Preliminary data indicate that the NB.1.8.1 variant has mutations in the spike protein that may increase the variant’s transmissibility and that result in marginal immune evasion compared to other currently circulating variants, such as LP.8.1. However, current data do not indicate that the NB.1.8.1 variant is associated with increased severity or different symptoms compared to other circulating lineages. As of 23 May 2025, the WHO considered the public health risk of NB.1.8.1 to be low. Current COVID-19 vaccines are expected to provide protection against severe illness due to NB.1.8.1 infections.

As of 10 June 2025, the NB.1.8.1 variant has not been detected in South Africa, although SARS-CoV-2 testing throughout the country is limited and few specimens are being submitted for sequencing. Data from the NICD’s respiratory illness syndromic surveillance programmes, which operate in selected public and private hospitals and outpatient facilities, show that the number of SARS-CoV-2 infections is currently low.

Currently, South Africa is seeing an increase in influenza cases due to the winter season. Individuals who are unwell with respiratory symptoms should practice regular hand washing, cover coughs and sneezes, and avoid contact with people who may be at high risk of severe respiratory illness. The public is reminded to practice hand and respiratory hygiene (cover coughs and sneezes). Monitoring of SARS-CoV-2 variants continues as part of national syndromic surveillance for respiratory illness and the Network for Genomic Surveillance in South Africa (NGS-SA).

Update: New COVID-19 variant NB.1.8.1 detected in Ekurhuleni wastewater; surveillance and testing ongoing

The new COVID-19 variant known as Nimbus or NB.1.8.1 has been detected in a wastewater surveillance sample collected on the 3rd June in the City of Ekurhuleni, Gauteng Province. Testing and sequencing with more recent wastewater samples is ongoing. Details may be found on the NICD SARS-CoV-2 dashboard at (https://wastewater.nicd.ac.za/). SARS-CoV-2 continues to cause very few outpatient or inpatient respiratory illnesses and testing rates amongst the general population remain low. To date, the NICD has not detected this lineage through our sentinel syndromic surveillance systems. However, global experience has shown that wastewater surveillance is able to detect new variants in communities before clinical surveillance confirms their presence.

Whilst NB.1.8.1 has been designated a SARS-CoV-2 variant under monitoring by global health authorities, newer variants of SARS-CoV-2 are continually replacing older ones, as viral mutation leads to immune escape. It is not unexpected to find NB.1.8.1 in South Africa, as travel and trade between countries and affected areas allows ongoing importation and transmission of infectious agents.

The severity of the NB.1.8.1 variant in South Africa is presently unknown. High levels of immunity to SARS-CoV-2 exist in South Africa which may lead to a less severe course of disease in infected persons.

During the winter season, preventing spread of respiratory illnesses including influenza, RSV and SARS-CoV-2 remains important. The public are advised to continue with good hand hygiene practices, covering the mouth when coughing and maintain distance from others when ill. When appropriate, ill persons may wear a mask, especially around individuals at higher risk of severe disease.

READ THE FULL UPDATE HERE

Summary 

XEC is a recombinant SARS-CoV-2 Omicron variant derived from the JN.1 descendent lineages KS.1.1 and KP.3.3. It was first detected in Germany in June 2024, and was designated a variant under monitoring (VUM) by the World Health Organization (WHO) on 24 September 20241,2.

The XEC subvariant has increased in prevalence globally, and is currently the dominant lineage constituting 45% of SARS-CoV-2 sequences submitted to GISAID in January 20253. In South Africa, XEC was first detected in a specimen collected in Gauteng in September 2024 (1/218, 0.5%), and increased in prevalence to 15.8% (9/57) of SARS-CoV-2 sequences in December 2024, while the KP.3.1.1 lineage remained the dominant lineage (27/57, 47.4%). As of 23 January 2025, in South Africa, 16 XEC cases have been detected (Western Cape (n=9), Gauteng (n=6) and Mpumalanga (n=1)). However, due to limited testing and sequencing, the prevalence and spread of the subvariant is difficult to define. The detection of the XEC subvariant in wastewater samples began in August 2024, with a prevalence of 1%. The proportion of XEC in wastewater samples increased to 3% in September 2024, and 7% in October, before declining to 1% in November 20244. Current data from the wastewater surveillance programme is pending. Data from the NICD’s respiratory illness surveillance programmes showed a slight increase in SARS-CoV-2 infections in December and January, likely reflecting increased SARS-CoV-2 transmission over the festive season5.

