Drivers of adaptive evolution during chronic SARS-CoV-2 infections

Abstract

In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations in variants of concern (VOCs), which has led to the hypothesis that VOCs emerged from chronic infections. In this study, we searched for drivers of VOC-like emergence by consolidating sequencing results from a set of 27 chronic infections. Most substitutions in this set reflected lineage-defining VOC mutations; however, a subset of mutations associated with successful global transmission was absent from chronic infections. We further tested the ability to associate antibody evasion mutations with patient-specific and virus-specific features and found that viral rebound is strongly correlated with the emergence of antibody evasion. We found evidence for dynamic polymorphic viral populations in most patients, suggesting that a compromised immune system selects for antibody evasion in particular niches in a patient's body. We suggest that a tradeoff exists between antibody evasion and transmissibility and that extensive monitoring of chronic infections is necessary to further understanding of VOC emergence.

Fig. 1. Substitutions in SARS-CoV-2 observed in chronically infected patients and comparison to sequences of circulating viruses.

a, Comparison of substitutions observed in chronic infections to VOC LDMs and to substitutions dominated by genetic drift during globally dispersed acute infections. Shown are the number of substitutions observed along the SARS-CoV-2 genome, in bins of 500 nucleotides. The upper panel displays substitutions observed at any timepoint of the 27 chronic infections. The middle panel displays LDMs of the five currently recognized VOCs. The lower panel displays substitutions observed globally during the first 9 months of the pandemic, mostly before the emergence of VOCs. Asterisks mark bins enriched for more substitutions using a one-tailed binominal test, after correction for multiple testing (P < 0.05; Methods and Supplementary Table 8). The genomic positions are based on the Wuhan-Hu-1 reference genome (GenBank ID NC_045512), and the banner on the top shows a breakdown of ORF1a/b into individual proteins and domains of the S protein (see main text). b, A network of co-occurring substitutions across patients with chronic SARS-CoV-2 infection. Each colored circle represents a locus, and a black asterisk and dot represent a significant enrichment under a one-tailed Fisher’s exact test with P < 0.05 and P < 0.1, respectively, after correction for multiple testing. Blue asterisks represent enrichment of co-occurring substitutions in globally observed sequences using a one-tailed X² test, with P < 0.05 and P < 0.1, respectively, after correction for multiple testing (Methods).

Fig. 2. Viral rebound is associated with antibody evasion.

a, Results of a random forest classifier used to explain an outcome of antibody evasion. The effect of each feature on model outcome is shown: mean SHAP absolute values (left) and individual SHAP values for each feature, ordered based on contribution (right). The color range corresponds to the values of each feature, from red (high value) to blue (low value). b, Illustration of individuals who experienced viral rebound and mutations associated with antibody evasion. Ct values are used here as an inversed proxy for VL and are presented according to the day of infection (denoted as number of days after the first positive PCR test), with the dashed red horizontal line and shaded area representing a negative or borderline result, respectively. Blue dots represent samples that were sequenced. Only amino acid replacements in the S protein are shown, with predicted antibody evasion mutations shown in bold (Supplementary Table 1). Positive samples from BAL, ETA or sputum are indicated in brown. Antibody-based anti-COVID-19 treatments are represented by dashed vertical lines on the day of administration. ALL, acute lymphoblastic leukemia; APS, antiphospholipid syndrome; CLL, chronic lymphocytic leukemia; ETA, endotracheal aspirates; P, patient.

Fig. 3. Illustration of polymorphic populations observed across patients.

Each series of boxed lines represents a patient, and each line represents a sequenced timepoint with time-since-infection on the right. The different open reading frames are color-coded. For each patient, only mutations relative to the first timepoint sequenced that appeared at a frequency ranging from 20% to 100% are shown. Most samples were nasopharyngeal, except those marked by asterisks, which were obtained from endotracheal aspirates.