REFERENCES
Abdel-Moneim, A. S., & Abdelwhab, E. M. (2020). Evidence for SARS-CoV-2
Infection of Animal Hosts. Pathogens , 9 (7), 529.
https://doi.org/10.3390/pathogens9070529
Bogner, P., Capua, I., Cox, N. J., & Lipman, D. J. (2006, August 31). A
global initiative on sharing avian flu data. Nature . Nature
Publishing Group. https://doi.org/10.1038/442981a
Boni, M. F., Lemey, P., Jiang, X., Lam, T. T. Y., Perry, B. W., Castoe,
T. A., … Robertson, D. L. (2020). Evolutionary origins of the
SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic.Nature Microbiology , 5 (11), 1408–1417.
https://doi.org/10.1038/s41564-020-0771-4
Bosco-Lauth, A. M., Hartwig, A. E., Porter, S. M., Gordy, P. W.,
Nehring, M., Byas, A. D., … Bowen, R. A. (2020). Experimental
infection of domestic dogs and cats with SARS-CoV-2: Pathogenesis,
transmission, and response to reexposure in cats. Proceedings of
the National Academy of Sciences of the United States of America ,117 (42), 26382–26388. https://doi.org/10.1073/pnas.2013102117
Braun, K. M., Moreno, G. K., Halfmann, P. J., Baker, D. A., Weiler, A.
M., Haj, A. K., … Friedrich, T. C. (2020). Transmission of
SARS-CoV-2 in 1 domestic cats imposes a narrow 2 bottleneck 3.BioRxiv , 2020.11.16.384917.
https://doi.org/10.1101/2020.11.16.384917
Carlos, R. S. A., Mariano, A. P. M., Maciel, B. M., Gadelha, S. R., de
Melo Silva, M., Belitardo, E. M. M. A., … Albuquerque, G. R.
(2021). First genome sequencing of SARS‐CoV‐2 recovered from an infected
cat and its owner in Latin America. Transboundary and Emerging
Diseases , tbed.13984. https://doi.org/10.1111/tbed.13984
Centers for Disease Control and Prevention (CDC). (2020). CDC 2019-Novel
Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel. Retrieved
December 31, 2020, from
https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html
Chaintoutis, S. C., Papadopoulou, E., Melidou, A., Papa, A., & Dovas,
C. I. (2019). A PCR-based NGS protocol for whole genome sequencing of
West Nile virus lineage 2 directly from biological specimens.Molecular and Cellular Probes .
https://doi.org/10.1016/j.mcp.2019.06.002
Chan, J. F. W., Kok, K. H., Zhu, Z., Chu, H., To, K. K. W., Yuan, S., &
Yuen, K. Y. (2020). Genomic characterization of the 2019 novel
human-pathogenic coronavirus isolated from a patient with atypical
pneumonia after visiting Wuhan. Emerging Microbes and Infections ,9 (1), 221–236. https://doi.org/10.1080/22221751.2020.1719902
Chao, Y. X., Rötzschke, O., & Tan, E. K. (2020, July 1). The role of
IgA in COVID-19. Brain, Behavior, and Immunity . Academic Press
Inc. https://doi.org/10.1016/j.bbi.2020.05.057
Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L.,
… Ruden, D. M. (2012). A program for annotating and predicting
the effects of single nucleotide polymorphisms, SnpEff: SNPs in the
genome of Drosophila melanogaster strain w1118; iso-2; iso-3.Fly , 6 (2), 80–92. https://doi.org/10.4161/fly.19695
Coppée, F., Lechien, J. R., Declèves, A. E., Tafforeau, L., & Saussez,
S. (2020). Severe acute respiratory syndrome coronavirus 2: virus
mutations in specific European populations. New Microbes and New
Infections , 36 , 100696.
https://doi.org/10.1016/j.nmni.2020.100696
Corman, V. M., Landt, O., Kaiser, M., Molenkamp, R., Meijer, A., Chu, D.
K. W., … Drosten, C. (2020). Detection of 2019 novel coronavirus
(2019-nCoV) by real-time RT-PCR. Eurosurveillance , 25 (3).
https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045
de Morais, H. A., dos Santos, A. P., do Nascimento, N. C., Kmetiuk, L.
B., Barbosa, D. S., Brandão, P. E., … Biondo, A. W. (2020).
