Rail operators and Transport for London (TfL) are cutting services because of the rising number of staff self-isolating.
Reduced timetables have been introduced on railways across England in an attempt to improve reliability after a spate of last-minute cancellations.
Around 600,000 people in England and Wales were instructed to self-isolate by the NHS Covid-19 app in the week to July 14.
TfL has announced no London Underground trains will run on the Circle or Hammersmith and City lines this weekend as more than 300 members of staff are self-isolating.
It warned there will also be changes to the District and Metropolitan lines, and short notice cancellations elsewhere.
London Underground managing director Andy Lord said: “We apologise to customers for the impact on Tube services, while we deal with staff shortages across the network due to self-isolation.
“We are committed to running a frequent and reliable service, but with a reduced number of staff available it’s not always possible.
“I’d encourage anyone travelling in the coming days to check before they travel and thank them for bearing with us during this difficult time.”
Thameslink and Southern will cut its weekday timetables on five routes from Monday “until further notice”.
It warned further changes could be required, including at weekends.
Steve White, chief operating officer at parent company Govia Thameslink Railway, said: “Regrettably, we have had to make the difficult decision to reduce some weekday services.
“Unfortunately, like other industries across the country, coronavirus continues to affect our operations.
“We have fewer colleagues available at the moment due to a significant increase recently in the number of our people affected by COVID-19.
“Our colleagues have continued to work tirelessly throughout the pandemic and we’re really sorry for any inconvenience caused by the latest changes.
“By bringing in a reduced timetable now, it will help to reduce short-notice cancellations and give customers more certainty.
“We strongly advise passengers to check before they travel, including at weekends.”
Avanti West Coast is also cutting trains from Monday on its routes between London Euston and Manchester, Birmingham and North Wales.
A spokesman said this is to “manage staff shortages and ensure a reliable service”.
London Northwestern Railway will introduce a revised timetable with fewer services from Saturday.
The firm’s customer experience director Lawrence Bowman said: “No-one wants to see trains being cancelled, particularly at short notice.
“But we are experiencing more of this, across all our services, as increasing numbers of staff are getting pinged by the Test and Trace app.
“We are sorry that we have had to make the decision to alter some services.
“However, the changes will help us run a more reliable and consistent timetable for passengers across our network.”
Northern said it is “expecting disruption” this weekend due to “more people being asked to self-isolate”.
Routes in and out of Sheffield are likely to be the worst hit.
The operator said: “Our teams work really hard to find cover for services, however we find it more difficult to find cover for isolating colleagues over the weekends.”
ScotRail said a “very limited number of trains” have been cancelled due to staff shortages, but it has not amended its timetables.
A spokeswoman for industry body the Rail Delivery Group said: “Rail companies are working hard to keep passengers safely on the move as restrictions ease and more people travel to work or to see friends and family.
“As cases increase more rail employees are being pinged by the NHS contact tracing app and being asked to self-isolate.
“While train companies are doing everything they can to minimise any disruption, there may be an impact on services, so we are asking people to check before they travel using app alerts which were upgraded during the pandemic as part of our safer travel pledge.”
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