Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France
Authors: Anthony Levasseur
Philippe Colson
Philippe Gautret
Nhu Ngoc Nguyen
Jérémy Delerce
Hervé Chaudet
Didier Raoult
Jean Christophe Lagier
Thi Loi Dao
Van Thuan Hoang
Journal: Clinical Microbiology and Infection (2021)
Discipline: IMMUNOLOGY
Keywords: Coronavirus disease 2019; Marseille; Mutation; N501Y; Severe acute respiratory syndrome coronavirus 2
Affiliations: Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet nam., Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France., Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France., Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France. Electronic address: .

Abstract:  Objectives: To compare the clinical and epidemiological aspects associated with different predominant lineages circulating in Marseille from March 2020 to January 2021. Methods: In this single-centre retrospective cohort study, characteristics of patients infected with four different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants were documented from medical files. The outcome was the occurrence of clinical failure, defined as hospitalization (for outpatients), transfer to the intensive care unit (inpatients) and death (all). Results: A total of 254 patients were infected with clade 20A (20AS), 85 with Marseille-1 (M1V), 190 with Marseille-4 (M4V) and 211 with N501Y (N501YV) variants. 20AS presented a bell-shaped epidemiological curve and nearly disappeared around May 2020. M1V reached a very weak peak, then disappeared after six weeks. M4V appeared in July presented an atypical wave form for 7 months. N501YV has only recently appeared. Compared with 20AS, patients infected with M1V were less likely to report dyspnoea (adjusted odds ratio (OR) 0.50, p 0.04), rhinitis (aOR 0.57, p 0.04) and to be hospitalized (aOR 0.22, p 0.002). Patients infected with M4V were more likely to report fever than those with 20AS and M1V (aOR 2.49, p &lt; 0.0001 and aOR 2.30, p 0.007, respectively) and to be hospitalized than those with M1V (aOR 4.81, p 0.003). Patients infected with N501YV reported lower rate of rhinitis (aOR 0.50, p 0.001) and anosmia (aOR 0.57, p 0.02), compared with those infected with 20AS. A lower rate of hospitalization was associated with N501YV infection compared with 20AS and M4V (aOR 0.33, p &lt; 0.0001 and aOR 0.27, p &lt; 0.0001, respectively). Conclusions: The four lineages have presentations that differ from one another, epidemiologically and clinically. This supports SARS-CoV-2 genomic surveillance through next-generation sequencing. 

Retracted: No

PubPeer comments:
  The percentage of Covid-19u2013positive patients in whom severe illness developed was 5.6% (9 of 162 patients) in the placebo group and 12.5% (1 of 8 patients) in the vaccine group u2014 a difference of 6.9 percentage points (95% confidence interval [CI], 6.4 to 7.6) (P 0.001 by the chi-square test of proportions). (Reference cited: Campbell I. Chi-squared and Fisher-Irwin tests of two-by-two tables with small sample recommendations. Stat Med 2007;26:3661-3675.) I m not following how these estimates are even possible with this data. Without correction (not recommended due to an expected event count of ~ 0.47 in the vaccine group), Pearson s Chi-squared test gives a p-value of .415. With Yates correction, the p-value is .964. Fisher s exact test gives a p-value of .391. The Wald confidence interval for the difference in proportions ranges from -16.24% to 30.13%. Considering the extremely small number of subjects in the vaccine group, what statistical test could possibly generate estimates this precise or highly significant? Campbell s paper doesn t help to clarify this -- it includes several tests, none of which replicated their figures. ,