Tag: sequencing

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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. 

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WHO webinar on genomic surveillance and SARS-CoV-2 sequencing capacity

In this webinar, WHO and FIND co-host a discussion on sequencing capacity for SARS-CoV-2 and global initiatives to strengthen genomic surveillance.

Co-chaired by Natacha Milhano, WHO Public Health Laboratory Strengthening Unit, and Dr Dhamari Naidoo, WHO South-East Asia, it featured the following speakers and topics:

  • Dr Lisa Carter: Genomic surveillance strategy for pathogens with epidemic or pandemic potential
  • Dr Anita Suresh: Mapping and building genomic surveillance capacity for COVID-19 and beyond
  • Dr Senjuti Saha: Towards building capacity and accelerating genomic surveillance: one step at a time 
  • Dr Sikhulile Moyo: Pathogen genomics of SARS-CoV-2: Lessons from Botswana.

Participants shared learnings from the experiences of Botswana (Moyo) and Bangladesh (Saha) on building next generation sequencing capacity, and the global strategy launched by WHO on 31 March 2022 (Carter).

The presentation on 20 April 2022 was in English, with simultaneous interpretations in Arabic, French, Portuguese, Russian and Spanish.

Watch the webinar on YouTube

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FIND partners with CSIR-IGIB to strengthen SARS-CoV-2 genomic surveillance in India

FIND has partnered with CSIR-IGIB (Institute of Genomics and Integrated Biology) to help India fight COVID-19 by boosting sequencing capacity across the country. 

The partnership aims to decentralize genomic surveillance of SARS-CoV-2 by setting up “MicroLabs”. These will enable sequencing, analysis and interpretation of sequencing data with minimal turnaround time and infrastructure limited settings.

The goal is to optimize and scale the capacity needed to identify SARS-CoV-2 variants of concern (VOC) and variants of interest (VOI).

The partnership will also  identify genomic hotspots and mutations associated with disease severity that are critical for surveillance and public health action.

Read the report here

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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

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Global genomic surveillance strategy for pathogens with pandemic and epidemic potential, 2022–2032

Looking at the decade 2022-2032, WHO presents a global genomic surveillance strategy for pathogens with pandemic and epidemic potential.

The goal is to strengthen and scale surveillance of these pathogens to enable quality, timely and appropriate public health actions across local to global surveillance systems.

WHO’s strategy outlines five objectives with accompanying actions that need implementation plans.

It also highlights considerations to build global genomic surveillance over the next 10 years, as well as monitoring and evaluation mechanisms.

The report includes two annexes:

  • Strategy development and stakeholder engagement
  • Key WHO assets for the strategy.

Read report here

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Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health, 8 January 2021

WHO released its publication, Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health, on 8 January 2021.

As the genomes of SARS-CoV-2 are able to be sequenced almost within real time, this enables increased speed to inform public health responses.

This has led to more laboratories investing in viral genome sequencing. Before starting such a programme, however, the intended goals of sequencing must be understood and a strategy for analysis in place, as well as a plan for how findings will be used.

Decisions about sequencing goals should be made in a multidisciplinary framework that includes representatives of all stakeholders. Funding sources must also be identified, and ethical aspects evaluated.

To maximize public health impact, usable and timely results need to be produced and communicated.

This document, available in English and Portuguese, provides this type of guidance for laboratories on maximizing the impact of SARS-CoV-2 sequencing activities now and in the future.

Read the guide here