisting of either four male or four female cats per group. Each group was divided in two subgroups, which were housed in two separate pens A and B: cats X.1 and X.2 were housed together in Pen A from D0 until D6 and in Pen B from D7-23, and cats X.3 and X.4 were housed together in Pen B from D0-6 and in Pen A from D7-23, where X=experimental group. All four cats identified by X.1 were inoculated on D0 and all cats identified by X.2 were housed together with X.1 except of on the day of inoculation of cats X.1 (D0). On D6, cats X.1 and X.2 were removed from Pen A and cats X.3 and X.4 were placed in (contaminated) Pen A; while cats X.1 and X.2 were then placed in (clean) Pen B in which cats X.3 and X.4 had been housed until then. Thus, four independently housed pairs of cats were used to assess direct transmission (X.1 and X.2) and contamination of the environment (pen) where new naïve cats (two per contaminated pen: X.3 and X.4) were introduced following the removal of the pair of cats used to assess direct transmission. The sample size was calculated based on published data (10). Of the direct transmission pairs, the four donor cats became infected following inoculation, and three of those transmitted infection to their corresponding contact cats. Of the eight cats exposed to the contaminated pens, only one got infected. Below, we provide the detailed results of the observed infection characteristics and the quantitative assessment of transmission.

Clinical signs and pathology
Two of the four inoculated cats occasionally showed mild serous nasal discharge. All 12 cats that had direct contact or indirect contact with the inoculated cat remained without clinical signs. The body weights of all 16 cats remained constant. A video-based analysis of activity of the direct transmission pairs revealed no changes in activity post inoculation compared to before inoculation (baseline measurement), indicating that inoculated and direct contact cats displayed a similar activity pattern regardless of SARS-CoV-2 inoculation/direct exposure (Supplemental Material 1). One cat from Group 4 (Cat 4.3) died on D18 and was necropsied the same day. It was confirmed that the death was unrelated to SARS-CoV-2 infection. All other cats were euthanized on D23. As expected, no lesions were observed in gross pathology, and there were no substantial differences in relative lung weights between the animals upon necropsy (data not shown). Lung tissue showed no SARS-CoV-2-related histopathology. However, mild lung changes -such as lymphoplasmacytic bronchoadenitis, bronchusassociated lymphoid tissue (BALT) hyperplasia, infiltrates of macrophages and few neutrophils in alveolar lumina -were observed in inoculated animals, and in direct and indirect contact animals (data not shown) suggesting these changes were nonspecific. Other evaluated organs (nasal conchae, trachea, tracheobronchial lymph node, duodenum, ileum, colon, mesenterial lymph node and pancreas) showed also no substantial histopathological findings. No viral antigen could be detected by immunohistochemistry in any of the investigated tissues (data not shown). (…)

Figure 2. E-gene and subgenomic PCR results on swabs.
For total E-gene PCR, the mean log10 RNA copies/mL from two technical replicates of the same swab are shown. The replicates were generated by isolating RNA from the swab sample in duplicate and subsequent PCR. The sgPCR was performed once with the RNA sample from the replicate that showed a lower Ct value in the total E-gene PCR. Shapes indicating the results are jittered so that overlapping shapes can still be observed. The red line indicates the day of removal of cats 1 and 2 from Pen A and housing them in Pen B. Response of authors: According to epidemiological theory, sustained transmission of a pathogen is explained by the R0 estimate. When R0 >1, one can expect sustained transmission and an epidemic to take place; while when R0 < 1, one could expect that transmission won't be sustained and infection will die out. The statistical analysis and the repetitions in the experiment allowed this assessment (see also Velthuis et al, 2002). We acknowledge that the wording of 'sustained transmission' can be interpreted as 'sustained in a population'. We therefore changed the appropriate sections in the manuscript for clarification.
In the abstract: These data indicate that transmission between cats is efficient and can be sustained (R 0 >1), however, the infectiousness of a contaminated environment decays rapidly (mean duration of infectiousness 1/2.73 days).
Despite this, infections of cats via exposure to a SARS-CoV-2-contaminated environment cannot be discounted if cats are exposed shortly after contamination.
In the discussion section: This study explored direct and indirect transmission of SARS-CoV-2, lineage B.1.22, among domestic cats in an experimental setting. We particularly quantified the duration of infectiousness of an environment with contaminated surfaces. We found that the infectiousness of contaminated surfaces would decay within 8.8 (95%CI: 1.5 -31.2) hours, making transmission via contaminated surfaces alone inefficient, but it cannot be excluded yet. We also provide further confirmation that cat-to-cat transmission is efficient.
However, when using sgPCR as an indicator for successful transmission, similar R 0 were estimated for datasets 3 and 4, which were 2.5 (95%CI: 0.97 -5.15) and 2.12 (95%CI: 0.92 -4.08), respectively (Table 1). These estimates are in agreement with those made by (10) using published data from direct transmission experiments R 0 = 3.0 (95% CI: 1.5 -5.8) or from household infections R 0 = 2.3 (95%CI: 1.1 -4.9) and provide further certainty that cat-to-cat transmission is efficient. In addition, the analysis also indicates that transmission is a result of both close contact interaction between cats and the contamination of the shared environment, with the later having a lower contribution (1/3 of the overall contribution) to the risk of transmission. (…) 1st Revision -Editorial Decision We appreciate your consideration of the reviewers' comments and for the submission of a revised version addressing the issues raised. As you will see from the referees' comments that additional information needs to be provided. Please fully address the comment from reviewer 2, particularly point 4 in regards to length of infectivity. We ask that this be provided, before we consider you manuscript further.
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