Natural Infection by SARS-CoV-2 in Companion Animals: A Review of Case
Reports and Current Evidence of Their Role in the Epidemiology of
COVID-19. Frontiers in Veterinary Science , 7 (October),
1–10. https://doi.org/10.3389/fvets.2020.591216
Drechsler, Y., Alcaraz, A., Bossong, F. J., Collisson, E. W., & Diniz,
P. P. V. P. (2011, November). Feline Coronavirus in Multicat
Environments. Veterinary Clinics of North America - Small Animal
Practice . Vet Clin North Am Small Anim Pract.
https://doi.org/10.1016/j.cvsm.2011.08.004
Gallais, F., Velay, A., Wendling, M.-J., Nazon, C., Partisani, M.,
Sibilia, J., … Fafi-Kremer, S. (2020). Intrafamilial Exposure to
SARS-CoV-2 Induces Cellular Immune Response without Seroconversion.MedRxiv , 2020.06.21.20132449.
https://doi.org/10.1101/2020.06.21.20132449
Gaudreault, N. N., Trujillo, J. D., Carossino, M., Meekins, D. A.,
Morozov, I., Madden, D. W., … Richt, J. A. (2020). SARS-CoV-2
infection, disease and transmission in domestic cats. Emerging
Microbes and Infections , 9 (1), 2322–2332.
https://doi.org/10.1080/22221751.2020.1833687
Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B.,
Callender, C., … Neher, R. A. (2018). NextStrain: Real-time
tracking of pathogen evolution. Bioinformatics , 34 (23),
4121–4123. https://doi.org/10.1093/bioinformatics/bty407
Halfmann, P. J., Hatta, M., Chiba, S., Maemura, T., Fan, S., Takeda, M.,
… Kawaoka, Y. (2020). Transmission of SARS-CoV-2 in Domestic
Cats. New England Journal of Medicine , 383 (6), 592–594.
https://doi.org/10.1056/nejmc2013400
Hou, Y. J., Chiba, S., Halfmann, P., Ehre, C., Kuroda, M., Dinnon, K.
H., … Baric, R. S. (2020). SARS-CoV-2 D614G variant exhibits
efficient replication ex vivo and transmission in vivo. Science ,370 (6523), eabe8499. https://doi.org/10.1126/science.abe8499
Kim, D., Lee, J. Y., Yang, J. S., Kim, J. W., Kim, V. N., & Chang, H.
(2020). The Architecture of SARS-CoV-2 Transcriptome. Cell ,181 (4), 914-921.e10. https://doi.org/10.1016/j.cell.2020.04.011
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment
with Burrows-Wheeler transform. Bioinformatics , 25 (14),
1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N.,
… Durbin, R. (2009). The Sequence Alignment/Map format and
SAMtools. Bioinformatics , 25 (16), 2078–2079.
https://doi.org/10.1093/bioinformatics/btp352
Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., … Tan, W.
(2020). Genomic characterisation and epidemiology of 2019 novel
coronavirus: implications for virus origins and receptor binding.The Lancet , 395 (10224), 565–574.
https://doi.org/10.1016/S0140-6736(20)30251-8
Luan, J., Lu, Y., Jin, X., & Zhang, L. (2020). Spike protein
recognition of mammalian ACE2 predicts the host range and an optimized
ACE2 for SARS-CoV-2 infection. Biochemical and Biophysical
Research Communications , 526 (1), 165–169.
https://doi.org/10.1016/j.bbrc.2020.03.047
Patterson, E. I., Elia, G., Grassi, A., Giordano, A., Desario, C.,
Medardo, M., … Decaro, N. (2020). Evidence of exposure to
SARS-CoV-2 in cats and dogs from households in Italy. Nature
Communications , 11 (1), 6231.
https://doi.org/10.1038/s41467-020-20097-0
Plante, J. A., Liu, Y., Liu, J., Xia, H., Johnson, B. A., Lokugamage, K.
G., … Shi, P. Y. (2020). Spike mutation D614G alters SARS-CoV-2
fitness. Nature , (September).
https://doi.org/10.1038/s41586-020-2895-3
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree 2 -
Approximately maximum-likelihood trees for large alignments. PLoS
ONE , 5 (3). https://doi.org/10.1371/journal.pone.0009490
Rambaut, A., Holmes, E. C., O’Toole, A., Hill, V., McCrone, J. T., Ruis,
C., … Pybus, O. G. (2020). A dynamic nomenclature proposal for
SARS-CoV-2 lineages to assist genomic epidemiology. Nature
Microbiology , 5 , 1403–1407.
