Vaccine Inequity Increases the Risk of New SARS-CoV-2 Variants Emerging

Figure 1: Vaccination rates by population size and country income level. High and upper middle income countries have vaccinated far more of their populations than have most low and lower middle income countries.

Global inequities in access to Covid-19 vaccines reflect entrenched flaws in current approaches to financing for health, pandemic preparedness, and the vaccine supply chain. Pharmaceutical companies resist technology transfer and waivers of trade-related intellectual property. Vaccine “nationalism” sees high-income countries hoarding doses. Investment in the human resources and infrastructure needed for resilient health systems has lagged for decades. Vaccine hesitancy, often fueled by mis- and disinformation, inhibits vaccine uptake in all countries; yet, in countries reliant on donor funding, it is sometimes erroneously cited as a cause for low coverage, rather than a challenge to be tackled with robust resources and coordinated, well-informed programs.

When low- and lower-middle-income countries lack access to the resources they need for vaccination programs, they are at high risk for Covid-19 surges. Furthermore, the finances and underlying infrastructure to respond effectively to the disease are already severely constrained. Vital resources, like well-staffed and well-equipped intensive care units, oxygen supplies, and personal protective equipment (PPE) for health care workers, are all stretched to their limits. This taxes already-overburdened health systems, diverting staff and stockpiles away from other essential programs, resulting in negative downstream health consequences. Longstanding services for infectious diseases like tuberculosis, malaria, and HIV, as well as noncommunicable diseases like cancer and diabetes, have been severely disrupted during Covid-19. Well-established childhood immunization campaigns—one of the defining successes of global health—have suffered, with an estimated 22 million children worldwide missing their first measles vaccine in 2020, the largest drop in 20 years. Fueled by limited access to vaccines and a lack of programs that support uptake, the pandemic in low- and lower-middle income countries can become a vicious cycle. Covid-19 cases surge, straining already overburdened health systems and exacerbating conditions that may allow Covid-19 infections and deaths to increase further.

Figure 2: Countries that have published more than 2000 sequences to GISAID in the last 180 days. Sequencing capacity varies greatly based on income level, what % of cases are sequenced, how many sequences are shared, and submission latency. Of these, high income countries are alone in the capacity to sequence more than 5% of cases. It is important to note that political constraints and legitimate concerns around the benefits of sharing data may also affect the percentage of cases sequenced, beyond strict capacity limits.

Variants emerging in areas lacking both vaccination and genomic surveillance may have the chance to become widespread before they can be detected and contained. The Delta variant, currently the dominant strain worldwide, was first identified in late 2020 in India, but was not recognized as a public health threat until March 2021, in part because India was sequencing less than 1% of positive samples. It is now the dominant variant globally.

Figure 3: Visualizing the timeline of Omicron sequences collected and submitted to GISAID by country, with circle sizes representing number of Omicron samples collected per date, the line spanning from earliest collected sample to latest submitted sequence, color denoting continent, and ordered top-down by earliest date of collection.

The excellent work of South African scientists and other contributing researchers shows how effective genomic surveillance can be at identifying and tracking variants and enabling a rapid response. The value of genomic surveillance can be further enhanced by expanding it to underserved populations, both domestically and globally. The swift announcement of Omicron was a benefit to the global community, yet it was met with travel bans against African nations, without comparable bans on other countries with documented Omicron cases. These bans have been criticized by scientists as being ineffective, inhibiting the very transparency that had alerted the world to the variant, and interfering with the ability of researchers to study it. Inequitable application of policies is yet another facet of the global imbalance that fuels pandemics.

In spite of these persistent issues, a steady expansion of genomic surveillance capabilities around the world will aid global surveillance efforts. The Africa CDC’s Institute of Pathogen Genomics is playing a crucial role in coordinating and supporting expansion of capabilities and data sharing, and comparable programs have been initiated to improve genomic surveillance in other low- and lower-middle-income regions. The Rockefeller Foundation, through its Pandemic Prevention Institute, is supporting initiatives in India, at the University of Ghana’s West African Centre for Cell Biology of Infectious Pathogens, and at the Nigeria-based Africa Centre for Excellence in Genomics of Infectious Disease. The Pandemic Prevention Institute is also supporting the work of The Centre for Epidemic Response and Innovation (CERI), a consortium of public health officials, scientists and clinicians associated with the South African Medical Research Council (SAMRC), the Department of Science and Innovation (DSI), Stellenbosch University and the University of KwaZulu-Natal (UKZN). Headed by Professor de Oliveira, CERI has the goal of improving genomic surveillance on the African continent. In addition to its own sequencing technology, CERI’s Genomics Africa Fellowship Program is training scientists from countries throughout Africa, who can then support genomic surveillance in their own countries.

This expanded capability will help support the ability to track Covid-19 and guide responses in some regions, and additional public and private investment in surveillance initiatives are still needed to provide effective global surveillance. Genomic surveillance alone will not, however, solve the problem of continued spread caused by low vaccination rates and resulting high transmission rates. Scaling up genomic surveillance and swift data sharing depends on countries and communities seeing the benefits of sharing information—including access to the resources needed to respond. The emergence of the Omicron variant has illustrated to the world the need for vaccine equity and global genomic surveillance. Programs that expand sequencing capacity will aid in attaining comprehensive surveillance. Controlling the pandemic depends on using genomic data to track the virus, as well as taking the steps needed to end the inequities that contribute to the emergence of variants that may threaten the globe.