Functional and Morphological Disorders of Taste and Olfaction in COVID-19-Patients (preprint)

Objectives: To test the prevalence and evolution of acute olfactory and gustatory functional impairment and of their morphologic correlates in COVID-19 patients who require hospitalization due to COVID-19-related respiratory conditions. Key-words: COVID-19, taste, olfaction, electrogustometry, contact endoscopy Design: Electrogustometric (EGM) - thresholds at the tongue area supplied by the chorda tympani, at the soft palate and at the vallate papillae area were recorded bilaterally. Olfaction was examined by Sniffin’ sticks. The patients’ nasal and oral mucosa (fungiform papillae, fpap) were examined by contact endoscopy. Setting: Tertiary referral medical centre. Patients: 53 consecutive hospitalized patients (23 males, 30 females, age 42,54 ± 10, 95 yrs) with RT-PCR-confirmed COVID-19 diagnosis were included. Patients have been examined twice: just after hospital discharge and 4-6 weeks later. Main outcome measures: EGM-thresholds and taste strips, Schniffin-Sticks, Contact-Endoscopyesults: EGM-thresholds in patients were significantly higher at both instances than those of healthy subjects. EGM-thresholds at the second measurement were significantly lower than those at the first measurement. Accordingly, patient-reported gustatory outcomes were improved at the second measurement. The same pattern has been found using Sniffin’ sticks. Significant alterations in form and vascularization of fPap have been detected in patients, especially at the first instance. Conclusions: COVID-19 affects both gustatory and olfactory functions. It also affects in parallel the structure and vascularization of both nasal and oral mucosa, although the nasal mucosa to a much less, non-significant, extent. Our findings suggest that COVID-19 may cause a mild to profound neuropathy of multiple cranial nerves.

Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains (preprint)

This study aims to highlight SARS-COV-2 mutations which are associated with increased or decreased viral virulence. We utilize, genetic data from all strains available from GISAID and countries regional information such as deaths and cases per million as well as covid-19-related public health austerity measure response times. Initial indications of selective advantage of specific mutations can be obtained from calculating their frequencies across viral strains. By applying modelling approaches, we provide additional information that is not evident from standard statistics or mutation frequencies alone. We therefore, propose a more precise way of selecting informative mutations. We highlight two interesting mutations found in genes N (P13L) and ORF3a (Q57H). The former appears to be significantly associated with decreased deaths and cases per million according to our models, while the latter shows an opposing association with decreased deaths and increased cases per million. Moreover, protein structure prediction tools show that the mutations infer conformational changes to the protein that significantly alter its structure when compared to the reference protein.

Population genomics insights into the recent evolution of SARS-CoV-2 (preprint)

The current coronavirus disease 2019 (COVID-19) pandemic is caused by the SARS-CoV-2 virus and is still spreading rapidly worldwide. Full-genome-sequence computational analysis of the SARS-CoV-2 genome will allow us to understand the recent evolutionary events and adaptability mechanisms more accurately, as there is still neither effective therapeutic nor prophylactic strategy. In this study, we used population genetics analysis to infer the mutation rate and plausible recombination events that may have contributed to the evolution of the SARS-CoV-2 virus. Furthermore, we localized targets of recent and strong positive selection. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from non-human hosts appeared to have taken place in the past. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., Hedgehog and Sparrow. Even though recombination events within human hosts cannot be directly assessed, due to the high similarity of SARS-CoV-2 genomes, we infer that recombinations may have recently occurred within human hosts using a linkage disequilibrium analysis. In addition, we employed an Approximate Bayesian Computation approach to estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian and Northern American cohorts, and we demonstrated that a rapid exponential growth in population size can support the observed polymorphism patterns in SARS-CoV-2 genomes.