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Of 13 samples taken between April 8 and 14, 11 were found to carry the subvariants XBB.1.9.1, XBB.1.16 and XBB.1.16.1, the first having been detected in Hanoi last week.
The other two samples were infected with the XBB.1.5 subvariant that the city first detected early this month.
The new variants have been reported in dozens of countries, leading to a rise in Covid cases in places such as Thailand and India.
They could be the reason for a surge in infections in HCMC and many cities and provinces in Vietnam in recent days, the city's health department said, adding that a recent survey on herd immunity in the city found only 94.2% carrying antibodies, down from 98.7% last September.
Although there have been no reports showing a connection between the rise in infections and severity, HCMC Health Department said more cases will result in more hospitalizations, particularly among elder people, those with health complications or not fully vaccinated against Covid.
Covid infections in HCMC have increased since mid-April. The city recorded 193 new cases on Saturday compared to 47 cases on April 18.
The Health Ministry has also recorded a rise in Covid-19 cases nationwide, more than half of whom are asymptomatic and less than 2% are severe cases.
Omicron has been the dominant coronavirus variant for 16 months, with more than 500 subvariants detected globally. Most of the subvariants are highly contagious, but there has not been clear evidence about them leading to more severe cases.
