Curious case of SARS-CoV-2 Delta variant in a dog

In late 2019, a novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged in Wuhan, China, and has since become one of the most economically impactful pandemics to date. As the world went into lockdown, molecular genetics research familiarized the public with different mutations undergone by the (SARS-CoV-2).

Study: Near-Complete Genome of SARS-CoV-2 Delta (AY.3) Variant Identified in a Dog in Kansas, USA. Image Credit: Pyrstai / Shutterstock.com

Background

The 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.

Despite 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.

To date, 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. Investigations 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.

However, 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 a recent 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.

About the study

A 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.

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 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 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.

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.

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 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.

Furthermore, 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.

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. 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.

Implication

The current study indicates that there was a fair chance of the virus being transmitted from the host to the animal, 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.

Journal reference:
Sreetama Dutt

Written by

Sreetama Dutt

Sreetama Dutt has completed her B.Tech. in Biotechnology from SRM University in Chennai, India and holds an M.Sc. in Medical Microbiology from the University of Manchester, UK. Initially decided upon building her career in laboratory-based research, medical writing and communications happened to catch her when she least expected it. Of course, nothing is a coincidence.

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