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The Window of Opportunity to Vaccinate Africa

Paper9th February 2022

Chapter 1

Executive Summary

On 17 January 2022, there were estimated to be 125 million active Covid-19 infections worldwide – ten times the peak of the Delta wave. It is likely that more than 50 per cent of the globe will have been infected by March 2022. Despite these numbers, we were lucky – it didn’t lead to mass death and blanket lockdowns. However, a new, more transmissible and more deadly variant may test this luck, and we cannot afford to be unprepared.

It is therefore critical that countries in the early stages of an Omicron-driven wave of infections understand how it will play out and how to prepare for it, and for them to act now rather than when it’s too late.

This paper reviews the impact of Omicron in South Africa, Kenya, Tunisia and Nigeria and finds:

  1. that populations with high levels of seroprevalence, either through vaccination or prior infection, fare well against Omicron.

  2. a decoupling of positive cases from hospital admissions, severe illness and death.

  3. that countries’ economic recoveries have been set back by Omicron.

  4. a six-month window between Covid waves driven by the emergence of new variants.

  5. a move away from blanket lockdowns as a response.

These impacts were significant, but they are acute symptoms of a chronic and recurring inaction. The Omicron wave is the fourth to have swept through Africa. It is almost inevitable – without further action – that a fifth wave will appear: it is just a matter of when.

With this in mind, we recommend that countries implement a two-track response focusing on preparation and prevention.

  1. Build long-term resilience now in areas such as data, and vaccine and testing infrastructure.

  2. Identify prior issues and engage in responsive policymaking: update policies ahead of time rather than in real time.

  3. Prioritise rollout of vaccines and boosters, and vaccinating children: all evidence points to increased protection from severe disease and death after vaccination.

  4. Recognise that lockdowns are not always the best course of action: as the virus changes, countries need to adapt.

  1. End vaccine inequity to slow emergence of new variants: we have a six-month window to ramp up vaccinations in Africa.

  2. Increase testing and genomic sequencing to reduce rate of transmission and keep societies and economies running.

  3. Take collective action: global leadership is needed for a globally agreed pandemic plan.

The Omicron flash flood may be receding, but if the past two years tell us anything it is that there is likely to be another on the horizon. Almost every six months over the past two years, we have observed a Covid wave, driven by new variants, sweep across Africa. These waves drive infections, increase mortality, and disrupt societies and economies. At this stage of the pandemic, we can be confident in this prediction although, thankfully, Omicron has had a comparatively soft impact. The arrival of a new, more transmissible and more deadly variant in mid-2022 may not be so kind, especially to those countries with low levels of protection.

This begs the question: what will the next six months look like?

The most likely scenario, which we have seen play out before, is that Omicron subsides, failing to produce herd immunity or durable protection. This will provide us with a six-month window to make progress towards meeting the World Health Organisation's (WHO) target of vaccinating 70 per cent of every country’s population to prevent a new variant from emerging in the middle of this year.

Chapter 2


Omicron unfolded in a vastly different way to previous Covid-19 waves. In countries with highly vaccinated populations, there were instant economic slowdowns, mass staff absences in critical areas such as health care and the supply chain, a rapid testing crunch, significant disruptions to travel, and price rises for commodities such as fuel. These issues have been exacerbated by a failure to adapt policies fast enough for them to be fully effective.

Countries with high proportions of unvaccinated populations have been hit slightly harder. These countries have faced the same socioeconomic challenges, coupled with an increase in severe disease and death. With the proliferation of variants, Covid-19 now poses a different and more complex threat than before and requires preparatory decision-making, fast and agile responses, and clear-eyed, collective global action and leadership.

In this paper, we set out what we now know about Omicron, how it has played out so far, how to mitigate its impacts, and what to do to prevent – or at least delay – another variant from emerging.

Chapter 3

Overview: What We Know of Omicron and Its Epidemiology

Omicron was first reported to the WHO on 24 November 2021. It has now spread to more than 150 countries and infected hundreds of millions of people worldwide. Omicron quickly outpaced Delta’s spread and today accounts for the majority of reported Covid-19 infections around the world.

