Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study

Abstract

Background: Host determinants of severe coronavirus disease 2019 include advanced age, comorbidities and male sex. Virologic factors may also be important in determining clinical outcome and transmission rates, but limited patient-level data is available.

Methods: We conducted an observational cohort study at seven public hospitals in Singapore. Clinical and laboratory data were collected and compared between individuals infected with different SARS-CoV-2 clades. Firth's logistic regression was used to examine the association between SARS-CoV-2 clade and development of hypoxia, and quasi-Poisson regression to compare transmission rates. Plasma samples were tested for immune mediator levels and the kinetics of viral replication in cell culture were compared.

Findings: 319 patients with PCR-confirmed SARS-CoV-2 infection had clinical and virologic data available for analysis. 29 (9%) were infected with clade S, 90 (28%) with clade L/V, 96 (30%) with clade G (containing D614G variant), and 104 (33%) with other clades 'O' were assigned to lineage B.6. After adjusting for age and other covariates, infections with clade S (adjusted odds ratio (aOR) 0·030 (95% confidence intervals (CI): 0·0002-0·29)) or clade O (B·6) (aOR 0·26 (95% CI 0·064-0·93)) were associated with lower odds of developing hypoxia requiring supplemental oxygen compared with clade L/V. Patients infected with clade L/V had more pronounced systemic inflammation with higher concentrations of pro-inflammatory cytokines, chemokines and growth factors. No significant difference in the severity of clade G infections was observed (aOR 0·95 (95% CI: 0·35-2·52). Though viral loads were significantly higher, there was no evidence of increased transmissibility of clade G, and replicative fitness in cell culture was similar for all clades.

Interpretation: Infection with clades L/V was associated with increased severity and more systemic release of pro-inflammatory cytokines. Infection with clade G was not associated with changes in severity, and despite higher viral loads there was no evidence of increased transmissibility.

Keywords: COVID-19; Clade; D614G; SARS-CoV-2; Severity; Transmission.

Fig. 1.

Epidemiological curve of COVID-19 cases, Singapore, January 22 to April 21, 2020 (n = 9956).

Fig. 2.

Plasma immune mediator levels of COVID-19 patients infected with different SARS-CoV-2 clades. Concentrations of 45 immune mediators were quantified using a 45-plex microbead-based immunoassay. (a) Heatmap of immune mediator levels in plasma samples of patients infected with different SARS-CoV-2 clades (clade S, n = 21; clade O (B.6), n = 10; clade G, n = 22; clades L and V, n = 46) during first collection timepoint upon hospital admission (median 5 days from symptom onset). Each colour represents the relative concentration of a particular analyte. Blue and red indicates low and high concentration, respectively. (b) Profiles of significant immune mediators of COVID-19 patients infected with different SARS-CoV-2 clades at the first collection timepoint upon hospital admission are illustrated as scatter plots. Immune mediator levels in plasma fraction samples from first collection timepoint during hospital admission (median 5 days from symptom onset) were compared amongst the patients infected with different SARS-CoV-2 clades. One-way ANOVA followed by post-hoc t-test with Bonferroni correction was performed on the logarithmically transformed concentration (*p < 0•05; **p < 0•01; **p < 0•0001). Immune mediator levels for healthy controls (n = 23) are indicated by the black dotted line. Patient samples with concentration out of measurement range are presented as the value of logarithm transformation of Limit of Quantification (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.).

Fig. 3.

Kinetics of viral replication of 16 SARS-CoV-2 virus isolates up to 96 h post-infection. S 3 isolates; L/V 7; G, 5; O (B.6). TCID: Tissue culture infectious dose.