A mysterious respiratory illness in dogs

A mysterious respiratory illness is afflicting dogs across America (Figure 1). Veterinary experts are puzzled as to the underlying cause, and hence how to treat. This disease mimics the symptoms of kennel cough, a common respiratory infection in dogs (from a variety of bacterial and viral pathogens), but lingers for a much longer duration. In some instances, it can be fatal to the infected dog.

A key question is whether the illness is caused by a bacteria or a virus. One piece of evidence is that antibiotics do not seem to work, and as a result the consensus favors a viral culprit. Of course an alternative explanation is that the pathogen is a bacteria that is resistant to all known doggy antibiotics. Coronavirus has largely been ruled out because the virus has not been detected in the dogs, and in addition, the number of documented Covid cases in dogs has been extremely low (link) with dogs experiencing mild to no symptoms. Most likely, coronavirus infects dogs poorly compared to humans.

A mysterious illness caused by an infectious pathogen always raises a red flag even in dogs. This occurrence is somewhat rare in humans as our catalog of human pathogens becomes ever more comprehensive. However in a previous post, I described an outbreak of hepatitis cases among children earlier this year that was not caused by one of the hepatitis viruses which are responsible for the vast majority of hepatitis cases. Ultimately, the World Health Organization (WHO) designated this outbreak as acute, severe hepatitis of unknown origin in children. 

Many months later the origin is coming into focus. Researchers took advantage of metagenomic sequencing of blood, liver, and stool samples to identify both RNA and DNA viruses from over 200 families. The idea is to sequence all of the DNA in a sample and identify any foreign (non-patient) sequences that can be matched to a viral genome database.  They found that the unexplained pediatric hepatitis cases were linked to being simultaneously infected by adeno-associated virus type 2 (AAV2) and specific other viruses such as human adenovirus (HAdV). 

Metagenomic sequencing refers to the sequencing of the genomes of numerous different species (i.e. viral and bacterial genomes). In the case described above, the researchers searched against a panel of known viruses, and so they could take advantage of existing DNA primers targeted against specific virus families.

A much greater challenge is when the suspected pathogen has not been previously characterized, and is not related to a known pathogen. Then one has to rely on random sequencing primers to sequence potentially novel genomes whose sequence is not in any database. Matching a known sequence is much easier than matching an unknown sequence. 

The problem with the random primer approach is that you will pick up all sorts of random DNA sequence. The noise could easily overwhelm and occlude any signal (i.e. DNA sequence from the pathogen). One can operate by a principle of exclusion and eliminate DNA sequences that are obviously not pathogen such as from the human host, but that still leaves a lot of foreign DNA that may not be related to the unknown pathogen (e.g. from food, pets, other infectious agents, mold, etc.).

A more traditional approach would be to try to culture the pathogen from a sample in the laboratory. But trying to grow an unknown pathogen in the lab is much more difficult than trying to sequence it. Pathogens usually do not grow well outside of their native host habitat, and only painstaking trial-and-error can identify culture conditions in the lab amenable for growth.

So ultimately metagenomics offers the best option, and over time the hope is that we will build a more comprehensive database of pathogen genomic sequences so that there will be fewer mysterious illnesses whether in humans or other mammals such as dogs.

Figure 1. A mysterious respiratory illness has been sickening dogs across the United States. The pathological agent has not been identified yet, but most likely it is not coronavirus (NBC News).