HPV. How do viruses persist outside the body?

Question

The main route of transmission of human papillomavirus (HPV) is generally believed to be sexual. While fomites have been postulated for inexplicable infections, sexual health professionals regularly counter that lying respondents are the more likely explanation.

Research into HPV seems to have mostly stalled and there are few in depth in-vitro studies into viability of the virus outside the body, the infectivity of fomites or their infective dose that I could find.

There are some footnotes and references to animal models, with claims that HPV can remain infective at least 7 days after desiccation but no upper limits. There is some more precise research but understanding the significance is difficult for layman.

For example research published in Nature stated HPV-16 "can remain viable and capable of transducing the reporter construct upon stimulation of cell cycle re-entry for at least 2 weeks, but most likely for no longer than 4 weeks."

How can one understand the viability and limits of viruses, and HPV in particular, outside the body?

To clarify: Despite the fanciful language of the bounty I'm not looking for certainty, but general principles of environmental virology and an overview of statistical observations in regards to HPV in particular.

Note: The various aspects which influence the persistence of viruses in the environment spoken of below are summarized with some additional detail in a literature review published in 2010 in Food and Environmental Virology.

Answer 1

bob1's answer is good, but I was already working on this one so I'll go ahead and post the parts that aren't redundant:

What does it mean for a virion to lose infectiousness?

To be 'infectious' a virus particle perform a set of tasks that result in more virus particles. A simplified list for HPV could be: attach to receptor on host cell > enter cytoplasm > enter nucleus > make proteins > copy DNA > assemble new virions from protein and DNA > exit cell. The first four tasks must be performed by proteins in the virion; if enough of these are degraded, the corresponding task cannot be completed, and the virion cannot infect a cell. This means that there are many different routes by which any particular virus might be inactivated. One of the references in the question suggests HPV can be inactivated by gunk from dead cells sticking to the otherwise-viable virions:

The greater inactivation of the virions in the extracts at 56 C may be due to denatured cellular protein, which visibly aggregated at 56 C and above, interfering with infection.

Viruses are not metabolically active on their own!

This means that damage cannot be repaired, and also that a functional protein cannot be 'reset' after it changes shape. To use the SARS-2 spike protein as an example, the spikes have energy stored in them like a mousetrap. If the transition from open to closed is triggered while the spike is bound to ACE2 on a host cell's membrane, the motion of the spike protein changing shape will bring the viral membrane in contact with the host membrane, fusion occurs, and the virion contents enter the host cytoplasm. If the transition is triggered before the spike is bound to a host receptor, that spike is 'dead'. SARS-2 virions have many spikes, but if all of them trigger prematurely, the virion as a whole becomes uninfectious. The transition from the high energy 'prefusion' state to the lower energy 'dead' or 'postfusion' state has to be energetically accessible in order to be triggered by the new host cell. This means that the risk of premature triggering is inescapable. Therefore, damage or premature transition of all copies of some viral protein that changes shape to allow cell entry is a likely candidate for inactivation for any viral species. This hasn't been investigated systematically, though, so there's no reference I can cite for this.

In papillomaviruses:

Unlike coronaviruses, HPV doesn't have a membrane that can fuse with the host's for cytoplasm entry. Instead, it is absorbed by endocytosis, then the capsid disassembles, and L2 disrupts the endosome membrane. The details of how this happens aren't known, but it's likely that L2, which is protected inside the capsid most of the time, becomes exposed by structural changes to L1 which occur in the endosomes. This suggests to me that degradation of L1 is the main cause of viral inactivation outside of the cell. That hypothetical structural change of L1 would need to be identified before you could start to investigate if it's present in inactivated particles.

Answer 2

As far as I can tell this topic, specifically for human papillomavirus (HPV), hasn't been fully investigated. There is some literature on it (as cited by OP), but it is sparse, making this an open field for someone to investigate. As such there is no certainty about how long a sample can persist in the environment as a huge number of factors come into it.

However, this is a difficult topic to investigate - how do you mimic in the laboratory the conditions under which you would find the virus in a natural shedding? In terms of HPV, no-one seems to have fully investigated just how the virus is deposited in terms of how it is shed in a natural manner from warts. It is assumed in the literature that it is in the form of keratinised squamous epithelial cells with virus inside, and probably naked virus too. These will have different profiles of decay in the various environments because of the natures of the different forms.

In terms of environments for persistence, there are a huge number of factors that might play into it. Here are a few of the known significant ones: heat (max temperature and min temperature as well as freeze/thaw cycles), light (particularly UV from sun), humidity (overall in environment and local to the place were the virions are), salinity (beach?), chemical (e.g. chlorine at a pool), how the virus is deposited, and last but not least, what the virus is in (a skin cell? mucus? naked virion?)

HPV is a non-enveloped virion containing double-stranded DNA. The virion is composed of 72 capsomers each consisting of 5 copies of the structural protein L1 and forms a strucutre with icosahedral symmetry. The capsid is capable of self-assembly under the right conditions, which means that it is likely quite stable (relative to some other viruses), as it can potentially re-form if damaged by heat or something similar.

The virus enters the cell through abrasions or micro-traumas of the skin surface, where it invades the squamous epithelium and only grows in those keratinized cells. It can also invade and grow in epithelial tissues of some mucosa such as the nasal passages, throat and vagina. Some of these tissues are shed containing virus through abrasion and natural shedding of the epithelial surfaces.

Now that we have a bit of the biology out of the way:

How do we test for persistence of a virus in the laboratory? Actually it is quite simple, generally you grow and purify the virus (or a surrogate similar virus) and then place some as droplets on the surface you wish to test. You then subject it to the conditions that you want to mimic and see how long you can detect it for.

The methods of detection vary depending on the virus and study. Some will use molecular detection methods like the ability to PCR amplify genetic material from the virus as a surrogate for genetic damage making the virus incapable of replication. The other most commonly used is to try to propagate the virus from swabs taken from the surface it was applied to. This doesn't work for all viruses, as some are not culturable, or are very difficult to culture (e.g. for SARS-CoV-2, only about 30% of positive samples can be cultured, but for measles virus very close to 100% can be cultured). If the virus is not culturable, it may be that it can get into the cell and either replicate but not escape the cell, or that replication is incomplete, so genes are expressed, but no virions formed. If either of those two options are go then the presence/viability of the virus on the surface can be determined by looking for activity of one or more viral genes.

I can't give you landmarks for HPV, and the exact sequence of events is unknown for any of the viruses I know anything about, but in general viruses tend to be non-viable before you can no-longer detect genetic material. Exactly how long each of these takes depends highly on the virus. For instance, take two quite topical viruses - SARS-CoV-2 and influenza, both enveloped (less stable) RNA viruses with similar size and structures and similar routes of transmission. Viable influenza persists for about 2 weeks on stainless steel, but only 1 week on cotton, but you can detect the RNA for up to 17 weeks, while CoV-2 only persisted for 1 week on steel, but RNA could be detected for the full duration of the study (though I can tell you personally from my CoV-2 as yet unpublished results >14 days on some surfaces under some conditions at room temp).