Add Resources - Scaling Up & Sustainability

Current testing tools uncompromised by new COVID-19 variant of concern Omicron (B.1.1.529)

Available diagnostics do pick up Omicron infections

In November 2021 a new variant of the SARS-CoV-2 virus was identified. 

The World Health Organization declared it a variant of concern, especially as it is more transmissible than the variants that preceded it. 

There were initial concerns that Omicron would also evade testing, as some PCR tests did not pick up the virus because it had a deletion in one of its genes. 

However, the other PCR gene targets were still identified. 

At the time FIND conducted a rapid assessment of available evidence and also confirmed that rapid antigen tests would still pick up an Omicron infection. 

Add Resources - Scaling Up & Sustainability

Enhancing response to Omicron SARS-CoV-2 variant

WHO released this technical brief and guide to prioritize actions for member states in January 2022.

It aims to enhance response to the Omicron SARS-CoV-2 variant, designated by WHO as a variant of concern on 26 November 2021. Based on the information available, the overall risk related to Omicron was identified as being very high.

The brief is divided into three main sections:

  • An executive summary of key current technical information
  • Current evidence on Omicron
  • Priority actions for member states.

Previous versions of this technical brief are available on this link.

Read the full WHO brief here

Add Resources - Research & Development

How genomics can help track new SARS-CoV-2 variants

Sequencing data key for monitoring virus and understanding impact of therapeutics.

This report on SARS-CoV-2 variants, developed and published for FIND (11 March, 2021) by PHG Foundation, explains how genomics helps to monitor the evolution of coronavirus “variants of concern”, or VOCs.

It outlines how genomic surveillance and sequencing have supported identification of new variants as well as the impact these variants have had on diagnostic tests and public health measures. 

This process has also significantly advanced vaccine design and development. 

Ongoing surveillance is required not only for known VOCs, but also for new “variants of interest” (VOIs).

Thinking ahead
Data produced has enabled further understanding of the variants, helping to inform future surveillance and the impact mutations may have on vaccines, diagnostics and therapeutics. 

Various countries have invested in sequencing infrastructure and resources to help combat the virus, and have put public health measures in place in response. 

Continued investment in sequencing capabilities and data sharing, as well as a variety of skills and expertise from multiple backgrounds, is needed to make genomic surveillance successful. 

In addition, it is important to limit the spread of the virus to prevent the emergence of additional variants which may be even more transmissible. 

Sequencing data continues to be key for monitoring the virus and understanding the impact of therapeutics.

An appendix on resources actively monitoring VOCs is included.

Read the full report here

Resource Centre - Publications

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1,2,3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

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Resource Centre - Publications

An early warning system for emerging SARS-CoV-2 variants

Global sequencing and surveillance capacity for SARS-CoV-2 must be strengthened and combined with multidisciplinary studies of infectivity, virulence and immune escape, in order to track the unpredictable evolution of the ongoing COVID-19 pandemic.

In June 2020, the World Health Organization (WHO) SARS-CoV-2 evolution working group was established to track SARS-CoV-2 variants and their specific genetic changes and to monitor viral characteristics and their impact on medical and non-medical countermeasures, including vaccines against COVID-19. In November 2021, this working group transitioned to a formal WHO Technical Advisory Group on Virus Evolution (TAG-VE), with the aim of developing and implementing a global risk-monitoring framework for SARS-CoV-2 variants, based on a multidisciplinary approach that includes in silico, virological, clinical and epidemiological data.

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Resource Centre - Publications

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69–70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69–70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08–0.09) and 0.10 (95% CI: 0.09–0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.

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