ABSTRACT
Throughout the SARS-CoV-2 pandemic, several variants of concern (VOC) have been identified, many of which share recurrent mutations in the spike protein's receptor binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we show that immunosuppressed patients with hematologic cancers develop distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. Furthermore, we provide the first evidence for a viral reservoir based on intra-host phylogenetics. Our results on viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable as well as an alternative explanation for some long-COVID cases. Our findings also highlight that protracted infections should be treated with combination therapies rather than by a single mAbs to clear pre-existing resistant mutations.
Subject(s)
NeoplasmsABSTRACT
Syndromic surveillance for respiratory disease is limited by an inability to monitor its protean manifestation, cough. Advances in artificial intelligence provide the ability to passively monitor cough at individual and community levels. We hypothesized that changes in the aggregate number of coughs recorded among a sample could serve as a lead indicator for population incidence of respiratory diseases, particularly that of COVID-19. We enrolled over 900 people from the city of Pamplona (Spain) between 2020 and 2021 and used artificial intelligence cough detection software to monitor their cough. We collected nine person-years of cough aggregated data. Coughs per hour surged around the time cohort subjects sought medical care. There was a weak temporal correlation between aggregated coughs and the incidence of COVID-19 in the local population. We propose that a clearer correlation with COVID-19 incidence could be achieved with better penetration and compliance with cough monitoring.
Subject(s)
COVID-19 , Respiratory Tract InfectionsABSTRACT
3D printed alternatives to standard flocked swabs were rapidly developed to provide a response to the unprecedented and sudden need for an exponentially growing amounts of diagnostic tools to fight the pandemics of COVID-19. In light of the anticipated shortage, an hospital-based 3D printing platform was implemented in our institution for the production of swabs for nasopharyngeal and oropharyngeal sampling based on the freely available open-sourced design made available to the community by University of South Florida's Health Radiology and Northwell Health System teams as replacement for locally used commercial swabs. Validation of our 3D printed swabs was performed by a head-to-head diagnostic accuracy study of the 3D printed Northwell model with the cobas PCR Media swabs sample kit. We observed an excellent concordance (total agreement 96.8%, Kappa 0.936) in results obtained with the 3D printed and flocked swabs indicating that the in-house 3D printed swab can be used reliably in a context of shortage of flocked swabs. To our knowledge, this is the first study to report on autonomous hospital-based production and clinical validation of 3D printed swabs.
Subject(s)
COVID-19ABSTRACT
SARS-CoV-2 whole genome sequencing is an important molecular biology tool performed to support many aspects of the response to the pandemic. Freezing of primary clinical nasopharyngeal swab samples and shipment to reference laboratories is usually required since RNA sequencing is rarely available in routine clinical microbiology laboratories where initial diagnosis and support to outbreak investigations occur. The cobas PCR Media transport medium developed by Roche facilitates high throughput analyses on cobas multianalyzer PCR platforms. There is no data on the stability of SARS-CoV-2 RNA after freezing and thawing of clinical samples in this transport medium, but potential denaturing of the molecular template could impair test results. Our objective was to compare the quality and results of SARS-CoV-2 genomic sequencing when performed on fresh or frozen samples in cobas PCR Media. Viral whole genome sequencing was performed using Oxford Nanopore Technologies MinION platform. Genomic coverage and sequencing depth did not significantly differ between fresh and frozen samples (n=10). For samples with lower viral inoculum and PCR cycle threshold above 30, sequencing quality scores and detection of single nucleotide polymorphisms did not differ either. Freezing of cobas PCR Media does not negatively affect the quality of SARS-CoV-2 RNA sequencing results and it is therefore a suitable transport medium for outsourcing sequencing analyses to reference laboratories. Those results support secondary use of diagnostic nasopharyngeal swab material for viral sequencing without requirement for additional clinical samples.