Johnson & Johnson's (NYSE:JNJ) COVID-19 vaccine has had some challenges this year. From production issues to some disquieting reports of blood clots possibly being linked to the vaccine, it hasn't been the success the company was likely hoping it would be at this stage. Vaccines from Pfizer (NYSE:PFE) and Moderna (NASDAQ:MRNA) have generated far more revenue for those companies and appear to be the vaccines of choice for many people.

However, the delta variant may change that, as both Moderna and Pfizer are suggesting booster shots are necessary. And the Food and Drug Administration (FDA) recently authorized a third dose for people with weakened immune systems. Meanwhile, a new study has found the Johnson & Johnson vaccine to be highly effective against the delta variant, so booster shots may not be necessary for individuals who receive that vaccine. While a lack of boosters won't translate to more revenue from the vaccine, it's a development that could ultimately lead to Johnson & Johnson's vaccine rising in popularity and grabbing more market share.

A person receiving a vaccine from a healthcare worker.

Image source: Getty Images.

The underdog vaccine?

Johnson & Johnson expects to make $2.5 billion in revenue from its COVID-19 vaccine in 2021. That's a drop in the bucket for the mammoth business, which generated more than $80 billion in revenue in 2020.

Moderna's vaccine sales could reach $20 billion by the end of this year. And that's still well behind Pfizer, which estimates its vaccine sales will hit $33.5 billion this year as it leads the way, producing up to 3 billion doses in 2021. Moderna doesn't anticipate it will be able to produce that many doses annually until next year. In 2021, its production could reach 1 billion doses.

Johnson & Johnson only expects to produce up to 600 million doses of its single-shot vaccine this year, down from its earlier target of 1 billion. Its struggles stem in large part from difficulties at a plant in Baltimore run by Emergent BioSolutions, where concerns relating to cross-contamination led to a shutdown of its factory in March. The FDA only recently gave the plant the green light to reopen.

It also didn't help that some people felt, correctly or not, that J&J's vaccine wasn't as effective as the other ones granted Emergency Use Authorization by the FDA.

J&J's efficacy numbers don't tell the whole story

One of the challenges that Johnson & Johnson's vaccine has faced is that from the start, it didn't look like it stacked up well against the shots from Moderna and Pfizer. In January, the company reported that its vaccine was 66% effective in preventing moderate and severe cases of COVID-19. In preventing severe disease only, that figure rose to 85%. However, that looks far less impressive than the vaccines from Pfizer and Moderna, both of which demonstrated more than 90% efficacy when those companies reported the results of their trials in November 2020.

But the problem is that Johnson & Johnson's vaccine data were never a fair comparison: It only completed enrolling participants in the first phase of its vaccine trial a month later, in December 2020. By then, coronavirus had evolved and new variants of concern were emerging in the U.K., Brazil, and South Africa. In Moderna's and Pfizer's earlier trials, those variants would not have played as much of a role (if at all) in their overall efficacy rates as they did in Johnson & Johnson's trials; when looking at just the U.S., J&J's vaccine efficacy rose to 72% in preventing moderate and severe disease.

From the start, J&J's vaccine was disadvantaged because of the numbers, which inevitably led to comparisons. But there's a new study that could be much more promising for Johnson & Johnson and lead to greater demand for its shot.

High effectiveness against the delta variant

A new study from South Africa, called Sisonke, has shown Johnson & Johnson's vaccine to be highly effective against one of the most concerning variants around right now -- delta. The trial is massive and involves 480,000 healthcare workers (Johnson & Johnson's initial phase 3 trial was relatively large and had only 45,000 participants). Although the data hasn't been peer-reviewed, the initial numbers are extremely encouraging -- showing 71% efficacy in preventing hospitalizations in delta-related cases. And in terms of preventing death, the overall efficacy rose to 96%.

By comparison, studies on two doses of the Pfizer vaccine suggest efficacy rates could range between 42% and 96% against delta. Moderna has also had varying efficacy rates but it looks to be a bit higher, at around 76%. But what's common to both is that people need two doses of the vaccine, as a single dose offers weaker protection. And that's where the advantage could sway significantly in Johnson & Johnson's favor as its single-shot vaccine would be significantly easier to administer.

Is this a game-changer for Johnson & Johnson?

Johnson & Johnson's vaccine could quickly help countries around the world increase their vaccination rates. Without having to wait several weeks between doses, a single-shot vaccine that's effective against the delta variant could be in high demand.

If production-related issues are sorted out and concerns ease about its efficacy, Johnson & Johnson could make up some serious ground in the COVID-19 vaccine market. It has a long way to go in overtaking Pfizer and Moderna in market share, but the healthcare giant is a major player in the industry with significant resources. It could ramp up production to meet a surge in demand. And that's why investors shouldn't count out the role that vaccine sales may play in its future.

But there is danger in investing based on a specific COVID-19 variant. Things have been changing rapidly, and a new variant could emerge that renders all of the currently available vaccines nearly useless. And so while Johnson & Johnson's vaccine does look like it should rebound in the future, and even though it has an outside chance of overtaking both Moderna and Pfizer, those factors aren't enough to make it a sure thing; there's just too much uncertainty. The stock isn't all that safe over the long term either; Johnson & Johnson's legal troubles in other areas of its business are enough of a reason for me to stay away from the stock.

However, if you are comfortable with the risk and uncertainty and want exposure to the COVID-19 vaccine market, investing in Johnson & Johnson is still a better option than buying shares of a soaring stock like Moderna, which is trading more than $100 higher than price targets set by even some of the most bullish of analysts. And given that it is a bit of an underdog in this race, Johnson & Johnson's ability to produce some better-than-anticipated vaccine sales could lead to significant analyst upgrades, which, in turn, may lead to some great returns for shareholders who buy the stock today.

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.