A novel coronavirus with severe acute respiratory syndrome (SARS-CoV-2) emerged in Wuhan, China at the end of 2019 and has since become one of the most economically effective pandemics. When the world was locked down, molecular genetic research introduced the public to various mutations that the (SARS-CoV-2) has undergone.
To learn: Almost complete genome of the SARS-CoV-2 Delta variant (AY.3) identified in a dog in Kansas, USA. Image source: Pyrstai / Shutterstock.com
The presence of these mutations led to some of them being called Variants of Interest (VOI), such as Eta (B.1.525), Iota (B.1.526) and Kappa (B.1.617.1), depending on the preceding factors. In comparison, some strains with more serious mutations were identified as worrisome variants (VOC) such as Alpha (B.1.1.7 / Q), Beta (B.1.351.1,2,3), Delta (B.1.617.2.) / AY) and Gamma (P.1.) Variants. Taken together, all of these variants have been classified based on genomic sequencing, particularly with respect to the coding regions in the spike (S) protein within the SARS-CoV-2 genome.
Despite the current global introduction of vaccines, SARS-CoV-2-VOCs are still characterized by increased transferability, more serious disease outcomes, a reduction in neutralization in vaccinated people or errors in diagnostic detection.
To date, the theory of zoonotic transmission has been popular; however, the possibility of a reverse situation in which human-to-animal transmission occurred was not common. Investigations into possible animal reservoirs of SARS-CoV-2 with the original virus from China showed that cats and ferrets were approved for the virus, while dogs, pigs, chickens and ducks were significantly less susceptible to infection.
However, studies of the Delta variant have shown high levels of ribonucleic acid (RNA) and viral shedding by hamsters and Asiatic lions that cause mild to moderate clinical symptoms. There have been isolated reports that the Delta variant has also been isolated from dogs; However, there is a lack of sequencing data for the virus in dog hosts.
In a recent study, researchers document the detection and sequencing of an AY.3 virus from a 12-year-old collie who lives with an owner infected with SARS-CoV-2. The animal was admitted to the Kansas State Veterinary Health Center (KSU VHC) for unrelated symptoms and tested positive for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) two days after admission.
A 12-year-old collie was admitted to the KSU VHC because it collapsed after a trip. The dog was diagnosed with a hemoabdoma attributable to a bleeding spleen mass viewed on an abdominal examination with sonography for trauma (FAST) scan and abdominocentesis.
Chest x-rays showed a multilobar alveolar lung pattern with a mediastinal shift. Differential diagnoses for multilobar pneumonia, atelectasis, or multifocal pulmonary hemorrhage were made.
A splenectomy was performed the day after admission, while multifocal hepatic nodules and a mass of 5 × 4 cm (cm) were found on the left medial lobe of the liver during the operation. The postoperative pulmonary oximetry was between 88% and 90%, suggesting poor blood flow; therefore the dog was placed in an oxygen cage overnight. Chest x-rays showed pulmonary changes associated with progressive aspiration pneumonia and mild cylindrical bronchiectasis.
The dog was released 5 days after ingestion without the need for additional oxygen. The dog died two days after being released. No autopsies or additional examinations were carried out. The owner had tested positive for SARS-CoV-2 before the dog was admitted.
The nasal swab sample that was taken from the dog after admission to the KSU VHC was tested and confirmed SARS-CoV-2-positive with a Ct of 12.17 two days after admission. The positive nucleic acid was prepared for sequencing of the entire genome immediately after the qRT-PCR confirmation.
A total of 1,458,751 reads were assigned to the reference genome. The whole genome sequence obtained from the dog sample had several previously unidentified, unique, consensus-level changes in a SARS-CoV-2 genome that may have played a role in the rapid human-to-dog adaptation.
A complete SARS-CoV-2 coding region and partial 5 ‘and 3’ UTRs were extracted from the deep sequencing data. The genome had a length of 29,884 nucleotides with a GC content of 38.0% and codes for 12 open reading frames of the expected size. The genome was 99.96% identical to the closest genome (an internal sample, hCoV-19 / USA / KS-KSU-2046/2021, GISAID # EPI_ISL_3693315), which corresponds to 8 nucleotide differences. Of these nucleotide differences (4 in ORF1; 2 in S; 1 in M; 1 in N) three non-synonymous (NS) changes (1 in ORF1; 1 in S; 1 in N) were new for SARS-CoV-2 so far sequenced delta variants.
In addition, 5/7 of the subconsensus variants identified within the spike coding region in the dog sequence were also identified in the next internal human reference case. Taken together, the entire genomic sequence, as well as phylogenetic and subconsensus variant analysis, indicated that the virus that infected the animal was from a local outbreak cluster.
The exact cause of death wasn’t necessarily COVID-19 as the dog had a weakened immune system linked to the liver and spleen masses along with some of the classic COVID-19 symptoms like pneumonia, bronchiectasis, and lack of oxygen. The high RNA load in the nasal swab suggested that the dog may have shed viruses, which poses a risk of infection to susceptible people in the area.
The current study shows that there was a likelihood of host-to-animal transmission of the virus, although the exact causes of death remain controversial. The novel sequences found in the dog underscore the importance of screening pets for COVID-19 to reduce transmission rates in the surrounding community. These sequences could very well serve as clues for the identification of other variants and their role in the different species they infect.