Since late November 2021, scientists and public-health experts have been working around the clock to share the latest discoveries and insights into Omicron. What we know has so rapidly changed over the past two months that it is often difficult to take stock of the science.

The origins of Omicron are disputed and there is no transparent path of transmission linking it to past variants. Some plausible theories about its inception are well documented, although the definitive answer is unknown. These theories include silent person-to-person spread of Covid-19 that was not picked up through testing or genome sequencing, thereby allowing us to lose sight of the virus’s changes; persistent infection with a previous variant in a person with chronic infection, such as someone with an immune system weakened by HIV or another immunocompromising condition, that led to accumulation of additional mutations; or transmission from humans to mice with subsequent transmission back to humans.

The diversity of these theories demonstrates the rapid pace at which understanding of Omicron evolved in the initial months and the element of the unknown which has been present since the pandemic began.


Omicron is extremely transmissible – estimated to be four times more so than Delta – and its infectiousness has been likened to measles. This has been demonstrated through models from the Institute for Health Metrics and Evaluation (IHME) that estimate the number of global daily Covid-19 infections to be 30 times higher in mid-January 2022 than at the end of November 2021.

This extreme transmissibility – an average doubling time of two to three days – is likely a combination of immune evasion, virus mutation and intrinsic increased transmissibility. This is partly explained by the replication of Omicron in the upper respiratory tract being 70 times faster than in the lungs, resulting in more efficient expulsion of airborne particles.


We are familiar with the common symptoms of Covid-19: loss of taste and smell, stuffy and runny nose, fever, persistent cough, and sore head and throat. However, the symptoms observed for Omicron differ.

Common signs and symptoms that indicate infection with Omicron include a strange scratchy feeling in the throat, persistent tiredness, muscle aches, night sweats, diarrhoea and nausea or vomiting. But the most common sympton of all is nothing – most Omicron infections (between 80 and 90 per cent) are asymptomatic. Compared with previous variants, which were estimated to be asymptomatic about 40 per cent of the time, this is extraordinary.

It appears that this combination of mild symptoms and an increase in the proportion of cases that are asymptomatic has led to a global decline in the infection-detection rate from 20 per cent to 5 per cent.


The good news is that most evidence points to Omicron being less severe than other variants, with a reduced potential for hospitalisation and death compared with Delta – this has been borne out in real-life evidence from Denmark and South Africa.

Meanwhile, in the United States the ratio of hospitalisations to positive cases hospitalised has declined by 50 per cent compared with previous waves, and in Canada and South Africa, the proportion of patients who require intubation or are dying has declined by 80 to 90 per cent.

However, any reduction in severity should be treated carefully as Omicron’s increased transmissibility and exponential growth rate may outweigh any benefits of reduced severity, especially in under-vaccinated populations.

Chapter 4

Overview: What We Know About Vaccines, Treatments and Tests for Omicron

Vaccine-Induced Immunity

All available evidence points towards the majority of the current suite of vaccines remaining highly effective at preventing severe disease and death from Covid-19.

A study led by the UK Office for National Statistics, published in January 2022, found that those who had received any Covid-19 vaccine within three months, a second Pfizer vaccine within six months, or three vaccinations were all less likely to test positive than those who were not vaccinated. However, these effects are less significant than what has been observed previously, indicating a degree of diminished effectiveness against Omicron in the currently available vaccines.

A UK Health Security Agency surveillance report showed that the effectiveness of vaccines against symptomatic disease is lower for Omicron compared with Delta and that the protection wanes rapidly, with one report demonstrating a 40-fold reduction in the ability of antibodies from double-vaccinated individuals to protect against Omicron.

However, protection against hospitalisation remains high, particularly following a booster dose, which raises effectiveness against hospitalisation to 90 per cent. Regarding the level of immunity that a third dose provides individuals, Pfizer notes that a third dose of their mRNA vaccine increases the level of antibodies against Omicron 25-fold while a third dose also increases T-cell response (one’s innate immune cells) and protects against severe diseases. The duration of this protection is yet to be determined but from experience with prior variants, it is likely that it will be sustained for longer against severe disease than protection against symptomatic disease.

A fourth dose, as is being rolled out in Israel, has been assessed to increase antibody levels but not to a point that prevents infection with Omicron. It looks unlikely that fourth doses will be rolled out at a global scale any time soon.

