Virus variants causing breakthrough infections

The first study on the phenomenon of breakthrough SARS-CoV-2 infections among healthcare workers in the State has found that these individuals were infected by virus variant B.1.1.7 (which is a Variant of Concern) and variants with E484K and S477N mutations in spike protein, which are associated with immune escape.

The genomic analysis study of virus samples collected from healthcare workers who developed infection two weeks after they had received the second dose of vaccine was done by IGIB, New Delhi, in collaboration with the Government Medical Colleges at Kozhikode, Ernakulam and Idukki.

The pre print, “Genomic survey of SARS-CoV-2 vaccine breakthrough infections in healthcare workers from Kerala,” appears in OSF Preprints (

COVID-19 vaccines are an effective and potent tool to bring the pandemic under check. However, no vaccines are 100% effective in preventing infection. A small percentage of people who are fully vaccinated will still get COVID-19 if they are exposed to the virus.

Another reason for people getting infections after they are fully vaccinated is when the infections are caused by circulating virus variants, with potential immune escape mechanism, which might reduce the efficacy of vaccines.

These are called “vaccine breakthrough infections.”

In this study, virus samples were collected from six healthcare workers in Kozhikode, Idukki and Ernakulam. They were fully vaccinated but tested positive for COVID-19, 18-37 days after they received the second shot.

These were some of the earlier cases of breakthrough infections in the State.

Considering that the efficacy against symptomatic infection, post 15 days of the second dose of Covishield, with a 28 day inter-dose interval, is reported to be 76%, it should be expected that a small percentage of fully-vaccinated people may still get infected, researchers noted.

“What is most important is that all of them had only mild symptoms and that none progressed to a serious disease, which confirms that vaccines are effective in preventing serious disease or death due to COVID-19,” said Vinod Scaria, Principal Scientist, IGIB.

“We could obtain the neutralising antibody titres in the blood samples of two of our subjects, which were quite high, indicating good antibody response generated by the vaccines,” he said.

Four of the samples had N501Y variant in spike protein, while two samples had E484K (one of the mutations common to the B.1.351 or “South African variant” and P.1, the “Brazilian variant”) and S477N variants in spike protein respectively.

N501Y, E484K and S477N are key mutations in the receptor binding domain (RBD) of virus’ spike protein, with substantial evidence on immune evasion.

Dr. Scaria said the team intended to do an expanded study on breakthrough infections in Kerala and across the country as these are being reported among the general public also. Kerala is one of the pioneering States which has been systematically implementing genomic surveillance and sequencing studies.

Studying emerging lineages that cause breakthrough infections will help us explore the emerging genetic lineages and natural selection of viral escape mutants, he added.

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Printable version | Jun 20, 2021 2:33:32 PM |

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