KAMPALA: As Ugandan media report nine cases of the new Omicron COVID-19 variant in the country, a high level expert study has revealed details about how it came here.
“Eleven out of the 13 SARS-Cov-2 PCR positive samples collected from travelers arriving at Entebbe International Airport on 29th November 2021 were sequenced using the Illumina Miseq next generation sequencing platform (Covidseq assay kit) to generate high-quality genomes with over 90% coverage,” the report revealed on December 6.
It adds: “The travelers arrived from Nigeria, United Arab Emirates, South Africa, Democratic Republic of Congo and Netherlands aboard Ethiopian Airways, Uganda Airlines, Kenya Airlines and Airlink.
The study titled: “Report on SARS-CoV-2 genomic surveillance in Uganda” and dated
6th December, 2021, was commissioned on November 29, 2021 when the variant strain was first reported in the world media.
With the backing of the Medical Research Council, Uganda Virus Research Institute and London Scool of Hygene and Tropical Medicine, the report is the work of eminent Ugandan scientists.
MediaScape News understands that the researchers were:Deogratias Ssemwanga, Nicholas Bbosa, Hamidah Namagembe, Ronald Kiiza, Jocelyn Kiconco, John Kayiwa, Tom Lutalo, Alfred Ssekagiri, Julius Lutwama, Isaac Ssewanyana, Susan Nabadda, Henry Kyobe-Bbosa and Pontiano Kaleebu.
We reproduce the report as follows:
Background
Eleven out of the 13 SARS-Cov-2 PCR positive samples collected from travelers arriving at Entebbe International Airport on 29th November 2021 were sequenced using the Illumina Miseq next generation sequencing platform (Covidseq assay kit) to generate high-quality genomes with over 90% coverage.
The travelers arrived from Nigeria (n=5), United Arab Emirates (n=2), South Africa (n=2), Democratic Republic of Congo (n=1) and Netherlands (n=1) aboard Ethiopian Airways, Uganda Airlines, Kenya Airlines and Airlink.
Deep sequence reads were assembled using the Genome Detective software (1) and quality control of the sequences was done using Nextclade and Geneious programs followed by lineage classification using both PANGO lineage typing (2) and Nextclade (3).
Results
Seven (64%) out of the 11 SARS-CoV-2 genomes were classified as belonging to the Omicron variant (VOC) by both PANGOLIN (Phylogenetic Assignment of Named Global Outbreak LINeages) and Nextclade (Table 1). The other 4 genomes were of the Delta variant (also a VOC). The lineage and variant classification programs used in the analysis have been updated to detect the new Omicron B.1.1.529 variant.
Conclusion
We report for the first-time detection of the Omicron variant (B.1.1.529) in Uganda from samples taken from travelers arriving in the country through Entebbe International airport.
The Omicron variant has been designated as a variant of concern by the WHO and presents with some deletions and more than 30 mutations in the spike region. As the number of Omicron cases increases globally, there is a need for near real-time genomic surveillance to keep track of emerging and circulating variants for the effective control of the SARS-CoV-2 epidemic.
While giving her staus report to the nation on December 2, 2012, the Minister of Health Dr Ruth Aceng said: “I would like to appeal to the population to embrace and take seriously the COVID-19 vaccination exercise. Getting vaccinated and adhering to the Standard Operating Procedures (SOPs) will protect you and your loved ones from getting infected with COVID-19. The COVID-19 vaccine is safe, effective and free. It will protect our country from the devastating effects of COVID-19.
What You Need to Know about OMICRON:
According to the US’ Centre for Disease Control (CDC), Omicron Variant of SARS-CoV-2, B.1.1.529 was first reported on November 24, 2021 to the World Health Organization (WHO). This new variant was first detected in specimens collected on November 11, 2021 in Botswana and on November 14, 2021 in South Africa.
On November 26, 2021, WHO named the B.1.1.529 Omicron and classified it as a Variant of Concern (VOC). On November 30, 2021, the United States designated Omicron as a Variant of Concern, and on December 1, 2021 the first confirmed U.S. case of Omicron was identified.
CDC has been collaborating with global public health and industry partners to learn about Omicron, as we continue to monitor its course. CDC has been using genomic surveillance throughout the course of the pandemic to track variants of SARS-CoV-2, the virus that causes COVID-19, and inform public health practice. It is not yet known how easily it spreads, the severity of illness it causes, or how well available vaccines and medications work against it.
Infection and Spread
According to CDC, the Omicron variant likely will spread more easily than the original SARS-CoV-2 virus and how easily Omicron spreads compared to Delta remains unknown. CDC expects that anyone with Omicron infection can spread the virus to others, even if they are vaccinated or don’t have symptoms.
More data are still needed to know if Omicron infections, and especially reinfections and breakthrough infections in people who are fully vaccinated, cause more severe illness or death than infection with other variants.
Current vaccines are expected to protect against severe illness, hospitalizations, and deaths due to infection with the Omicron variant. However, breakthrough infections in people who are fully vaccinated are likely to occur. With other variants, like Delta, vaccines have remained effective at preventing severe illness, hospitalizations, and death. The recent emergence of Omicron further emphasizes the importance of vaccination and boosters.
Scientists are working to determine how well existing treatments for COVID-19 work. Based on the changed genetic make-up of Omicron, some treatments are likely to remain effective while others may be less effective.
Accordingly, vaccines remain the best public health measure to protect people from COVID-19, slow transmission, and reduce the likelihood of new variants emerging. COVID-19 vaccines are highly effective at preventing severe illness, hospitalizations, and death.
Scientists are currently investigating Omicron, including how protected fully vaccinated people will be against infection, hospitalization, and death. CDC recommends that everyone 5 years and older protect themselves from COVID-19 by getting fully vaccinated. CDC recommends that everyone aged 18 years and older should get a booster shot at least two months after their initial J&J/Janssen vaccine or six months after completing their primary COVID-19 vaccination series of Pfizer-BioNTech or Moderna.
Masks can offer protection against all variants and CDC continues to recommend wearing a mask in public indoor settings in areas of substantial or high community transmission, regardless of vaccination status.
Testing for OMICRON
Tests can tell you if you are currently infected with COVID-19. Two types of tests are used to test for current infection: nucleic acid amplification tests (NAATs) and antigen tests.
NAAT and antigen tests can only tell you if you have a current infection. Individuals can use the COVID-19 Viral Testing Tool to help determine what kind of test to seek.
Additional tests would be needed to determine if your infection was caused by Omicron.
Virus Characteristics
CDC scientists are working with partners to gather data and virus samples that can be studied to answer important questions about the Omicron variant. Scientific experiments have already started.