Health authorities confirmed that the genome of the teenager’s N501Y mutant strain was the Alpha variant B.1.1.7 and was not similar to samples found in Shenzhen. They also noted differences between the latest case and other similar strains reported in Hong Kong.

But the investigation was ongoing and further genetic analysis and comparison with recent imported cases with the N501Y strain were continuing, they said.

The 17-year-old girl was found to be carrying the Alpha variant and health authorities confirmed on Sunday her mother was also infected, likely with the same mutation. Six other new Covid-19 cases were recorded, involving arrivals from France, India, Indonesia, the Philippines and the United Arab Emirates. Fewer than five people tested preliminary-positive, but one was the girl’s 20-year-old sister.

The girl has no recent travel history, but a cluster of infections involving the Alpha variant has emerged in the Yantian district of Shenzhen, roughly an hour’s drive from downtown Hong Kong, which aroused suspicions the cases were linked.

But a medical source said a comparison of the genome sequencing of the infections found about 25 genetic differences between them, indicating Shenzhen was unlikely to be the source.

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The Alpha variant first emerged in Britain and has spread around the world, including to Indonesia and Taiwan. Respiratory medicine specialist Dr Leung Chi-chiu said health authorities should compare the teenager’s sample with the variant found on the self-ruled island to determine whether they were connected.

Close contacts of the teen’s family should also be tested for antibodies to determine whether they were infected earlier but had already recovered, he advised.

“This will help us find possible leaks in our infection-control measures, cut off transmission chains and effectively protect the city,” he said.

Leung urged authorities to consider tightening quarantine exemptions that apply to certain categories of people, such as senior executives of financial companies, and closely monitor the scope of their activities to avoid a repeat of the third wave of coronavirus infections, which was triggered by infected seafarers and aircrew who did not have to comply with standard quarantine rules.

Infectious disease expert Dr Joseph Tsang Kay-yan suggested the government should consider requiring residents returning from the mainland via the “Return2HK” scheme to undergo additional rounds of nucleic acid tests and antibody checks upon arrival.

“In view of the latest situation on the mainland, cross-border measures should be tightened to prevent a potential fifth wave of infections,” Tsang said.

Authorities should also consider asking people exempted from existing quarantine regulations who had visited the mainland recently to log their whereabouts in Hong Kong to further minimise risks of transmission, he said.

Under the scheme, Hongkongers in low-risk areas on the mainland as classified by the National Health Commission are exempted from mandatory 14-day quarantine upon arrival provided they test negative for Covid-19.

But the government listed several areas in cities in Guangdong and Anhui provinces as “at risk” places that would temporarily no longer be covered by the scheme.

These locations included: Liwan, Haizhu, Yuexiu, Panyu and Nansha in Guangzhou; the Xikeng and Anliang communities of Longgang in Shenzhen and six areas of its Yantian district; Chancheng and Nanhai in Foshan; and an area of Dianbai in Maoming. In Anhui, the suspension applied to Yuan district in Luan.

Hong Kong residents will be eligible to return from anywhere in mainland China without quarantine

A government spokesman earlier said that to further enhance risk management and better streamline border immigration, the list of medium or high-risk places would be further adjusted and no longer include individual buildings within subdistricts.

Meanwhile, Guangzhou and Foshan health authorities announced that from Monday noon, all residents would be barred from leaving unless they could show a negative Covid-19 nucleic acid test issued within the past 48 days. They were also advised to avoid all unnecessary travel out of the cities.

Shenzhen has recorded 11 infections involving the Alpha variant among 13 asymptomatic cases confirmed since May 21. The city is now classified as a low-risk area of the Covid-19 outbreak by the mainland authorities.

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Macau announced that from 6pm on Sunday, all individuals who had visited specific districts in Guangzhou or Foshan 14 days prior to arriving in the casino city must go to designated places for two weeks of medical observation.

In the case of the 17-year-old girl, her sister was found to have a high cycle threshold (CT) value, meaning she had a low viral load. The lower the CT value, the higher the viral level and the more infectious the person could be.

The older sister was admitted to hospital on Saturday after developing symptoms in quarantine the day before. But everyone at several places she visited during her incubation period must undergo compulsory testing.

On May 29, she went to Nina Mall 1 and 2, The Mills, D. Park shopping mall, Namco game centre at Citywalk II, Volcano Kitchen One and Chan Taiwan Cuisine in Tsuen Wan.

On May 23, she visited K11 Musea shopping mall, Cats Tea Room and Eslite Spectrum bookstore in Tsim Sha Tsui. She also went to Dragon Centre shopping centre and Kakurega Ramen Factory in Sham Shui Po.

Health authorities had ordered 21 days of compulsory quarantine for about 100 of the 17-year-old student’s close contacts as a precautionary measure.

The city’s overall infection tally stands at 11,858, with 210 related deaths.

Separately, Secretary for Labour and Welfare Law Chi-kwong said the vaccination take-up rate in care homes was low and warned that strict regulations at the premises would “continue indefinitely” if inoculation numbers remained sluggish.

As of May 31, a total of 2,261, or 3 per cent, of care home residents and 9,368, or 23 per cent, of staff had received at least one vaccine dose.

“We must review the problem in the short term, adjust our strategy and boost the vaccination take-up among care home residents and staff. Otherwise restrictions on care home visiting arrangements, outings, etc … will continue indefinitely,” Law wrote on his official blog.

More than 2.6 million jabs have been given so far, with over 1.1 million residents, or 14.8 per cent of the city’s 7.5 million population, fully vaccinated.