Genomic Surveillance Picks Up Hidden SARS-CoV-2 Delta Variant Spread in New Zealand

In a paper in Nature Communications, investigators at the University of Otago and other centers in New Zealand and the US outline SARS-CoV-2 Delta variant patterns detected in New Zealand through genomic surveillance between mid-August of 2021 and early December of that year. With genome sequence data for more than 3,800 SARS-CoV-2 isolates, the team saw previously unappreciated Delta variant spread within the country, along with genomic shifts in the virus, including an uptick in isolates containing a predicted truncation to the ORF7a accessory protein. "This genomic surveillance identified numerous examples of cryptic virus transmission by the apparent extinction and reappearance of genomically linked clusters," the authors report, adding that "we identified the emergence and dominance of a lineage possessing a 10-nucleotide frameshift deletion, likely rendering an accessory protein, encoded by the ORF7a gene, functionally impaired, within this outbreak."