Infection-Induced Immunity

People previously infected with Covid-19 continue to be less likely to test positive than people not previously infected. However, this effect is smaller than seen in the past.

Prior Covid-19 infection is also a less effective defence against Omicron, with the risk of reinfection now 16 times higher than during the Delta-dominant period. When Delta was rife, unvaccinated people were twice as likely to be reinfected than people who had been double-vaccinated.

The combination of a previous Covid-19 infection and being vaccinated is likely to confer up to 50 per cent more protection against Omicron than those who are only vaccinated or have only had a prior infection.

Studies show that infection-induced immunity against Covid-19 lasts for a period of three months. With Omicron, the window of protection from reinfection may be shorter due to its mutations and ability to evade infection-blocking antibodies.


Paxlovid, an antiviral drug manufactured by Pfizer, is increasingly the drug of choice for treating Omicron. It should be administered as soon as a diagnosis of Covid-19 has been made and within five days of onset of symptoms. The pill has been authorised for use in the US, the UK, the EU, Israel and some African countries.

Paxlovid has 89 per cent efficacy in preventing hospitalisations and death in high-risk patients, and evidence from Pfizer indicates that it remains effective against Omicron.

Other emerging antiviral drugs will also be key tools in the fight against Covid-19, preventing hospitalisation and death. This is even more important in under-vaccinated regions such as Africa, since they are cheap to produce, easy to store and simple to administer.

Chapter 5

Review: How Omicron Has Played Out in Africa

Given what we know about Omicron’s severity and characteristics, how has it played out in real life?

It is difficult to draw direct comparisons between different countries’ experiences due to varying vaccine- and infection-induced immunities and demographics. However, reviewing their experiences provides an insight into what can be reasonably expected to take place when Omicron or a future variant takes hold, and the challenges that governments will likely face.

Case Study: South Africa

It is estimated that 31 per cent of the South African population has received at least one vaccine, and that 80 per cent of the population has been exposed to Covid-19 since the beginning of the pandemic. In some parts of South Africa, sero-positivity is 79 per cent and 93 per cent respectively in unvaccinated and vaccinated people older than 50, an age group usually notorious for high rates of hospitalisation and death. This level of vaccine- and infection-induced immunity appears to provide a strong firewall against severe disease outcomes.

South Africa observed a rapid rise in case numbers and test-positivity rates. At one point, over 23,000 cases a day were being reported with an average of around 90 deaths per day. At the same time one year earlier, 19,000 cases a day were being reported with an average of around 500 deaths a day. In Gauteng, the epicentre of the outbreak in South Africa, approximately 5 per cent of Covid-19 cases were hospitalised during the Omicron wave, versus 19 per cent and 47 per cent during previous waves in the region.

Omicron led to a noticeable increase in Covid-19-related deaths. However, as most commentary has already noted, this has not corresponded with what would be expected given the significant number of infections – higher than had been observed in South Africa at any point in the pandemic.

While the increase in cases was rapid, the drop in cases was almost just as quick, likely driven by the apparent tidal-wave effect of Omicron. Today, South Africa continues to see a steady reduction in reported cases despite the comparatively light-touch restrictions that were put in place: curfews, restrictions on large gatherings and mandatory face-masking in public places. The government did not resort to strict lockdown measures as it had during prior Covid-19 waves and even began to loosen self-isolation rules for close contacts due to existing population immunity and a desire to avoid socioeconomic impacts such as loss of income and schooling time. However, this loosening was later put on hold.

As can be observed in Figure 1, South Africa appears to have escaped Omicron with a relatively minor impact on mortality and has seen a strong decoupling between cases and deaths.

Figure 1

Daily new confirmed Covid-19 cases and deaths per million people in South Africa

However, the destabilising impact of Omicron spread further than just cases and deaths.

Travel restrictions imposed on South Africa and its neighbouring countries by European Union countries, the United Kingdom and the United States severely hampered the South African and wider African Covid-19 response effort. Commercial flights that would normally be used to transport critical people, equipment and specimens were suddenly cancelled, so scientists and testing reagents could not reach South Africa and the genomic sequencing of Covid-19 samples was hindered.