As of 9 December 2024, the WHO considered the public health risk of XEC to be low2. There is currently no evidence that the subvariant is associated with increased disease severity or different symptoms compared to other circulating variants. Preliminary immunological data has suggested that that XEC may exhibit increased transmissibility and immune escape compared to its parent lineage, KP.36,7. However, current COVID-19 vaccines are expected to provide protection against severe illness due to XEC infection8. It is expected that SARS-CoV-2 will continue to evolve. Based on the available data, XEC does not represent a significant health threat for South Africa.

Individuals who are unwell with respiratory symptoms should practice regular hand washing, cover coughs and sneezes, and avoid contact with people who may be at high risk of severe respiratory illness. The public is reminded to practice hand and respiratory hygiene (cover coughs and sneezes). Monitoring of SARS-CoV-2 variants continues as part of national syndromic surveillance for respiratory illness and the Network for Genomic Surveillance in South Africa (NGS-SA).

Click here to read the full report

The XBB sublineage has been shown to have increased immune evasion compared to previous sublineages. Since its identification, the XBB sublineage has given rise to several more sublineages, including XBB.1, XBB.2, and XBB.3, that have been circulating in South Africa since October 2022. The XBB.1.5 sublineage was first detected in October 2022 in the USA and has since been detected in several other countries, with the first detection in South Africa from a sample collected late in December 2022. With the growing distribution of XBB.1.5, it was not unexpected that it would be detected in South Africa. XBB.1.5 has been shown to have a growth advantage in the USA compared to previous variants, which means it may outcompete other variants to become the dominant circulating variant in some settings. This sublineage is now being monitored as a “subvariant of concern”. The growth advantage is thought to be due to a substitution (F486P) in the spike protein that increases the binding of the virus to the human ACE2 receptor and therefore increases the transmissibility of the virus.

Thus far, it is not known if the severity of infection will be different to other Omicron sublineages. The World Health Organization (WHO) Technical Advisory Group on Virus Evolution is currently conducting an ongoing risk assessment on XBB.1.5.

Due to the widespread circulation of other Omicron sublineages, and the overall high population immunity in South Africa, the introduction of XBB.1.5 in South Africa may not necessarily result in a large wave of infections. Ongoing surveillance to track variants will continue to track the growth of XBB.1.5 in South Africa and information is published weekly on the NICD website. All private and public laboratories are requested to send positive SARS-CoV-2 specimens for genomic sequencing. Currently, no changes to the public health response are required, and individuals are encouraged to receive SARS-CoV-2 vaccination and boosters, as recommended by the National Department of Health, because vaccination has been shown to reduce the risk of hospitalisation and death.

Substantially lower numbers of hospitalisations and deaths were observed in this resurgence compared to any previous wave including the Omicron BA.1 wave. High levels of population immunity are likely a major contributor to the reduction in the burden of severe illness and death in South Africa, with a recent study by the South African National Blood Service estimating that 98% of South Africans have detectable antibodies to SARS-CoV-2. These antibodies are a result of infection, vaccination or a combination of the two.

In the context of high population immunity and lower disease severity the decision has been made to lift the COVID-19 regulations implemented as part of the National State of Disaster. However, it is important to keep in mind that SARS-CoV-2 will continue to circulate in the community, and therefore the potential for new variants or subvariants to emerge, and in turn cause surges in the number of cases exists. Therefore, continued monitoring of the SARS-CoV-2 trends and changes in early warning system indicators is important.

The National Institute for Communicable Diseases (NICD) will continue to monitor the trends in the number of SARS-CoV-2 tests performed, the positivity rate, and the number of cases. In addition, the trends in COVID- 19-related admissions and deaths will be monitored through the DATCOV hospital surveillance programme. We will also continue to monitor levels of SARS-CoV-2 in wastewater. Should there be any trend in these data suggesting a potential resurgence, the National Department of Health, NICD and others will be alerted to the early warning signals from the above surveillance programmes, and take early action to inform appropriate public health response.

Recommendations for control of COVID-19 following the lifting of COVID-19 regulations

Vaccination is the most effective method for preventing and controlling severe COVID-19, and people eligible for COVID-19 vaccines must get vaccines and boosters as indicated in the national programme. A South African study found that among individuals vaccinated with the Ad26.COV2.S (Johnson & Johnson–Janssen) vaccine, the vaccine effectiveness against hospitalization for COVID-19 was 74% (95% confidence interval [CI], 57 to 84) at 14 to 27 days post vaccination, and 72% (95% CI, 59 to 81) at 1 to 2 months.

