Many Countries Not Sharing SARS-CoV-2  Variants of Concern Sequence Data

A new study finds many countries aren’t publicly sharing most of their SARS-CoV-2 genome sequences from variants of concern (VOCs). A team of researchers determined that about 37% of countries with explicit reporting shared less than half of their VOC sequences in public repositories.

This trend is a serious impediment to global health efforts against the disease. As the authors write, “Genomic surveillance has been vital to the early detection of mutations, monitoring of virus evolution and evaluating the degree of similarities between circulating variants with vaccine strains, especially since SARS-CoV-2 vaccines became available.”

The study was published in Nature Genetics this week. The senior author is Hongjie Yu, of Fudan University, Shanghai, China.

Late last year, the U.S. and other countries praised South Africa for quickly detecting and sharing information about the omicron variant, which quickly became prevalent around the world. But keeping up with variants has become harder as they multiply.

For this study, researchers collected genomic data uploaded to public repositories including the Global Initiative on Sharing All Influenza Data (GISAID) between the beginning of the pandemic and 31 October 2021. That totaled approximately 4.8 million genomes from 169 countries.

They found SARS-CoV-2 genomic surveillance and sequencing availability varied markedly across countries, with 45 countries performing a high level of routine genomic surveillance and 96 countries with a high availability of SARS-CoV-2 sequencing. The team writes that they also saw “A marked heterogeneity of sequencing percentage, sequencing technologies, turnaround time and completeness of released metadata across regions and income groups.”

The researchers classified genomic surveillance strategies for 118 countries based on predefined criteria, including 78.7% (37/47) of WHO-defined African Region countries, 60.4% (32/53) of European Region countries, 54.3% (19/35) of countries in the Region of the Americas, 57.1% (12/21) of countries in the Eastern Mediterranean Region, 44.4% (12/27) of countries in the Western Pacific Region, and 54.5% (6/11) of countries in the South-East Asia Region.

They  found that most sequence data was produced on Illumina and Nanopore platforms. Most sequences were generated using second-generation sequencing technology, with 17.4% from third-generation sequencing and 0.3% from first-generation sequencing.

Following the first wave of coronavirus 2019 (COVID-19), SARS-CoV-2 variants have emerged and led to new surges of the disease across the globe. Some SARS-CoV-2 variants disappeared immediately, whereas others characterized by several key mutations adapted well, enabling their rapid spread.

As of January 2022, the World Health Organization (WHO) designated five VOCs associated with levels of increased transmissibility and immune resistance. These variants are: Alpha, Beta, Gamma, Delta, and Omicron. They were first detected in the United Kingdom, South Africa, Brazil, India and multiple countries, respectively.

As the authors write, “Since the first SARS-CoV-2 sequence was published in January 2020, the unprecedented rate of genome data generation was far greater than any other pathogen.”

Further, several studies have used sequence data to examine the evolution and spread of specific variants as they became dominant in certain countries or regions, supporting global genomic surveillance.

However, the paucity of genomic data from low- and middle-income countries in these studies is an impediment.