South Africa appeared to fare well in terms of other societal impacts that were seen in countries such as the UK. When the UK was in the midst of its Omicron-driven surge, it saw disruption to everyday life through mass staff absences, reduced economic output and a testing crunch. The surge led to the highest staff-absence rate since June 2020 and shrank the economy by a cumulative 0.5 per cent over December and January. South Africa, by contrast, did not experience the same phenomena.

Case Study: Kenya

Since the beginning of the pandemic, around 319,011 infections and 5,520 deaths have been reported in Kenya. Kenya, like most countries in sub-Saharan Africa, has relatively low vaccination rates. Only 12.5 per cent of the Kenyan population has received two doses of a Covid-19 vaccine.

As of mid-December, the test positivity rate was 11.5 per cent. During previous waves this was around 5 per cent. An increase in Covid-19-related deaths was reported but over the past three weeks the rates of infection and cases reported have steadily declined, indicating that Kenya, too, is emerging from its Omicron-driven wave.

Just prior to the detection of Omicron, the Kenyan government announced plans to require proof of vaccination for access to in-person government services, hospitality and public transport. Following a surge in Omicron cases they forged ahead with the vaccine requirement, extending it to supermarkets, weddings and funerals. The Kenyan government also held off implementing a lockdown, focusing instead on a lighter approach that included compulsory face masks indoors, the rollout of vaccine “booster” shots to everyone over the age of 18, and instructions to work from home if possible. This is consistent with other international approaches to Omicron, including that of the UK government, which was reticent to implement severe restrictions and all but ruled out moving to a full-scale lockdown of the kind that had been imposed in prior waves.

Figure 2

Daily new confirmed Covid-19 cases and deaths per million people in Kenya

Despite its modest impact on deaths, Omicron has presented the country’s tourism sector with another likely setback. The sector had already been hit hard by previous waves of Covid-19 and was transitioning to a recovery phase when Omicron emerged. At the start of the pandemic, the portion of Kenya’s GDP attributable to tourism fell by almost 50 per cent from $8.1 billion to $4.2 billion; the longer the pandemic rages on and the more variants that emerge, the greater the impact is expected to be.

The emergence of Omicron has also been directly attributed to the exacerbation of an ongoing fuel crisis in Kenya’s landlocked neighbour, Uganda. Fuel-delivery drivers crossing from Kenya to Uganda are required to display a negative test when crossing the border, but due to the surge in Omicron cases, tests are scarce and expensive. Some reports detail the queues into Uganda being up to ten days long, and alongside customs delays, driver strikes and protests, fuel prices have increased by more than 50 per cent in Uganda, while mass shortages of fuel across the country have seen traffic grind to a halt.

Case Study: Tunisia

Tunisia has experienced close to 860,000 infections and 26,000 deaths since the start of the pandemic, making it one of the hardest-hit African countries. Of its adult population, 54 per cent have had two doses of a Covid-19 vaccine.

There is a current spike in case numbers in Tunisia. An average of 9,000 new infections are reported daily – 120 per cent of its previous peak – and deaths have marginally increased, but not in line with the rapid increase in infections, indicating that the trend of a decoupling of infections and deaths continues to be observed.

Figure 3

Daily new confirmed Covid-19 cases and deaths per million people in Tunisia

Due to rising Omicron cases, the Tunisian government has imposed rules to curb transmission. Wearing face coverings in public places and on transport is mandatory and failure to comply may result in a fine or imprisonment. An initial two-week curfew, effective between 10pm and 5am, was imposed from 13 January 2022 and extended on 27 January 2022. All non-essential movement and protests in public and private places are banned during this period. Furthermore, proof of vaccination status is mandatory to gain entrance into public spaces for adults aged 18 and over.

The government has not closed Tunisian borders; however, entry requirements are tighter.

Other countries are advising their citizens to avoid travelling to Tunisia for non-essential purposes. For instance, the US Centres for Disease Control and Prevention has placed Tunisia in the “very high risk” category of its risk register, and advises US citizens travelling there to receive a full vaccination course before departure. Such advice, and the wider Covid-19 situation, has put a strain on the travel and tourism industry in Tunisia: the sector has seen a 64 per cent decrease in revenue and 50 per cent decrease in tourists.