Read more here 

BA.4 and BA.5 are two newly-designated Omicron lineages. They are currently still classified as the Omicron variant, meaning that they are not a new Variant of Concern (VOC); rather, they are Omicron viruses with a new combination of mutations. In terms of their mutations, BA.4 and BA.5 share mutations across their genomes with both BA.1 and BA.2 (also lineages of Omicron), but are most similar to BA.2. However, within spike, relative to BA.2, they possess the additional mutations: 69-70 deletion (causing S-gene target failure on the Thermo Fisher Scientific TaqPath COVID-19 PCR test, initially used as a proxy for BA.1), L452R (previously seen in Kappa, Delta, Epsilon variants), F486V, and R493 (i.e., no mutation at this position). BA.4 and BA.5 differ from one another in mutations that are outside of the spike gene but they are identical to each other in terms of spike mutations (1,2). For this reason, they are often discussed together.

2. Where have BA.4 and BA.5 lineages been detected?

The Omicron lineage BA.4 was first detected from a specimen collected on 10 January 2022 in Limpopo. As of 29 April 2022, BA.4 has been detected in all provinces. The percentage of sequences designated BA.4 has grown from <1% in January 2022 to > 35% in April 2022 (3).

The Omicron lineage BA.5 was first detected from a specimen collected on 25 February 2022 in KwaZulu-Natal. As of 22 April 2022, BA.5 has been detected in Gauteng, Limpopo, Mpumalanga, KwaZulu-Natal, the North West, and the Western Cape. The percentage of sequences designated BA.5 has increased from <1% in January 2022 to 20% in April 2022 (3).

Collectively, the percentage of sequences assigned to BA.4 and BA.5 have increased from <1% in January 2022 to >50% in April 2022 (3). Both lineages have been detected in countries outside South Africa, such as the USA, UK, and Botswana. These lineages are being closely monitored and data are being uploaded regularly. Weekly updates regarding SARS-CoV-2 in South Africa can be found at https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/surveillance-reports/.

3. Is it unusual to detect a new Omicron lineage?

It is not unusual to detect new Omicron lineages. As SARS-CoV-2 continues to spread, it continues to evolve and gain mutations. When a group of genomes all contain the same set of mutations, they are designated as a new lineage. There are many lineages of Omicron (4). While BA.4 and BA.5 are new Omicron lineages, they do not represent a new SARS-CoV-2 variant and are currently still classified as Omicron.

4. Is it possible that BA.4/BA.5 will replace Omicron in SA?

Omicron has been the dominant variant in South African since it emerged in November 2021. Initially, BA.1 was the dominant lineage, and remained dominant through January 2022. Omicron BA.2 started increasing in proportion in December 2021 and was dominant by February 2022. Omicron BA.3 never became dominant, but has been continually detected a low levels (3). BA.4 and BA.5 are still classified as lineages of the Omicron variant, and so if they become dominant, Omicron will still be the dominant variant in South Africa. BA.4 and BA.5 have increased in prevalence in SA, and as of 29 April 2022, together make up the majority of genomes.

5. Have there been any concerning new symptoms with BA.4/BA.5?

As of 29 April 2022, there are currently a relatively small number of BA.4 and BA.5 cases and so it is too early to definitively know if there are any new symptoms associated with these lineages. However, given that the lineages are still classified as Omicron, and that the majority of mutations (particularly within the spike protein) are the same, it is likely that symptoms will be similar.

6. Could the emergence of BA.4/BA.5 lineages result in an increase in COVID-19 cases in South Africa?

As the BA.4 and BA.5 lineages have some different mutations to other Omicron lineages it is possible that there may be some immune escape leading to an increase in the number of COVID-19 cases. However, South Africa has a high immunity due to previous infection and vaccination, which has been shown to protect against the risk of developing severe COVID-19 disease (5, 6, 7). There is currently no indication that this will change with BA.4/BA.5, however the situation will continue to be monitored closely.

7. Will current COVID-19 vaccines still work for BA.4 and BA.5?

Vaccination remains effective at preventing severe disease, and individuals are strongly encouraged to be vaccinated and receive appropriate booster doses according to the latest COVID-19 vaccination recommendations.

