Intra- vs. inter-host evolution of SARS-CoV-2 driven by uncorrelated selection - The evolution thwarted (preprint)

In viral evolution, a new mutation has to proliferate within the host (Stage I) in order to be transmitted and then compete in the host population (Stage II). We now analyze the intra-host single nucleotide variants (iSNVs) in a set of 79 SARS-CoV-2 infected patients with most transmissions tracked. Here, every mutation has two measures: i) iSNV frequency within each individual host in Stage I; ii) occurrence among individuals ranging from 1 (private), 2-78 (public) to 79 (global) occurrences in Stage II. In Stage I, a small fraction of non-synonymous iSNVs are sufficiently advantageous to rise to a high frequency, often 100%. However, such iSNVs usually fail to become public mutations. Thus, the selective forces in the two stages of evolution are uncorrelated and, possibly, antagonistic. For that reason, successful mutants, including many VOCs (variants of concern), have to avoid being eliminated in Stage I when they first emerge. As a result, they may not have the transmission advantage to outcompete the dominant strains and, hence, are rare in the host population. Few of them could manage to slowly accumulate advantageous mutations to compete in Stage II. When they do, they would appear suddenly as in each of the 6 successive waves of SARS-CoV-2 strains. In conclusion, Stage I evolution, the gate-keeper, may contravene the long-term viral evolution and should be heeded in viral studies.

SARS-CoV-2 breakthrough infections induce somatically hypermutated broadly neutralizing antibodies against heterologous variants (preprint)

Currently circulating SARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading acute-infection-induced germline antibodies isolated earlier in the pandemic. We identified that memory B cells from Delta variant breakthrough-infection patients expressed antibodies with more extensive somatic hypermutations (SHMs) allowing isolation of a number of broadly neutralizing antibodies with activities against heterologous variants of concerns (VOCs) including Omicron variant. Structural studies identified that SHM introduced altered amino acids and highly unusual HCDR2 insertions respectively in two representative broadly neutralizing antibodies - YB9-258 and YB13-292. Previously, insertion/deletion were rarely reported for antiviral antibodies except for those induced by HIV-1 chronic infections. Identified SHMs involved heavily in epitope recognition, they broadened neutralization breadth by rendering antibodies resistant to VOC mutations highly detrimental to previously isolated antibodies targeting similar epitopes. These data provide molecular mechanisms for enhanced immunity to heterologous SARS-CoV-2 variants after repeated antigen exposures with implications for future vaccination strategy.

Development and validation of an early warning score (EWAS) for predicting clinical deterioration in patients with coronavirus disease 2019 (preprint)

Background: Since the pandemic outbreak of coronavirus disease 2019 (COVID-19), the health system capacity in highly endemic areas has been overwhelmed. Approaches to efficient management are urgently needed. We aimed to develop and validate a score for early prediction of clinical deterioration of COVID-19 patients. Methods: In this retrospective multicenter cohort study, we included 1138 mild to moderate COVID-19 patients admitted to 33 hospitals in Guangdong Province from December 27, 2019 to March 4, 2020 (N =818; training cohort), as well as two hospitals in Hubei Province from January 21 to February 22, 2020 (N =320; validation cohort) in the analysis. Results: The 14-day cumulative incidences of clinical deterioration were 7.9% and 12.1% in the training and validation cohorts, respectively. An Early WArning Score (EWAS) (ranging from 0 to 4.5), comprising of age, underlying chronic disease, neutrophil to lymphocyte ratio, C-reactive protein, and D-dimer levels, was developed (AUROC: 0.857). By applying the EWAS, patients were categorized into low-, medium-, and high risk groups (cut-off values: two and three). The 14-day cumulative incidence of clinical deterioration in the low-risk group was 1.8%, which was significantly lower than the incidence rates in the medium- (14.4%) and high-risk (40.9%) groups (P

Failed detection of the full-length genome of SARS-CoV-2 by ultra-deep sequencing from the recovered and discharged patients retested viral PCR positive (preprint)

Over 10 percent of recovered and discharged patients retested positive for SARS-CoV-2, raising a public health concern whether they could be potential origins of infection. In this study, we found that detectable viral genome in discharged patients might only mean the presence of viral fragments, and could hardly form an infection origin for its extremely low concentration.

Prognostic factors for COVID-19 pneumonia progression to severe symptom based on the earlier clinical features: a retrospective analysis (preprint)

Background Approximately 15-20% of COVID-19 patients will develop severe pneumonia, about 10 % of which will die if not properly managed. Methods 125 COVID-19 patients enrolled in this study were classified into mild (93 cases) and severe (32 cases) groups, basing on their 3 to 7-days clinical outcomes. Patients' gender, age, comorbid with underlying diseases, epidemiological history, clinical manifestations, and laboratory tests on admission were collected and subsequently analyzed with single-factor and multivariate logistic regression methods. Finally, we evaluate their prognostic values with the receiver operating characteristic curve (ROC) analysis. Results Seventeen factors on admission differed significantly between mild and severe groups. Next, only four factors, including the comorbid with underlying diseases, increased respiratory rate (>24/min), elevated C-reactive protein (CRP >10mg/liter), and lactate dehydrogenase (LDH >250U/liter), were found to be independently associated with the later disease development. Prognostic value analysis by ROC indicated that individual factors could not confidently predict the occurrence of severe pneumonia, but that the combination of fast respiratory rate and elevated LDH significantly increase the predictive confidence (AUC= 0.944, sensitivity= 0.941, and specificity= 0.902). Three- or four-factors combinations, including elevated LDH and fast respiratory rate, further increased the prognostic value. Additionally, measurable serum viral RNA post-admission could independently predict the severe illness occurrence. Conclusions General clinical characteristics and laboratory tests, such as combinations consisting of elevated LDH and fast respiratory rate, and detectable viral RNA in serum post-admission could provide high confident prognostic value for identifying potential severe COVID-19 pneumonia patients.