Results and discussion
All dogs were found SARS-CoV-2 PCR negative. Out of the 22 cats tested,
one was SARS-CoV-2 Rt-qPCR positive with a Ct of 29 from the rectal swab
whereas nasopharyngeal swabs were negative. Another cat was found
positive for the feline coronavirus (Ct 25.6).
The RNA was sent to Institut Pasteur for confirmation of SARS-CoV-2 and
was confirmed PCR positive (CT 43, 30 and 32 with RdRp IP2, RdRp IP4 and
E genes).
The rectal swab extract found positive by RT-qPCR was subjected to
targeted iSeq100 system sequencing, and the run produced 3,858,853 raw
reads with a Phred quality score of 28. By using BWA-MEM, the mapping
against SARS-CoV-2 reference (NC_045512) allowed the retrieval of
high quality viral genomic sequences, with a read depth of 30x, covering
around 94% of the full length genome (sequence data has been deposited
in GISAID with accession number EPI_ISL_437349).
Sequence analysis of the cat SARS-CoV-2 genome showed that it belongs to
the Nextstrain (https://nextstrain.org/ ) proposed
phylogenetic clade A2a, which is consistent with
the phylogenetic analysis of the recent human French SARS-CoV-2.
Compared to the Wuhan reference sequence, and on the basis of the 94%
covered genome, the cat SARS-CoV-2 sequence displays eight nucleotide
mutations, with two not yet described in ORF1ab (T10800C and A13394G).
Among these mutations, five have led to amino-acids mutations, of which
four in ORF1ab (T265I, I3512T, K4377E and P4715L). It should also be
noted that the cat SARS-CoV-2 genome presents the amino-acid mutation
D614G in the Spike glycoprotein, specific of the clade A2
and encompassing most of the French SARS-CoV-2 sequences (figure 1).
The confirmed positive cat was a 9-year-old female of European breed. It
has been hospitalised on 13 April due to anorexia, vomiting and cough.
These clinical signs occurred 17 days after her owner has been sick from
COVID-19. The first samples (NP and R swabs, serum) were taken on 17 of
April, eight days after the beginning of symptoms. A second set of
samples was taken on cat that was healed (on 27 April) and the PCR
results were negative for both swabs. These results suggest a rapid
clearance of the virus from the intestinal tract, which is consistent
with experimental infection of cats suggesting presence of infectious
virus only until day 6 post-infection (Shi et al, 2020). Serological
analysis by MIA showed a strong positive signal against SARS-CoV-2 for
the two sera taken at 10 days apart (figure 2). The value of
fluorescence emitted was 36 times higher than the average of the values
emitted by control cats (sera sampled before the appearance of
COVID-19). A cross-reactivity was observed with the N SARS-CoV antigen
but given the high sequence identity between the two antigens, this
result was expected. Both sera were also confirmed positive by ELISA.
The mean value of the sixteen cats sampled before 2019 and the
apparition of the SARS-CoV-2 virus gave a mean OD value of 0,074, with a
standard deviation of 0,0116. Therefore, the cut-off was OD450nm : 0,109
(mean of negative values + 3x SD). The two sera taken at 10 days apart
gave a mean value of 0.682 and 0.356 respectively. These OD values,
clearly above the standard cut-off criteria (OD450 nm 0,109), reveal the
presence of specific antibodies to the SARS-CoV-2. The serological
results (MIA + ELISA) confirm that the cat was able to replicate
SARS-CoV-2.
Cats had already been tested positive for the SARS-CoV-2 in the United
States, Belgium, Hong Kong and Wuhan, China, where outbreaks occurred.
In the cases reported in Belgium and in the USA, clinical signs were
reported (diarrhoea, vomiting and breathing difficulty for the first and
respiratory illness for the second) whereas no clinical sign was
detected in Hong Kong. Experimentally, pulmonary lesions have been
described in young cats (Shi at al, 2020). Serological tests carried out
on cats in Wuhan demonstrated that that SARS-CoV-2 has infected cat
populations in Wuhan during the outbreak (15 of 102 tested were positive
in ELISA and 11 had neutralizing antibodies with titers ranging from
1/20 to 1/1080). The highest titers correspond to cats living with
owners with confirmed COVID-19 infection. No information on clinical
signs in any of the tested cats is available. Recently, Halfmann et al
(2020) showed the possible transmission of SARS-CoV-2 between domestic
cats in close contact.
As in previously identified cases worldwide, the French cat was living
with a person who was confirmed positive for COVID-19. However, a
previous study carried out on the animals of veterinary students of the
Alfort veterinary school (Enva, Maisons Alfort), also infected by
SARS-CoV-2 suggested that cats and dogs are not easily infected by the
SARS-CoV-2, even when they are in close contact with infected owners
(Temmam et al, 2020). Large serological analyses will be necessary to
evaluate the real circulation of the SARS-CoV-2 among pets.
Concerning the infection of dogs with SARS-CoV-2, two cases have been
reported in Honk- Kong in February and March 2020 (Sit, et al, 2020). In
both cases, dogs were placed under quarantine after their owner was
hospitalised due to COVID-19. Samples taken from the dogs were tested
positive for SARS-CoV-2 by RT-PCR and serological analysis. Both animals
did not exhibit any specific clinical signs. Shi et al, 2020 have
shown by experimental infection that dogs have low susceptibility to
SARS-CoV-2. In our investigations, none of the 11 dogs tested were PCR
positive despite having been in close contact with their infected owners
and exhibiting clinical signs.
Even though the risk of transmission of the SARS-CoV-2 to the cat
appears to be low, the authors therefore advise people with COVID-19 to
limit close contact with their cats, without compromising their welfare.