Case Study: Nigeria

Covid-19 cases appear to be on the decline in Nigeria. Case numbers are currently about 33 per cent below the previous peak level, but due to Omicron this had reached around 125 per cent of the peak before that. Since the start of the pandemic, about 252,428 infections and 3,126 deaths have been recorded. Double-vaccination levels in Nigeria sit at around 2.6 per cent of its adult population.

Figure 4

Daily new confirmed Covid-19 cases and deaths per million people in Nigeria

Despite comparatively low levels of vaccination and an increase in Omicron cases, blanket lockdowns were not implemented. Instead, religious gatherings were restricted to 50 per cent capacity; vaccines were encouraged, including boosters for the eligible; face masks and general hygiene were advised; and families were advised to limit the number of visitors to their homes. Furthermore, health workers were advised to apply necessary cautions and prepare for each admission as if it were a Covid-19 case.

While the public-health impact of Omicron could be seen in case numbers and a modest increase in deaths, the economic effects were felt through the imposition of travel bans by countries such as Canada, Saudi Arabia, the UAE and the UK, as well as through the internal restrictions imposed by the Nigerian government – all of which hindered the already volatile recovery of the domestic and international travel industries.

Chapter 6

What Are the Main Takeaways From These Experiences?

Omicron poses a more complex threat to societies than prior waves because of its rapid transmissibility that renders previously effective tools such as lockdowns futile. Therefore, it has required a different set of decisions from leaders whose countries have faced Omicron, and has afforded us new knowledge that can be used to prepare for the next stage of the pandemic.

Five main trends have been observed:

  1. Populations with high levels of seroprevalence either through vaccination or prior infection fare well against Omicron.

  2. A decoupling of positive cases from hospital admissions, severe illness and death.

  3. Countries’ economic recoveries have been set back by Omicron.

  4. The peak of Covid waves, driven by the emergence of new variants, are roughly separated by a six-month window.

  5. A move away from blunt lockdowns as a response.

Implications for Future Covid-19 Responses

The fourth wave in Africa was likened to a flash flood in the way that it rose, peaked and then rapidly dropped off, with the WHO noting that Africa had exited the fourth wave after just six weeks while previous waves in Africa lasted anywhere from 28 to 33 weeks.

During the midst of the Omicron-driven surge, the South African government eased its Covid-19 restrictions. This was motivated by a pragmatic focus on the capacity of the health system and the severity of the infections, rather than raw case numbers. This indicates a strong move towards living alongside Covid. This is likely to be replicated throughout Africa, with the Africa Centres for Disease Control and Prevention in lockstep agreement that lockdowns are no longer the best way to contain Covid-19, and countries such as Kenya, Nigeria and Tunisia implementing tight rules but not the blanket lockdowns seen in past waves.

This change acknowledges that for many countries a gradual return to normality has begun. However, this is a forced consequence of not being able to sufficiently vaccinate the population and instead needing to rely on infection-induced immunity. This may seem like a cost-effective approach given the complexities and challenges, both on the supply and demand side, of running a mass-vaccination campaign; however, the science shows that this is a false choice. Transmission, severe disease and death are all significantly reduced by vaccination. Consequently, this slows down the emergence of new variants, buying more time for the world to build and distribute the tools needed to exit the pandemic phase and move to a more sustainable, less damaging stage.

Some commentaries predict that Omicron is the end of the pandemic; others say that we should now treat Covid-19 as endemic, while Dr Anthony Fauci believes that we still do not know, and that it remains an open question as to whether or not Omicron will provide a widespread level of protection because of the variability implicit with new variants emerging. In any case, if we want to reach a point where Covid-19 is no longer significantly disruptive to our lives, the single biggest threat is the emergence of another variant that is deadlier, more transmissible, that eludes the immune response to prior variants or vaccines, or all of the above.