Sailleau, C., Dumarest, M., Vanhomwegen, J., Delaplace, M., Caro, V.,
Kwasiborski, A., … Le Poder, S. (2020). First detection and
genome sequencing of SARS-CoV-2 in an infected cat in France.Transboundary and Emerging Diseases , 67 (6), 2324–2328.
https://doi.org/10.1111/tbed.13659
Segalés, J., Puig, M., Rodon, J., Avila-Nieto, C., Carrillo, J.,
Cantero, G., … Vergara-Alert, J. (2020). Detection of SARS-CoV-2
in a cat owned by a COVID-19-affected patient in Spain.Proceedings of the National Academy of Sciences of the United
States of America , 117 (40), 24790–24793.
https://doi.org/10.1073/pnas.2010817117
Shi, J., Wen, Z., Zhong, G., Yang, H., Wang, C., Huang, B., … Bu,
Z. (2020). Susceptibility of ferrets, cats, dogs, and other domesticated
animals to SARS-coronavirus 2. Science , 368 (6494),
1016–1020. https://doi.org/10.1126/science.abb7015
Shi, Z., & Hu, Z. (2008). A review of studies on animal reservoirs of
the SARS coronavirus. Virus Research , 133 (1), 74–87.
https://doi.org/10.1016/j.virusres.2007.03.012
Sievers, F., & Higgins, D. G. (2014). Clustal Omega. Current
Protocols in Bioinformatics , 2014 , 3.13.1-3.13.16.
https://doi.org/10.1002/0471250953.bi0313s48
Staines, H., Kirwan, D., Clark, D., Adams, E., Augustin, Y., Byrne, R.,
… Planche, T. (2020). Dynamics of IgG seroconversion and
pathophysiology of COVID-19 infections. MedRxiv ,
2020.06.07.20124636. https://doi.org/10.1101/2020.06.07.20124636
Temmam, S., Barbarino, A., Maso, D., Behillil, S., Enouf, V., Huon, C.,
… Eloit, M. (2020). Absence of SARS-CoV-2 infection in cats and
dogs in close contact with a cluster of COVID-19 patients in a
veterinary campus. BioRxiv , 2020.04.07.029090.
https://doi.org/10.1101/2020.04.07.029090
Totton, S. C., Sargeant, J. M., & O’Connor, A. M. (2020). How could we
conclude cat-to-human transmission of SARS-CoV-2? Zoonoses and
Public Health . Wiley-VCH Verlag. https://doi.org/10.1111/zph.12788
Wan, Y., Shang, J., Graham, R., Baric, R. S., & Li, F. (2020). Receptor
Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on
Decade-Long Structural Studies of SARS Coronavirus. Journal of
Virology , 94 (7). https://doi.org/10.1128/jvi.00127-20
Wilm, A., Aw, P. P. K., Bertrand, D., Yeo, G. H. T., Ong, S. H., Wong,
C. H., … Nagarajan, N. (2012). LoFreq: A sequence-quality aware,
ultra-sensitive variant caller for uncovering cell-population
heterogeneity from high-throughput sequencing datasets. Nucleic
Acids Research , 40 (22), 11189–11201.
https://doi.org/10.1093/nar/gks918
Wölfel, R., Corman, V. M., Guggemos, W., Seilmaier, M., Zange, S.,
Müller, M. A., … Wendtner, C. (2020). Virological assessment of
hospitalized patients with COVID-2019. Nature , 581 (7809),
465–469. https://doi.org/10.1038/s41586-020-2196-x
Wu, A., Peng, Y., Huang, B., Ding, X., Wang, X., Niu, P., …
Jiang, T. (2020). Genome Composition and Divergence of the Novel
Coronavirus (2019-nCoV) Originating in China. Cell Host and
Microbe , 27 (3), 325–328.
https://doi.org/10.1016/j.chom.2020.02.001
Wu, F., Zhao, S., Yu, B., Chen, Y. M., Wang, W., Song, Z. G., …
Zhang, Y. Z. (2020). A new coronavirus associated with human respiratory
disease in China. Nature , 579 (7798), 265–269.
https://doi.org/10.1038/s41586-020-2008-3
Zhang, Q., Zhang, H., Gao, J., Huang, K., Yang, Y., Hui, X., …
Jin, M. (2020). A serological survey of SARS-CoV-2 in cat in Wuhan.Emerging Microbes and Infections , 9 (1), 2013–2019.
https://doi.org/10.1080/22221751.2020.1817796