I'm sure the people negotiating the scope of any waiver have figured out that might be many levels of patents. By the way, if companies were waiving their own patents "voluntarily" under pressure from the U.S, no TRIPS or other waivers would be needed.
First a small background - patents are territorial. No USPTO issued U.S. patent has any relevance to what happens in India and visa versa. Of course pharmaceutical companies tend to pursue the grant of patents in many countries. To make a vaccine in India would require suspension of Indian patent rights that might belong to a, possible U.S. based, vaccine developer.
As you say in the question, there is quite a bit of technology involved in producing vaccines. Some building block things are patented and others are trade secrets. Building block patents are held by multiple companies and there is some cross-licensing between them.
As of May 8th, I do not believe any patents have been issued for COVID vaccines themselves. Some COVID related patents have been issued for testing, etc. And there are certainly building block technology patents related to mRNA.
From a comment on the Patently-O blog
I have a Derwent alert set us that informs me every time a patent
issues with “SARS” or “COVID” in the claims or title. So far, none of
these grants concern a vaccine. The largest category so far are test
technologies. The next largest concern algorithms that purport to
predict something COVID-related (where the next outbreak is likely to
emerge, how a given patient’s disease is likely to progress, etc). The
smallest category so far is putative therapies (mostly second medical
use claims for existing FDA-approved drugs, but also some novel herbal
blends).
The claims directed to SARS-CoV2 vaccines are still being examined,
but none have yet granted. Of course, as previously noted, all the
vaccines approved in the U.S. are covered by one or more granted
patents directed to the novel vaccine platforms.
What the WTO is discussing, and the president has endorsed, is a waiver of terms of an international treaty. The signatories of the TRIPS treaty have agreed to have national patent systems with certain minimum provisions. If a country unilaterally suspended enforcement of some patents in their country, other countries could impose tariffs or otherwise try to commercially punish that country in the sphere of international trade for violation of TRIPS. The waiver would presumably cover trade secrets as well as patent rights. What is taught by an issued patent is published for all to see in that patent but waiving trade secret rights does not automatically produce the trade secrets on a platter.
Theoretically the steps would be - (1) the signatories to TRIPS can agree to wave its terms that allow commercial retaliation among themselves for weakening patent and trade secret rights locally. There would be some defined scope in terms of the technology addressed and the time frame of the waiver.
(2) In a specific country, they could pass a law or use something like executive action to suspend specific IP rights that had been granted or might be granted by that country in the near future.
(3) Someone in that country could try to make a vaccination.
Without know-how transmitted by the organization that developed the vaccine they would have a very, very hard time doing so. The text and drawings of a patent are not a specific easy to follow recipe. The original companies involved might be incented, either financially or by political pressure, to provide this technology transfer. However, they will must likely say that the best use of that time and talent is further ramping up their own production capacity, and it is probably true.
Alternatively, a country might import vaccine from a third country that had patent rights suspended. Patents do not just confer the right to stop others from making, but also selling, importing and using the patented invention in the country who issued the patent. So one country could make it under a suspended patent right and many other countries could import from their due to their similar action suspending patents.
