Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence

Shay Leary; Silvana Gaudieri; Abha Chopra; Suman Pakala; Eric Alves; Mina John; Suman Das; Simon Mallal; Phillips Jane Phillips

Evidence of viral adaptation to selective pressures as it spreads among diverse human populations has implications for the ongoing potential for changes in viral fitness over time, which in turn may impact transmissibility, disease pathogenesis and immunogenicity. Geographic differences in viral sequence diversity and epidemiological profiles of disease are likely to reflect the spread of founder viruses, which first entered different SARS-CoV-2 naïve populations. However, the extent to which selection pressures operating within those populations also impact SARS-CoV-2 diversity is currently not known. Functional effects of new genetic changes need to be considered in ongoing public health measures to contain infection around the world and in the development of universal vaccines and antiviral therapy. Here we describe a new emerging strain of SARS-CoV-2 within the LGG clade that appears to be the result of a homologous recombination event that introduced three adjacent nucleotide changes spanning two residues of the nucleocapsid protein. That strain expanded rapidly in Europe in March 2020. This protein forms an integral part of the virus lifecycle and is known to be highly immunogenic.