Joe,
If you read the PNAS article and then read the NBC (not fake news) article, you can see how they've butchered the material and you don't need to go beyond the second sentence to find this...
Flu viruses mutate every year and it turns out the methods used to make flu vaccines cause them to mutate even more, the researchers found.
First half, correct. Second half, misleading. Yes the Flu virus mutates every year. Yes, the methods used to make flu vaccines leave the flu vaccine itself open to mutation. That vaccine is open to mutation based on how it is grown in the egg system. The flu vaccine does not cause the flu virus that we are susceptible to, to mutate. The avian egg growth system may cause the flu virus
in the vaccine, to mutate. Huge difference, but it can lead to issues in efficacy. There is considerable research efforts to finding another vaccine systems that reduce the % probability of antigenic mismatches between vaccine virus and circulating virius - but the egg system is stable, and fully equipped to do the job. The virus just has the ability to outsmart it sometimes. The same virus has the ability to outsmart us, and continually find ways to mutate and adapt.
Big Pharma is involved in the manufacture process of flu vaccine and this is another reason that the enlightened public can trend so heavily against it. Big Pharma is bad... etc, but that's another topic. GSK, Sanofi Pasteur and Novartis are the 3 main players (smaller companies don't get involved in the manufacture and sale of the flu vaccine of the year - primarily due to the scale of manufacture needed in the short time span window).
Public Health Agencies and funded research labs (think universities, CDC etc) examine the strains from each hemisphere which has a different flu season and are able to work on predictive models based on strains that are found in the opposing hemisphere in their respective flu season. From this the PHAs provide seed strains to the main pharmaceutical companies who either have in house regulated manufacturing capabilities (a rare and no mean feat feature of a pharmaceutical company), or a strong relationship with a Contract Manufacturing System who is on alert to produce the quantities needed to match the demand. Each vaccine is usually comprised of 3-4 strains, 4 being the most recent successful flu development. There are models actively being researched to find a universal vaccine which is efficacious independent of strain. Timelines projected for this around 8-10 years.
Drug development is an insanely complex logistical challenge. Supply chain, release and stability data and the drug passport considerations that are required to accompany any product designed for human use - on top of the proof of concept and R&D work that precedes any human designed manufacture is mind blowing in its enormity.