Technological advancements have made sequencing quicker and more affordable, but collaboration, outreach, and trust are needed to achieve representative samples from underserved populations.

The course of the Covid-19 pandemic depends not only on how the SARS-CoV-2 virus changes, but on how communities respond to it. Public health officials can only make decisions to protect their communities if they know how much virus is circulating locally, which viral variants are present, and whether variants are emerging that may be more virulent or transmissible, or less susceptible to vaccines or medications. The only way to do this is through adequate genomic sequencing, which may not be available in communities that need it. Improvements in sequencing technology, training, and lab availability can help overcome barriers to representation and strengthen sequencing capacity and fill in large gaps in genomic data in the US and around the world. Collaboration and trust are crucial for working with communities to track the virus and get ahead of the pandemic.

Sequencing detects variants.

A diagnostic PCR test can tell whether SARS-CoV-2 is present in a sample–but in most cases not which variant. This is because the test detects limited, preselected portions of viral genes. In contrast, whole genome sequencing reveals the entirety of the SARS-CoV-2’s genetic material, also known as its genome. Once a full genome is sequenced, scientists can share data globally and compare it to an array of other genomes collected in global databases such as GISAID. Comparative analysis lets them identify mutations–or changes–from the original (wild type) virus sequenced and shared with the global GISAID community in January 2020. This analysis can spot an accumulation of mutations that could change how a variant virus behaves. Changes like increased transmissibility, an altered clinical course, decreased effectiveness of therapeutic treatments, or vaccine escape may lead to designation as Variants of Interest (VOI) or Variants of Concern (VOC), which are given Greek letter names by the World Health Organization (WHO). While the Delta variant continues to be the dominant lineage worldwide, the WHO designated the Omicron variant as a new VOC on November 26.

Extensive laboratory studies can help determine the role of specific mutations, which can help predict the hallmarks of newly identified variants. The table below lists some important mutations in the viral spike protein that have been shown to affect the characteristics of the five WHO-designated VOCs, including Omicron. Mutations in other proteins may also affect the properties of viral variants.

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