Kenyan scientists have identified a new branch of the Covid-19 Omicron variant, which they say was responsible for the unusual outbreak of ‘flu’ that many Kenyans reported in April and May.
Kenya was the first country in the world to report the new lineage, which scientists first detected in Lamu, then Kilifi, Kwale, Mombasa, Kiambu and Nairobi. They have named it FY.4.
It has since been reported in at least 11 other countries: United Kingdom, United States, China, Canada, Germany, France, Italy, Spain, Australia, Austria and Sweden.
The new lineage was discovered by researchers at the Kemri-Wellcome Trust programme in Kilifi.
“Surveillance of SARS-CoV-2 in Kenya has detected the emergence of a new Omicron lineage with unique spike and ORF3a gene mutations,” Kemri-Wellcome Trust reported.
“Detection of FY.4 lineage coincided with an increase in SARS-CoV-2 cases in Kilifi and has also been detected in other parts of the country.
“Growth estimates suggest the potential for continued increase in geographical spread of FY.4,” they said.
Patients with the new variant present mainly with cough (98 per cent of them), fever (78 per cent) and nasal discharge (74 per cent), while 7 per cent present with difficulties in breathing.
The report has been published on the preprint-server Medrxiv, awaiting publication in a journal.
Scientists are still observing the new variant but said previous studies have shown similar mutations make the virus more infectious.
“Further analysis on the immunological impacts of the observed mutations and any transmission advantage arising are ongoing,” they said.
The reporting comes as the World Health Organisation said most countries are no longer reporting Covid-19 data, yet the disease is still killing people.
“In the past month, only 25 per cent of countries and territories have reported Covid-19 deaths to WHO,” said WHO boss Dr Tedros Ghebreyesus in his weekly media briefing.
“And only 11 per cent have reported hospitalisations and ICU admissions. This doesn’t mean that other countries don’t have deaths or hospitalisations, it means they are not reporting them to WHO.”
Kenya continues to report Covid-19 data to WHO but stopped making its reports public in January this year.
The WHO tally shows at least 343,918 test-confirmed Covid-19 cases and 5,689 Covid-19-related deaths in Kenya so far.
As of April 1, 23.7 million vaccine doses had been administered.
Dr Tedros said all countries should report Covid-19 data to WHO or in open sources, especially on death and severe disease, genetic sequences, and data on vaccine effectiveness.
He said all countries should continue to offer vaccination, especially for the most at-risk groups, who are most likely to be hospitalised or to die.
“The virus continues to circulate in all countries. It continues to kill and it continues to change,” he said.
“The risk remains of a more dangerous variant emerging that could cause a sudden increase in cases and deaths.”
Dr Tedros said his new recommendations were made by the review committee that he established this year when he declared an end to the Covid-19 emergency in May.
“We urge all countries to sustain collaborative surveillance for Covid-19, to detect significant changes in the virus, as well as trends in disease severity and population immunity,” he said.
The Kemri scientists said they continue to conduct SARS-CoV-2 genomic surveillance across five health facilities in Kilifi, where samples are collected weekly from people presenting with acute respiratory illness.
They said the Lamu sample with the new variant was collected in March.
That month, SARS-CoV-2 positivity rate in Kilifi also increased from a background level of 1.2 per cent in the week commencing March 27, and peaked at 42.9 per cent, in the week commencing April 24.
However, the positivity rate dropped in the first week of May to 23.5 per cent and ranged between five per cent to 7.7 per cent over the next three weeks.
“The increase in the positivity rate starting late March coincided with detection of a new Omicron lineage, namely, FY4,” they said.
In April and May, the new FY4 variant was the predominant lineage, representing 97 per cent of all the detected lineages.
