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How many connections per second are being made from the EC2 instance to the RDS instance? You may be running into a DNS quota issue where the single EC2 instance is sending too many packets too quickly to resolve the RDS DNS entry.
Info about this: https://docs.aws.amazon.com/vpc/latest/userguide/vpc-dns.html#vpc-dns-limits
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Thank you for your answer. The number of connections is very close to zero at the moment.
Things are working again today but I assume I will run into the DNS issue again some day.