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Vaccine breakthrough shown to occur in practice with COVID-19 South African variant

In vitro neutralising assays suggest an increased escape for some COVID-19 variants of concern but whether this occurs in real world settings remains largely unknown.

Two COVID-19 mutations labelled “variants of concern (VOC)” are the ones first identified in the UK (B.1.1.7) and South Africa (B.1.351). According to the World Health Organization, a variant of concern is one for which there is evidence of increased transmissibility, more severe disease or a significant reduction in neutralisation by antibodies. In vitro data on neutralisation of VOC are mixed, with some studies indicating that vaccines such as the BNT162b2 offer a high level of protection whereas others show a significant reduction in neutralisation. Nevertheless, whether vaccines offer sufficient protection against these VOCs in clinical practice is uncertain. In trying to assess whether these VOCs could overcome the immune response generated by vaccination with BNT162b, a team of Israeli doctors from Clalit Health Services, Haifa and Western Galilee, Israel, performed a case-controlled study to examine whether BNT162b-vaccinated individuals with documented COVID-19 infection were more likely to be infected with either VOC compared with unvaccinated individuals. Their hypothesis was the both VOCs were able to surmount protection offered by the BNT162b vaccine and identified patients with documented COVID-19 and matched them to an unvaccinated control.

Data were available for 149 individuals who had been fully vaccinated and tested positive. Complete viral genome sequencing was performed and revealed how B.1.1.7 was the predominant strain of the virus in circulation whereas the B.1.351 variant was present in less than 1% of the samples. Among those who were fully vaccinated, 5.4% were infected with B.1.531 compared to 0.7% of unvaccinated individuals. In contrast, there was no difference in the rates of infection with B.1.1.7 in vaccinated and unvaccinated individuals (89.9% vs 92.6%).

Commenting on their results, the authors noted that while their study was not designed to examine the effectiveness of the BNT162b vaccine against the different VOCs, the data shows an increased incidence of B.1.351 in vaccine breakthrough among fully vaccinated individuals. However, given that the incidence of B.1.351 in circulation was very low, the authors suggested that selection did not favour this latter VOC but felt how their results emphasised the importance of tracking viral variants and that vaccination was the safest and most effective means of preventing onward transmission of the virus.

Kustin T et al. Evidence for increased breakthrough rates for SARS-CoV-2 variants of concern in BNT162b mRNA vaccinated individuals. Med Rxiv 2021