Cool! We Now Have New Delta Sub-Variants Such As AY.3 Infecting Dogs! College of Veterinary Medicine, Kansas State University Reports Case Study

Coronavirus News: Researchers from the College of Veterinary Medicine, Kansas State University-USA have reported a case study involving a dog being infected with a new Delta sub-variant called AY.3. To date, it must be noted that there is literally no concerted effort of genomic sequencings of samples taken from domestic animals or even wild animals let alone constant testing to see if they have been infected with the SARS-CoV-2 coronavirus. The findings have enormous implications as zoonotic transmissions and recombinant events with other animal-based viruses could result in a catastrophic phenomenon.

 
SARS-CoV-2 descriptions of infection and transmission have been increasing in companion animals in the past year. Although canine susceptibility is generally considered low, their role in the COVID-19 disease cycle remains unknown.
 
In this study, the researchers detected and sequenced a delta variant (AY.3) from a 12-year-old Collie living with owners that previously tested positive for SARS-CoV-2. It is unclear if the dogs’ symptoms were related to SARS-CoV-2 infection or underlying conditions. The whole genome sequence obtained from the dog sample had several unique consensus level changes not previously identified in a SARS-CoV-2 genome that may play a role in the rapid adaptation from humans to dogs. Within the spike coding region, 5/7 of the subconsensus variants identified in the dog sequence were also identified in the closest in-house human reference case. Taken together, the whole genome sequence, and phylogenetic and subconsensus variant analyses indicate the virus infecting the animal originated from a local outbreak cluster. The results of these analyses emphasize the importance of rapid detection and characterization of SARS-CoV-2 variants of concern in companion animals.
 
The study findings were published in the peer reviewed journal: Viruses
https://www.mdpi.com/1999-4915/13/10/2104/htm
 
The ongoing COVID-19 pandemic that first started as a result of the emergence of the SARS-CoV-2 in Wuhan China has to date caused the deaths of more than 5 million people globally according to official figures reported. (In reality the figures could be as high as 2.5- to 3-fold!) A total of more than 247 million people have been infected with the virus so far and the virus is still continuing to wreak havoc globally despite the advent of COVID-19 vaccines whose efficacy is now being questioned.

Molecular genetics research and genomic surveillance familiarized the general public with different mutations undergone by the (SARS-CoV-2).
 
The ever-growing presence of these mutations led to some of them being labeled variants of interest (VOI), like the Eta (B.1.525), Iota (B.1.526), and Kappa (B.1.617.1), depending on preceding factors. Comparatively, some strains with more serious mutations were labeled as variants of concern (VOC) like the 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 on the basis of genomic sequencing, specifically related to the coding regions in the spike (S) protein within the SARS-CoV-2 genome.
 
Even with the current rollout of vaccines globally, SARS-CoV-2 VOCs continue to be characterized by increased transmissibility, more severe disease outcomes, reduction in neutralization in vaccinated individuals, or failures in diagnostic detection.
 
/> The theory of zoonotic transmission was popular; however, the possibility of the reverse situation in which transmission from humans to animals occurred has not been common.
 
Past research into potential animal reservoirs of SARS-CoV-2, using the original virus from China, indicated that cats and ferrets were permissible to the virus, while dogs, pigs, chickens, and ducks were considerably less susceptible to infection.
 
Alarmingly however, new studies on the Delta variant have shown high levels of ribonucleic acid (RNA) and viral shedding from hamsters and Asiatic lions that produce mild to moderate clinical signs. There have been isolated reports of the Delta variant being isolated from dogs as well; however, there is a lack of sequencing data from the virus in canine hosts.
 
In this new study, researchers document the detection and sequencing of an AY.3 virus from a 12-year-old Collie living with a SARS-CoV-2-infected owner. 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 post-admission.
 
The 12-year-old male Collie was admitted to KSU VHC for collapsing following travel. The dog was diagnosed with a hemo-abdomen secondary to a bleeding splenic mass viewed on an abdominal-focused assessment with sonography for trauma (FAST) scan and abdominocentesis.
 
Interestingly thoracic radiographs showed a multilobar alveolar pulmonary pattern with a mediastinal shift. Differential diagnoses for multilobar pneumonia, atelectasis, or multifocal pulmonary hemorrhage were conducted.
 
A detailed splenectomy was performed the day following admission, while multifocal hepatic nodules and a 5 × 4 centimeter (cm) mass on the left medial liver lobe were noted during surgery. Pulmonary oximetry performed after surgery was between 88% and 90%, indicating poor perfusion; therefore the dog was housed in an oxygen cage overnight. Thoracic radiographs showed pulmonary changes consistent with progressive aspiration pneumonia and mild cylindrical bronchiectasis.
 
The study team reported that the dog was released 5 days after admission without the requirement for supplemental oxygen. The dog died two days after discharge. No post-mortem examination or ancillary testing was performed. The owner had tested positive for SARS-CoV-2 prior to the dog’s admission. (It should be noted that the dog was fortunate to receive the kind of detailed medical care as many humans in third world countries like Thailand cannot even access such detailed and precise care unless you have lots of money! Check more on the type of treatments for COVID-19 that poor people have to deal with in the Coronavirus News Sections of Thailand Medical News.)
 
Interestingly the nasal swab sample collected from the dog following 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 prepped for whole-genome sequencing immediately following qRT-PCR confirmation.
 
In all, a total of 1,458,751 reads were mapped 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 might have played a role in the rapid adaptation from humans to dogs.
 
A detailed and complete SARS-CoV-2 coding region and partial 5′ and 3′UTRs were extracted from the deep sequencing data. The genome was 29,884 nucleotides in length with a GC content of 38.0% and encodes 12 open reading frames of the expected sizes. The genome was 99.96% identical to the next closest genome (an in-house sample, hCoV-19/USA/KS-KSU-2046/2021, GISAID# EPI_ISL_3693315) equating to 8 nucleotide differences. Of these nucleotide differences (4 in ORF1; 2 in S; 1 in M; 1 in N), three nonsynonymous (NS) changes (1 in ORF1; 1 in S; 1 in N) were novel to the SARS-CoV-2 Delta variants sequenced thus far.
 
Of particular significance, 5/7 of the subconsensus variants identified within the spike coding region in the dog sequence were also identified in the closest in-house human reference case. Taken together, the whole genome sequence, as well as the phylogenetic and subconsensus variant analyses, indicated the virus infecting the animal originated from a local outbreak cluster.
 
However, the exact cause of death was not necessarily COVID-19, as the dog had a compromised immune system associated with the hepatic and splenic masses, apart from some of the classic COVID-19 symptoms like pneumonia, bronchiectasis, and lack of oxygenation.
 
Importantly the high RNA load in the nasal swab suggested the dog may have been shedding virus, causing a risk of infection to susceptible individuals in the surroundings.
 
Alarmingly, the study findings indicate that there was a fair chance of the virus being transmitted from the host to the animal and the reverse, though the exact reasons for death remain debatable. The novel sequences found in the canine emphasize the importance of screening pets for COVID-19 to reduce transmission rates in the surrounding community. These sequences could very well be leads in identifying more variants and their roles in the different species that they infect.
 
More importantly, more genomic surveillance is needed as we could end up with a recombinant event and the spread of a totally new virus strain!
 
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