The Pfizer vaccine against COVID-19 has proven to be a spectacular success in Israel, with more than half of the population and most of those over 40 already having received both shots. Youngsters from age 12 will apparently be eligible for the vaccination in a few weeks. It has defeated the original COVID-19 strain, as well as British, New York, and other variants. 

Now, a joint study at Tel Aviv University (TAU) and the Clalit Research Institute of Clalit Health Services – the country’s largest health maintenance organization – has found that the Pfizer vaccine is somewhat less effective against the South African variant compared to its great success against the British variant.  

At this stage, it is difficult to quantify the reduction in the vaccine’s effectiveness against the South African variant, wrote Prof. Shay Ben-Shachar (head of Precision Medicine of at Clalit Innovation), Dr. Doron Nezer, (director of Community Medicine at Clalit), and Prof. Adi Stern of the TAU’s School of Biomedicine and Cancer Research, However, researchers estimate that this reduction is not extreme.

The study, published but not yet peer-reviewed on the Medrxiv website under the title Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals,” it is the first study of its kind to examine the real-world effectiveness of the Pfizer vaccine in protecting against the COVID-19 variant originating in SouthAfrica. 

Researchers have found that the South African variant is significantly more likely to break through the protective effect of two doses of the vaccine compared to the British COVID-19 variant, which is by far the most common strain affecting the world. The researchers say that at this stage, the exact reduction in effectiveness cannot be accurately assessed from these data, but estimate that the vaccine remains protective against this variant. Fortunately, the South African variant has not spread widely and remains very rare in Israel.

The researchers examined some 400 members of Clalit Health Services who tested positive for COVID-19 14 days or more after receiving the first dose of the vaccine (“breakthrough cases”) and 400 unvaccinated matched members of similar age, sector, gender and place of residence that had lab-confirmed COVID-19 at the same time period. 

All viral samples underwent genetic sequencing and identified a prevalence of less than one percent of the South African variant among the overall cohort. However, among individuals who had been infected after receiving two doses of the vaccine, the prevalence rate was eight times higher than the rate in the unvaccinated matched individuals.  

This means that the Pfizer-Biontech vaccine – though highly protective – probably does not provide the same level of protection against the South African (B.1.351) variant of the coronavirus. The results indicate that the South African variant is capable, to some degree, of breaking through the vaccine’s defenses. At the same time, this ability is probably limited, since over time this variant’s prevalence in the overall population remains low. 

The study also compared the ability of the British (B.1.1.7) variant and the original COVID-19 virus strain, to break through the vaccine’s defenses. The data indicate that in fully vaccinated individuals (at least one week after the second dose) no difference was detected between the rates of the two variants among those vaccinated vs. unvaccinated. However, in 250 partially vaccinated individuals (from two weeks after the first dose to one week after the second dose), the rate of the British variant was disproportionally higher compared to unvaccinated persons.  This means that the vaccine is most effective against the British variant only after the second dose. 

“We examined the resistance of the various variants found in Israel – the British and the South African – to Pfizer’s vaccine,” said Stern. “We wanted to know whether the rate of these variants is higher among vaccinated compared to unvaccinated individuals, and unfortunately the answer is yes: we found a disproportionally higher rate of the South African variant among people vaccinated with a second dose, compared to the unvaccinated group.  This means that the South African variant is able, to some extent, to break through the vaccine’s protection.”

Stern stressed, however, that this variant remains uncommon within the vaccinated population and that the study does not precisely indicate the level of protection against the South African variant because its prevalence in Israel remains extremely low – about one percent of all cases.

“Our results may give cause for concern, but the low prevalence is encouraging,” she added. “It means that even if the South African variant does break through the vaccine’s protection, it has not spread widely through the population – unlike the British variant, which currently accounts for a large proportion of COVID-19 cases in Israel. One possible explanation is that the extensive spread of the British variant is blocking the spread of the South African variant.”

Ben-Shachar added that “the results of this study indicate the importance of expanding the genetic sequencing of lab-confirmed cases to detect any future outbreak of the South African variant or other new variants. The findings signal that we cannot yet regard the pandemic as a thing of the past, and it still remains important to continue social distancing and using masks.”