Virus evolution affected early COVID-19 spread

Abstract

As the SARS-Cov-2 virus spreads around the world afflicting millions of people, it has undergone divergent genetic mutations. Although most of these mutations are expected to be inconsequential, some mutations in the spike protein structure have been hypothesized to affect the critical stage at which the virus invades human cells, which could affect transmission probability and disease expression. If true, then we expect an increased growth rate of reported COVID-19 cases in regions dominated by viruses with these altered proteins. We modeled early global infection dynamics based on clade assignment along with other demographic and meteorological factors previously found to be important. Clade, but not variant D614G which has been associated with increased viral load, enhanced our ability to describe early COVID-19 growth dynamics. Including clade identity in models significantly improved predictions over earlier work based only on weather and demographic variables. In particular, higher proportions of clade 19A and 19B were negatively correlated with COVID-19 growth rate, whereas higher proportions of 20A and 20C were positively correlated with growth rate. A strong interaction between the prevalence of clade 20C and relative humidity suggests that the impact of clade identity might be more important when coupled with certain weather conditions. In particular, 20C an 20A generate the highest growth rates when coupled with low humidity. Projections based on data through April 2020 suggest that, without intervention, COVID-19 has the potential to grow more quickly in regions dominated by the 20A and 20C clades, including most of South and North America.

Estimating and explaining the spread of COVID-19 at the county level in the USA

“…This naïve analysis picked strain 19B as having a lower transmission rate than other strains ( P = 0.014, Supplementary Methods: Analysis of Nextstrain metadata of SARS-CoV-2 strains). Strain 19B does not have the G614 mutation, although strain 19A (also without the G614 mutation) did not have lower transmission than G614-containing strains, suggesting possible differences among strains separate from or in addition to the G614 mutation 25 .…”

“…3). This uncertainty underscores the need for more information about strain differences affecting SARS-CoV-2 transmission 23,25 .…”

Functional importance of the D614G mutation in the SARS-CoV-2 spike protein

“…Further, quantitative estimates of the basic reproductive number R 0 from infection incidence data suggest that viruses bearing S(G614) are 31% more transmissible than D614, although this analysis did not consider the effect of concomitant changes at other loci in the circulating viral strains [ 41 ]. Various studies have identified co-segregation of changes in other viral genes along with the D614G mutation in spike, such as the P323L mutation in the viral polymerase RdRp which may attenuate replication to compensate for the increased transmissibility of D614G viruses [ 40 , 42 , 43 ].

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Consultant psychiatrists’ experience of the impact of the COVID-19 pandemic on mental health services

“…One recent study in Galway reported no increase in the rate of presentations of self-harm/suicidal ideation but noted an increase in the lethality of presentations between March 1 st and May 31 st 2020 compared to the same time period (McIntyre et al, 2020. There was no evidence of an increase in the actual suicide rate in the Cork area in March-August 2020 (N=15) compared to the same time period in 2019 (N=15), based on real-time surveillance of suicide in Cork (Corcoran, 2020),…”