Philip Pullman’s return to the world of Lyra Belacqua, La Belle Sauvage, has picked up its first award: the Waterstones book of the year.

The novel, which is already a bestseller on both sides of the Atlantic, begins 10 years before Northern Lights and tells the story of an apocalyptic flood and how a young boy, Malcolm, teams up with an older girl, Alice, to save the infant Lyra from a sinister plot.

Pullman pronounced himself delighted to have won an award chosen by booksellers, which he called “the most important channel between the publishers and the public”.

“Writers are at one end of a complicated network that includes editors, reviewers, designers, printers, and many other real people – as well as phantoms such as the writer the readers imagine and the readers the book seems to expect,” he said. “Part of this great living network or ecology of the book world is the ancient and distinguished profession of bookselling, which I respect and value very much.”

La Belle Sauvage is the first volume in a trilogy, The Book of Dust, which will follow Malcolm, Alice and Lyra into adult life, a journey that has already taken a darker turn. The villain is a rapist and a paedophile who breaks the conventions of Lyra’s world in a terrifying scene where he abuses his own spiritual companion, or daemon. According to Pullman, the darkness in his second trilogy is partly because the world has changed since Northern Lights was published in 1995 and partly because of changes in the author himself.

“There’s no question that the times are darker,” Pullman said. “For one thing, the internet has made it possible for a mean and cruel part of human nature to express itself without being shamed or punished. Social sanctions don’t work when you can hurt people in perfect anonymous safety. Perhaps I’m getting a little more cynical as a result. Another thing might be that this story will concern itself with Lyra’s life as an adult, and she’s going to find some things difficult.”

While the His Dark Materials trilogy was written in answer to Milton’s Paradise Lost, The Book of Dust responds to Spenser’s The Faerie Queene, which the author said has a “different kind of stance towards the events of the story themselves. If Paradise Lost is an epic, then The Faerie Queene is a romance, and that was the kind of stance I was trying out. There’s also the influence of folktales and fairytales, with which I’ve been deeply concerned in the past few years. I think those influences might become even clearer in the second and third parts of the story.”

La Belle Sauvage also draws on more recent inspiration, he continued, with the immediate threat of climate change an “inevitable” inspiration for the flood that drowns his alternative Oxford. “But it also derives partly from the Murray-Darling river basin floods in southern Australia in 1956, which I saw as a boy of nine. The impression of a vast body of water moving implacably across the entire world (or so it seemed) left a vivid memory that I’ve never lost.”

According to Waterstones managing director James Daunt, the excitement surrounding the title was intense even before last month’s publication, which came 17 years after the final volume of His Dark Materials.

“Sometimes when the anticipation is so much, there’s a slight let-down when it turns up and it isn’t quite what you expect. But this manages to be both a tremendously good read, so young people can read it and enjoy it, and also a sophisticated, challenging and thoughtful book that any reader of any age will benefit from.”

There is no prize money associated with the award, but the title is set to receive the “full and committed backing” of Waterstones shops throughout the festive period. This front-of-store promotion saw sales for last year’s winner, Sarah Perry’s The Essex Serpent, leap by 720% across the retailer’s 280 outlets. The 2015 winner, Coralie Bickford-Smith’s debut, The Fox and the Star, received an even more impressive boost, with sales across the chain increasing by 5,000%.

The selection of a novel that has already sold almost 200,000 copies in the UK, according to Nielsen BookScan, marks a departure for the award. Daunt admitted the retailer is unlikely to sell “enormously more copies” because of the award, but the panel couldn’t ignore the weight of nominations coming from staff who recognise both the quality of Pullman’s novel and the part he has played in the rejuvenation of bookselling.

“Commercially, I sit there thinking: ‘Can we give the prize to something else?’” he said, “because we’re going to sell lots of this book anyway. But when just about every bookseller in the business says it’s first Pullman and then something else, you end up saying ‘Well, the booksellers have spoken.’ It is the book of the year.”

Anticipation may have been intense among booksellers as well as Pullman’s fans, but the writer himself said that he has “never really been away” from Lyra’s Oxford: “I’ve been thinking about it pretty well every day. I live a lot of my time there.”