To this end, the primary takeaway from this paper is that for the Omicron-driven wave in South Africa, Kenya, Tunisia and Nigeria, and all previous waves, there is a rhythm in their impact (see Figure 4), and that they are extremely disruptive. Almost every six months, we have observed the impact of a new variant of concern that drives Covid infections, leads to increased mortality, and disrupts society and economies. From May 2020, several strains related to the original SARS-CoV-2 took hold in Africa leading to increased cases and deaths; this was followed by Beta from October 2020 until May 2021, Delta in July 2021 until November 2021, and Omicron in December 2021. These waves are illustrated by the following chart of South Africa’s Covid-19 experience.

Figure 5

Covid-19 waves in South Africa since March 2020

The emergence of new Covid-19 variants that continue to cost lives and disrupt society with regularity is almost predictable at this stage of the pandemic. Despite the many declarations that if we ride out this wave then herd immunity is on the horizon, the most likely scenario – that we have already seen play out multiple times – is that Omicron subsides having failed to produce herd immunity or durable protection. This will again give us a six-month window to vaccinate Africa and reduce the likelihood of a new wave sweeping across the continent midway through 2022.

The risk of resting on our laurels having ridden out the Omicron wave (mostly) successfully is that the next variant may not resemble Omicron. There is no guarantee that this variant will be less transmissible or less severe, or that vaccine- and infection-induced immunity will remain effective. However, it is guaranteed that if we do not use the tools available to us – such as vaccines – the pandemic phase will be extended by new variants, continued susceptibility to Covid-19 and long-term disruption to our everyday lives.

Accelerating efforts to vaccinate the world in the next six months is the only way to have a modicum of control over this cycle.

Chapter 7

What Have We Learnt and Where Do We Go From Here?

The key takeaways and recommendations can be split into two parts: how to prepare for Omicron; and how to prevent another Omicron.

  1. Build long-term resilience now: countries must prioritise building resilience in data, vaccine and testing infrastructure to provide greater institutional strength to withstand the pressures of future Covid-19 waves. The Tony Blair Institute for Global Change is working with a number of countries in Africa to support this long-term resilience-building.

  2. Prior issue identification and responsive policymaking: countries should institute policies ahead of time, following the science and anticipating what will happen next, rather than trying to institute policies in real time. Isolation requirements, for instance, should be updated in line with international experience to respond to inevitable staff shortages, and masking guidance updated to recommend N95 or KN95 masks rather than fabric or surgical masks. These are all steps that can and should be taken in advance of the next wave.

  3. Prioritise rollout of vaccines and boosters, and vaccinating children: all evidence points to significantly increased protection from severe disease and death after vaccination.

  4. Recognise that lockdowns are not always the best course of action: as the virus changes countries need to adapt. What worked in the past might not in the future and it may even hamper an effective response.

  1. Vaccinate to slow the emergence of new variants: the receding Omicron wave signals the beginning of a six-month window to work towards the WHO’s 70 per cent vaccination goal. Vital challenges will include seeking a reliable and predictable supply of vaccines with expiry dates of at least three months, and ramping up absorptive capacity.

  2. Testing and genomic sequencing: this will reduce the rate of transmission and keep societies and economies running. This includes widely available rapid tests that can be done at home, as well as testing in critical sectors such as supply chain and power generation.

  3. Collective action: it’s impossible for a single country to end the pandemic alone. This extends to prevention, detection and response. Efforts to establish a globally agreed pandemic plan should be accelerated.

Chapter 8


Omicron’s impact in shifting the Covid conversation has been undeniable, and it may well prove to be another step towards the beginning of the end of the pandemic phase for those populations that have sufficient protection through prior infection, vaccination or both. However, for those countries that are under-vaccinated – the majority of Africa – a return to normality is likely to be delayed to well beyond 2023.

This delay, driven primarily by vaccine inequity, means that countries the world over will need to learn lessons from Omicron about how to prepare for a new variant and build long-term resilience, as well as bolster preventative efforts focused on those under-vaccinated populations.

We know that there is a pattern to the impact of Covid-19 waves in Africa: whether by chance or biology, every six months we have seen a new Covid wave, driven by a new variant, sweep across Africa.

In some senses, the world was lucky with Omicron – it didn’t lead to mass death and extended lockdowns – but a new, more transmissible and more deadly variant in the future may test this luck. We cannot afford to be badly prepared; we need to make the most of this six-month window to vaccinate Africa.

Lead Image: Getty Images


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