Impact of lockdown on Covid-19 case fatality rate and viral mutations spread in 7 countries in Europe and North America

Abstract

Background: Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the first coronavirus disease 2019 (COVID-19) outbreak in China and has become a public health emergency of international concern. SARS-CoV-2 outbreak has been declared a pandemic by WHO on March 11th, 2020 and the same month several Countries put in place different lockdown restrictions and testing strategies in order to contain the spread of the virus.

Methods: The calculation of the Case Fatality Rate of SARS-CoV-2 in the Countries selected was made by using the data available at https://github.com/owid/covi-19-data/tree/master/public/data . Case fatality rate was calculated as the ratio between the death cases due to COVID-19, over the total number of SARS-CoV-2 reported cases 14 days before. Standard Case Fatality Rate values were normalized by the Country-specific ρ factor, i.e. the number of PCR tests/1 million inhabitants over the number of reported cases/1 million inhabitants. Case-fatality rates between Countries were compared using proportion test. Post-hoc analysis in the case of more than two groups was performed using pairwise comparison of proportions and p value was adjusted using Holm method. We also analyzed 487 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 from January 2020 to April 2020 in Italy, Spain, Germany, France, Sweden, UK and USA. SARS-CoV-2 reference genome was obtained from the GenBank database (NC_045512.2). Genomes alignment was performed using Muscle and Jalview software. We, then, calculated the Case Fatality Rate of SARS-CoV-2 in the Countries selected.

Results: In this study we analyse how different lockdown strategies and PCR testing capability adopted by Italy, France, Germany, Spain, Sweden, UK and USA have influenced the Case Fatality Rate and the viral mutations spread. We calculated case fatality rates by dividing the death number of a specific day by the number of patients with confirmed COVID-19 infection observed 14 days before and normalized by a ρ factor which takes into account the diagnostic PCR testing capability of each Country and the number of positive cases detected. We notice the stabilization of a clear pattern of mutations at sites nt241, nt3037, nt14408 and nt23403. A novel nonsynonymous SARS-CoV-2 mutation in the spike protein (nt24368) has been found in genomes sequenced in Sweden, which enacted a soft lockdown strategy.

Conclusions: Strict lockdown strategies together with a wide diagnostic PCR testing of the population were correlated with a relevant decline of the case fatality rate in different Countries. The emergence of specific patterns of mutations concomitant with the decline in case fatality rate needs further confirmation and their biological significance remains unclear.

Keywords: COVID-19; Case fatality rate; Europe; Lockdown strategy; Mutation; SARS-CoV-2; Testing capacity; US.

Fig. 1

a Calculated case fatality rate curves for USA, Italy, Sweden, Germany, Spain, France and UK as explained by Baud and colleagues [11]. Bars indicate the 95% of confidence interval. b Case fatality rate of a normalized by the ρ factor, i.e. by the number of PCR tests performed per 1 M population over positive cases per 1 M population up to the 30th of April, 2020. Bars indicate the 95% of confidence interval. The normalization leads to the formation of three main groups: group 1 includes Germany, group 2 includes Italy, USA and Spain and group 3 includes UK, France and Sweden

Fig. 2

Bubble plot representation of the 30th of April Case Fatality Rate (a) and of the 30th of April Normalized Case Fatality Rate of USA (in light blue), Italy (in red), of UK (black line), France (in magenta), Spain (in green), Sweden (in yellow) and Germany (in cyan). In a, the CFRs are distributed within a large range of values, whereas in b the normalized CFRs values are clustered in three well-distinct groups: Germany forms the first group, Italy, Spain and USA the second group and, finally, Sweden, UK and France the third group with the higher normalized CFR value

Fig. 3

SARS-CoV-2 recurrent mutations occurrence over time, divided per geographic area. The graph reports evolution of nonsynonymous (top) and silent (bottom) mutation patterns from January 2020 to April 2020 in Italy, Spain, France, Germany, UK, Sweden and in the USA. The frequency of each mutation in each country and for each month was normalized to 100%, i.e. to the total number of genomes analyzed in that frameshift and collected in that specific country. Recurrent nonsynonymous mutation pattern is characterized by the occurrence of mutations at nt14408, nt 23403 and nt28881–28882–28883 (RdRp and spike protein, respectively), while the most found silent mutations are at nt241 and nt3037 (localized in the leader protein and in the nsp3)