Limiting such early-life viruses may be “essential” for a healthy immune system and long-term respiratory health, researchers said.
But Professor Debby Bogaert, author on the study and Edinburgh University chair of paediatric medicine, said there was no reason to believe Covid would not present a similar risk when caught by newborn babies.
Respiratory infections in later development are a major health concern for children, responsible for 15 per cent of global deaths of under fives.
They are also one of the three main causes of visits to doctors and hospitals in early childhood.
Researchers said the prevention of viral infection in newborns, or strengthening immune systems with specially designed products, could reduce the risk.
Prof Bogaert said the team was surprised to discover viral infections so early in life, as they are usually asymptomatic and go unnoticed.
They studied mucosa samples from the noses of 114 babies at various stages of life as part of the Microbiome Utrecht Infant Study, which has been running for six years.
"We hypothesised that the first three to six months were going to be essential,” Prof Bogaert said.
“We never expected that ultimately, we would tailor it down further and further to the first days to weeks of life.”
These infections seem to play a “really key role” in affecting the development of the immune system, which was then linked with the risk of infections over the following year.
“Limiting the number of viral encounters in those first days to weeks of life might be essential for a healthy immune and microbiome development, and consequently long-term respiratory health,” she said.
Prof Bogaert added: “I don't think it would be different for Covid. I think it will behave as one of those respiratory viruses and we have to be careful when the children are extremely young.”