For me, "to be alive" means that the "living" entity (whether that is a virus, or a prokaryote, or a whole multi-cellular organism) has the possibility of multiplying itself in a (occasional mutations not considered) conservative manner. Meaning: The offspring must carry the traits of the parent(s). For viruses and prokaryotes, the offspring will be a perfect copy of the parent, whereas eukaryotic offspring will be 50% of one parent, and 50% of the other parent. In short, life is the possibility of multiplying in a conservative manner.

So, according to the above definition, a virus is a living entity (not all scientists agree on this, but again, this is my personal opinion). So when is a bacteriophage "dead"?

I see two options:

• Structural defects

Concrete examples: the correct receptors are missing, the tail is not complete, the DNA is not packed, certain enzymes in the capsid are missing, ...

• Genetic defects

Concrete examples: The genome has gathered too many mutations or is damaged, the genome was not completely packaged, ...

So, you can have an intact phage particle, but with an empty capsid. The structure is intact, it can attach to a host, but doesn't inject a viral genome. Or an infected host cell can release complete phage genomes upon lysis, but the capsid was not built around it. I would consider these phage "particles" as dead.

What happens with these dead phages? They will eventually be broken down, into amino acids and nucleotides, or even smaller compounds, and recycled when they are used as building blocks for new life.

So, to answer your questions:

• The whole particle will be broken down and recycled eventually. It will not stay "intact".
• An intact structural capsid, does not necessarily mean that the phage is active. The genome can be missing.

This is my opinion, but I'm always open to discuss this further.

Kind regards.

Hi Dieter,

Thank you for your answers.

I am very happy to know one more researcher that considers viruses are living. Actually I was shocked when the first time a researcher told me that he didn't think viruses are living entities.

I agree with your opinions to my questions. So here, I have a further question, and would like to know your opinions:

I suppose you know about 'phage cocktail'. What will be a good way to determine the titer of each phage in the cocktail without their bacterial hosts?

Dear Zinan xu,

This is a completely new question, and should therefore be posted as a new topic.

In response to that, the first question is: Why would you want to do that? Why would you want to know the phage titer, when you don't have the host?

A quick answer would be: color the DNA of the phage particles - assumed the preparation is pure and only contains phages - and count the phage-dots using a fluorescent microscope, maybe this is even possible using FACS? Using a microscope would only be qualitatively, not quantitatively. This is just a thought, I have no experience in this.

Hi Dieter,

Thanks for your answer.

Actually, this question is related with the first one, because someone proposed to use qPCR to determine the titer of each phage in a phage cocaktail, of course on the condition that they already got the unique sequences of each phage in the cocktail. I was wondering if the method could work, so asked the first question. According to your answers to the first questions, this qPCR method could also detect the nucleic acid of the dead phages.

Anyway, many thanks for your answers. And i will post the second question as a new one.

Hi Zinan xu and Dieter,

On the one hand, I see a phage as a collection of proteins and nucleic acids, which will denature when exposed to non-ideal circomstances. I do not consider it to be alive. The bacterium-phage duo, on the other hand, is a living entity, exposed to the forces of evolution.

Best wishes,

Jean-Paul

Hi Jean-Paul,

Welcome to join the discussion. Really glad to see your opinions on this topic, very intersting and do make sense. Thanks for the contribution!

Regards,

Zinan

qPCR should work. High-throughput sequencing (e.g. Illumina) too, when you take an internal standard.