Authors: Josie Everatt, Daniel G. Amoako, Dikeledi Kekana, Jocelyn Moyes, Mignon du Plessis, Sibongile Walaza, Nicole Wolter, Anne von Gottberg, Cheryl Cohen

Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa

References

1. Tegally et al., “Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages”. 2022. https://krisp.org.za/manuscripts/MEDRXIV-2022-274406v1-deOliveira.pdf
2. UKHSA, SARS-CoV-2 variants of concern and variants under investigation in England, Technical briefing 40. 8 April 2022, accessed 29 April 2022 at https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1067672/Technical-Briefing-40-8April2022.pdf
3. https://www.nicd.ac.za/wp-content/uploads/2022/04/Update-of-SA-sequencing-data-from-GISAID-29-Apr-2022.pdf
4. https://www.pango.network/summary-of-designated-omicron-lineages/
5. Wolter, et al. “Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study.” The Lancet vol. 399,10323 (2022): 437-446. doi:10.1016/S0140-6736(22)00017-4
6. Madhi, et al. “Population Immunity and Covid-19 Severity with Omicron Variant in South Africa.” The New England Journal of Medicine vol. 386,14 (2022): 1314-1326. doi:10.1056/NEJMoa2119658
7. Kleynhans, et al. “SARS-CoV-2 Seroprevalence after Third Wave of Infections, South Africa.” Emerging Infectious Diseases vol. 28,5 (2022): 1055-1058. doi:10.3201/eid2805.220278

Vaccines have been shown in controlled trials and in the evaluation of national vaccination programmes (e.g. United Kingdom) to reduce severe disease and mortality by up to 95-97%. This lifesaving effect has continued, even as variants have emerged. Taking a vaccine will protect you and your loved ones from a devastating illness and/or death. Recently, vaccines have also been shown to reduce transmission of COVID-19 from one person to another. As early as the first clinical trials, vaccines have been shown to reduce but not prevent mild to moderate illness.

As COVID variants has emerged, laboratory research has shown that protection against COVID-19 is related to antibody levels. Booster vaccination with the JnJ or Pfizer vaccine is a reliable and safe way of increasing antibody levels.

2. Why are booster shots recommended?

Booster vaccination increases antibody levels and ‘T-cell responses’ to SARS-CoV-2. Laboratory testing has shown that high antibody levels are more effective at neutralising variants of SARS-CoV-2. Therefore booster vaccines are helpful to improve protection from infection, especially during the fourth wave which is predominantly due to the Omicron variant.

3. Are booster shots safe?

Side effects of booster vaccines are similar to side effects from a first vaccine. Common side effects include tiredness, body aches, and pains, low-grade fever, pain at the injection site. Persons who have a booster vaccine may experience these common side effects more frequently. These side effects resolve completely within 24-48 hours.

Occasionally, very rare side effects (for example, myocarditis, which may occur at 12.6 cases/million doses of Pfizer vaccine) may occur slightly more frequently after a second (or booster) vaccine. If you have experienced any side effects after your first vaccine, you should report the side effect on the MedSafety app (see https://aefi-reporting.sahpra.org.za/report-aefi.html) , and discuss the need for a booster with your health care provider.

4. Who should get a booster shot, and when?

Cominarty® (Pfizer) vaccine:

• From 23 February 2022, individuals older than 18 years of age who received their first dose of the Pfizer vaccine can get their second dose after 21 days (previously, this was 42 days).
• Individuals older than 18 years of age who received their second dose of the Pfizer vaccine can get their third booster dose after 90 days (previously this was 180 days).

Johnson & Johnson vaccine:

• From 21 February 2022, individuals older than 18 years of age who received their first dose of the J&J vaccine can get their second booster dose after 60 days.

5. Can you mix and match vaccines?

You are now able to get a mixture of the J&J and Pfizer vaccines against Covid-19 in South Africa. You just have to be fully vaccinated with the one, then ask for the other as a booster, after either 60 or 90 days, depending on which you got first.

6. Which booster shot will be administered?

The decision regarding which vaccine to administer as a booster should be guided by vaccine availability. If both vaccines are available, homologous boosting should be preferred, unless the vaccine requests to receive a heterologous booster dose, or has a history of experiencing an adverse event following immunisation. (Please remember that all adverse events following immunisation must be reported).

7. Will a booster help against omicron?

Yes. There is good evidence that booster vaccination increases antibody levels to the spike protein of the SARS-CoV-2 virus and that higher antibody levels offer more protection against variants, including Omicron.

