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Study of major congenital anomalies following COVID-19 vaccination and SARS-CoV-2 infection

January 2022: This study, published in Nature Communications, looks at the risk of major congenital conditions following COVID-19 vaccines or SARS-CoV-2 infection.

A population-based matched cohort study of major congenital anomalies following COVID-19 vaccination and SARS-CoV-2 infection

Calvert, C; Carruthers, J; Denny, C; Donaghy, J; et. al.

Nature Communications

Published Online on: 6 January 2023

Available online at: https://doi.org/10.1038/s41467-022-35771-8 

Summary in plain English 

Having an infection with SARS-CoV-2 (the virus that causes COVID-19 disease) can impact the health of a pregnant woman and her baby. Some viruses can cause ‘congenital conditions’, which form in early pregnancy as a baby develops.

Congenital conditions can affect both the body’s structure and how it works. They can be:

  • External: a visible physical condition, such as a cleft lip or spina bifida
  • Internal: an invisible condition, such as a heart defect. 

Why did we carry out this research?

Rates of COVID-19 vaccination are lower amongst pregnant women than non-pregnant women of the same age. A key reason for this is concerns around vaccine safety.

However, existing literature suggests that the COVID-19 vaccine is safe to use during pregnancy.

Read about some of our previous research in this area

Other studies have assessed the risk of major congenital conditions in early pregnancy due to the COVID-19 vaccine and SARS-CoV-2 infection. However, the studies did not include a full range of congenital conditions, and some had other method limitations.

We wanted to understand the impact of COVID-19 vaccination or SARS-CoV-2 infection on babies developing congenital conditions.

What data did we use?

To carry out this study, we looked at health data in the ‘COVID-19 in Pregnancy in Scotland Study’ (COPS) until July 2022.

The dataset contains records for all clinically recognised pregnancies in Scotland from 2015 onwards. This includes pregnancies that were not carried to full term for any reason.

In our vaccination analysis, we included

  • 6,731 babies whose mothers received a COVID-19 vaccination in early pregnancy (between 6 weeks before conception and 19 weeks and 6 days of pregnancy)
  • 20,193 babies whose mothers were unvaccinated in early pregnancy (control sample)

Most babies whose mothers were vaccinated in early pregnancy received either the Pfizer-BioNTech (73.7%) or Moderna (7.9%) vaccine.

In our infection analysis, we included

  • 1,574 babies whose mothers had confirmed SARS-CoV-2 infection in early pregnancy
  • 4,722 babies whose mothers were uninfected in early pregnancy (control sample)

In both analyses, we only included babies from pregnancies reaching at least 12 weeks gestation.  Babies whose mothers had both infection and vaccination in early pregnancy were excluded.

We used routine health records to identify any babies with a major congenital condition where

  • The baby was live born and diagnosed at any point up to the end of the neonatal period (28 days after birth)
  • The pregnancy ended in a miscarriage or stillbirth at 20 weeks and 0 days of pregnancy or later
  • The pregnancy ended in a termination of pregnancy at any stage

What did we find?

We did not find a link between having a COVID-19 vaccine and major congenital conditions

  • 153 out of 6,731 (2.3%) babies of vaccinated mothers had a major congenital condition
  • 467 out of 20,193 (2.3%) babies of unvaccinated mothers had a major congenital condition

Similarly, we did not find a link between having SARS-CoV-2 infection and major congenital conditions

  • 32 out of 1,574 (2.0%) babies of infected mothers had a major congenital condition
  • 85 out of 4,722 (1.8%) babies of uninfected mothers had a major congenital condition

We also checked the results by including pregnancies which did not reach at least 12 weeks gestation. Again, we found no evidence of a link with either vaccines or infection.

Why was this research important?

In this study, we have found no link between mothers having a SARS-CoV-2 infection or COVID-19 vaccine during early pregnancy and their babies having a major congenital condition.

This research provides reassurance on the safety of the COVID-19 vaccine in early pregnancy. COVID-19 vaccination remains the best way for women to protect themselves and their babies from the risk of SARS-CoV-2 infection in late pregnancy.


This plain English summary was written by EAVE II Patient and Public Involvement (PPI) Lead Lana Woolford in consultation with COPS researchers and the EAVE II Patient Advisory Group.

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