The European Union has toughened its demands on fish in British waters as part of a post-Brexit trade deal, as the chief negotiator, Michel Barnier, revealed he had coronavirus, fuelling doubts about the timetable for an agreement.

Fishing is set to be one of the most bruising chapters of the EU-UK negotiations, with both sides seeking an agreement by 1 July, a deadline called into question by the coronavirus crisis.

An EU legal text published on Wednesday evening revealed a tougher approach on fishing rights, compared with an earlier version. The new text sets the goal of “upholding … existing reciprocal conditions on access to waters and resources”, whereas the previous version set the bar at “defining clear and stable rules”.

The changes – demanded by EU member states – underline that national governments are taking a harder line on fishing rights than the EU’s chief negotiator, who wants flexibility in the negotiating room.

Member states, led by France, Belgium, Denmark and Ireland, are insisting on maintaining the status quo on access rights for their fishing fleets. The British government wants to tear up arrangements formalised decades ago so that it can increase its share of the catch in British waters.

The two sides exchanged legal texts on Wednesday, before Barnier announced he had tested positive for the coronavirus, heaping further doubt on the timetable for a deal by the end of the year.

“I am doing well and in good spirits. I am following all the necessary instructions, as is my team,” Barnier wrote on Twitter. “For all those affected already, and for all those currently in isolation, we will get through this together.”

In a video message recorded in a book-lined room, he added: “Everyone among us has a role to win this collective battle, this war against the virus.”

A UK government spokesperson said: “We send Michel Barnier our best wishes for his recovery.”

Confirmation that the virus has spread to the highest levels of the EU negotiating team is bound to fuel calls for both sides to extend the transition period that ends on 31 December 2020.

At his daily press conference on Wednesday, Boris Johnson denied reports he would seek an extension of the transition, saying it was “not a subject that is being regularly discussed”.

The latest round of talks, due to take place in London this week, were cancelled because of the coronavirus outbreak. The two sides have been unable to agree so far on other ways of talking. The UK has said both sides are considering “alternative ways to continue discussions”, such as video conferencing and conference calls.

The European commission’s chief spokesman, Eric Mamer, said the negotiations would be carried forward. “We believe that there are ways to ensure that even in the current circumstances, negotiations can continue to take place.” The main focus, he said, was “textual analysis” of the legal documents exchanged by both sides.

But online talks pose problems for the Brussels negotiators. Even the smallest discussions can include 10 to 20 people on each side, coming and going, during one three- or four-hour session. The European commission has asked all “non-critical” staff to work at home, a message reinforced by the Belgian government when a nationwide lockdown came into force on Wednesday.

Meanwhile, civil servants across Whitehall are being deployed to work on the coronavirus. The next round, due to start on 6 April, is now in doubt, as the EU executive and all European governments turn their attention to fighting the coronavirus crisis.

Terry Reintke, a German Green MEP, who helped to set up the European parliament’s EU-UK friendship group, told the Guardian it was “absolutely insane” to stick to the original timetable, which is meant to result in a wide-ranging deal on trade, fishing rights and security being agreed by the end of the year.

“I don’t think it’s going to be possible. I really hope the British government and the British parliament will come to their senses.”

She added that a deal was not just “people meeting in a room”, but time for parliamentary scrutiny, informed by experts. The European parliament, which has to approve the final deal, has drastically reduced its activity, with many MEPs unable to leave their home countries.

Fabian Zuleeg, the head of the European Policy Centre, a Brussels thinktank, said not extending the transition was “reckless when faced with unprecedented crisis”.

“Remote facilities cannot replace the multiple exchanges that take place during a negotiation round, let alone replicate the personal relationships that make a negotiation work,” he wrote. “That is particularly crucial in this case, where the timetable is already tight.”

The British government has not revealed whether it intends to publish its draft legal text, which was sent to the EU team on Wednesday.

“We are sharing ours in confidence as a negotiating document, as part of the ongoing negotiating process,” a government spokesman said. “We will keep under review which documents it is appropriate to publish during the course of negotiations and whether it is useful to make them available more widely.”