8. What if I’m immunocompromised, does the timing of the third shot differ?

Persons who are immunocompromised should receive an additional Pfizer or Johnson and Johnson vaccine dose at least 28 days after receiving their last dose. Persons who are immunocompromised should be referred by their doctor for a booster dose

Presently, persons are considered immunocompromised if they have

• Haematological or immune malignancy
• Moderate to Severe Primary immunodeficiency disorder
• HIV infection with CD4 count < 200 cells/µL within the last 6 months
• Asplenia
• Individuals receiving the following treatments:
  • High dose steroids or systemic biologics (e.g. for autoimmune conditions)
  • Long term renal dialysis
  • Transplant recipients (Solid organ or bone marrow)

The additional vaccine dose should be of the same vaccine type as the initial dose (or doses).

Isolation for Asymptomatic COVID infection

People with asymptomatic COVID-19 infection do not need to isolate. However they should be advised to:

• Wear a mask whenever interacting with people, for the next 5 days from the date of the test
• Avoid social gatherings (3 or more people) for 5 days from date of test
• Avoid being with others socially in indoor spaces, for 5 days from date of test
• Specifically avoid socially interacting with the elderly (>60 years) and anyone with co-morbidities (diabetes, lung disease, heart disease, kidney disease, cancer, uncontrolled HIV, immunocompromised), for 5 days from date of test.

Isolation for Mild Symptomatic COVID-19 infection

Those with symptomatic COVID infection who have mild disease (they do not require hospitalisation for COVID pnuemonia) should isolate for 7 days from the date of start of symptoms. There is no need for testing prior to de-isolation.

Read full update here 

The WHO, on the recommendation of the Technical Advisory Group on SARS-CoV-2 Virus Evolution, designated B.1.1.529 as Omicron, the fifth VOC, on 26^th November 2021. Concomitantly, there was a rapid increase in COVID-19 cases in Gauteng Province, from the week beginning 15 November 2021, with SARS-CoV-2 testing laboratories reporting an increase in the number of samples with S gene target failure (SGTF) when tested on the TaqPath COVID‑19 (Thermo Fisher Scientific, Waltham, MA, USA) PCR test. Subsequently, increases in COVID-19 cases and samples with SGTF were observed in other provinces in South Africa precipitating entry into a fourth wave of SARS-CoV-2 infections. By 16 December 2021, Omicron had been detected in 87 countries, with many countries reporting community transmission.

The Omicron VOC has a high number of mutations, some of which are concerning due to predicted immune evasion and increased infectivity. While the Omicron variant shares a few common mutations with the C.1.2 (a highly mutated lineage previously identified in South Africa), Beta and Delta variants, it also has 22 additional substitutions (including insertions and deletions) not seen in any other VOC or variant of interest (VOI) to date. Among them, the Δ69-70 amino acid deletion in the spike gene, previously observed in Alpha, is known to cause SGTF on the TaqPath COVID‑19 PCR test.

Data on the clinical severity of the Omicron variant compared to previous SARS-CoV-2 variants are needed to guide public health planning and response. DATCOV-Gen is a prospective surveillance network linking real-time SARS-CoV-2 genome data to detailed epidemiologic and clinical data on hospitalised cases to allow rapid assessment of severity and clinical presentation of emerging SARS-CoV-2 VOCs. The study aimed to assess the severity of Omicron infections compared to Delta variant using SGTF as a proxy.

Read full study here 

At this stage, scientists are trying to establish if this new variant has increased transmissibility (ability to spread) and/or developed ways to escape some of our immune responses,” says NICD Acting Executive Director, Prof Adrian Puren. He adds however, that the severity of Omicron is yet to be determined and urges members of the public to be cautious and to reconsider attending events that may become super spreader events, such as indoor gatherings in poorly ventilated spaces or large gatherings.

Dr Michelle Groome, Head of the Division of Public Health Surveillance and Response at the NICD agrees that responsible actions and adherence to non-pharmaceutical interventions are key to limiting the impact of a fourth wave. “If individuals remain steadfast in implementing physical and social distancing, and by wearing their masks, transmission of the disease and ultimately the negative impact on our health sector will be lessened. COVID-19 vaccination remains key, and anyone over the age of 12-years who chooses to vaccinate, is encouraged to follow through and join those who have already rolled up their sleeves.”

Dr Groome concludes by saying that if anyone experiences COVID-like symptoms, that they should self-quarantine and monitor their symptoms for at least 10-days. “During the 10-day period you should avoid contact with others, continue to wear your mask and wash your hands often. Should any worrisome symptoms present, we recommend contacting your healthcare provider for assistance.”

To find out more about what to do if you think you have contracted COVID-19, click here.