Irish Medical Times Medical News for Healthcare Professionals 
Genome sequencing, conducted by the NVRL, has revealed the lineage of SARS-CoV-2 predominating across Ireland
Latest named strains of severe acute respiratory syndrome coronavirus (SARS-CoV-2), associated with Covid-19 disease circulating in Ireland, have been identified by the National Virus Reference Laboratory (NVRL), reports Valerie Ryan.
All SARS-CoV-2 strains are named alphabetically as “lineages”, starting with a letter followed by a number, under a naming system proposed by Rambaut and colleagues. At the same time, there is some overlap with the labelling system under GISAID (originally known as Global Initiative on Sharing All Influenza Data).
Genome sequencing, conducted by the NVRL, has revealed the lineage of SARS-CoV-2 predominating across Dublin, Wicklow, Kilkenny, Leitrim, Sligo, Limerick, Waterford, and Kerry as B.1.113, with three separable clusters in circulation during July.
According to the NVRL, in addition, Limerick and Cork have two distinct clusters of B.1 detected by genome sequencing.
The NVRL added that some distinct lineages had been detected in Ireland including B.1.113, B.1.1, B.1 and B.2.1.
The first SARS-CoV-2 genome sequence was released on January 10, and data on genome sequencing around the world are being shared rapidly by laboratories, in huge volumes, across GISAID, which has become an online repository for coronavirus data ever since.
Aside from the more detailed “lineages”, the GISAID initiative has identified seven SARS-CoV-2 subtypes or clades, mapping the evolution of the virus as it spreads across the world.
As in other countries, the variant G614 “spike mutation” form appears to have supplanted the original D614 as the dominant form of the virus in Ireland.
The spike protein is key for the highly transmissible SARS-CoV-2 virus to gain entry to a host cell and has become a target for vaccine development or blocking therapy.
The effect of the mutation of the virus genome as it moved to the G614 variant is a focus for scientific efforts and remains unanswered yet.
“The shift from D614 to G614 in the spike protein, is consistent with an increased replicative fitness advantage,” said the NVRL.
“The majority of genomes in circulation in July were clade G, and harboured the spike mutation D614G.”
Responding to a query from Irish Medical Times, as to whether the mutation was responsible for a heightened level of infectivity, the NVRL stated: “Data available in Ireland are insufficient to address this question.”
The NVRL added that a study in the UK, found hospitalised patients with G614 had higher viral titres in upper respiratory tract specimens but no difference in disease outcome (Korber et al, 2020).The available evidence suggested that G614 was not as important a predictor of disease severity as are underlying conditions, including immune compromise, advanced age or metabolic syndrome, according to the NVRL.
An analysis of genome variants worldwide found that several variants of the SARS-CoV-2 genome existed and that the D614G clade had become the most common variant since December 2019.
The analysis by Takahiko Koyama, Daniel Platt and Laxmi Parida was published in the July bulletin of the World Health Organization.
