The new flight programme came into effect on Sunday (8 November) and will provisionally run until 3 December, when the new measures designed to slow the spread of Covid-19 in England are due to be lifted.
Frequencies on various services operating from Heathrow have been reduced, while Virgin has suspended operations at Gatwick entirely.
It has also warned there could be further "ad hoc" changes to the lockdown schedule, including cancellations.
Virgin has temporarily suspended Montego Bay flights from 11 November to 23 November, when the route will resume as a twice-weekly service operating on Tuesdays and Fridays.
Twice-weekly Boston flights, meanwhile, will resume on 26 November.
Flights to Barbados and Antigua will operate on Wednesdays and Saturdays up to and including 18 November, before becoming a weekly Saturday service through to the end of the lockdown.
Virgin has also made alterations to its Atlanta, Delhi, Hong Kong, Johannesburg, Lagos, Los Angeles, New York, Miami, Mumbai, Shanghai and Tel Aviv schedules up to 3 December.
The carrier’s full lockdown schedule is available here.
A Virgin Atlantic spokesperson said passengers booked on cancelled flights would be contacted with the option to rebook, or request a refund.
Customers will be automatically provided credit equal to the value of the trip, which can be used to rebook for an alternative date – and allowing for two date changes, a destination change and name change for travel up to 30 December 2022.
Those with flights still scheduled to operate, customers booked up to 31 August 2021 can rebook with fees for a name change and two date changes waived for travel up to 30 December 2020.
All Virgin Holidays trips up to 2 December have been cancelled, and all Florida holidays until 9 December – including Walt Disney World holidays. Customers will be offered a digital voucher, or the option to request a full refund.
"We apologise for any disappointment or inconvenience caused to our customers, and remain so grateful for their patience during these extraordinary circumstances," the virgin spokesperson added.
“While we have reduced our passenger flying schedule, we’ll continue to serve many of Virgin Atlantic’s destinations on a reduced frequency and provide vital international connectivity from London Heathrow Terminal 2 for customers that need to fly, including journeys permitted for work, education or other legally permitted reasons."
