Validation of a MALDI-TOF MS method for SARS-CoV-2 detection on the Bruker Biotyper and nasopharyngeal swabs. A Brazil - UK collaborative study. (preprint)

We had developed a MALDI-TOF mass spectrometry method for detection of SARS-CoV-2 virus in saliva-gargle samples using Shimadzu MALDI-TOF mass spectrometers in the UK. This was validated in the USA to CLIA-LDT standards for asymptomatic infection detection remotely via sharing protocols, shipping key reagents, video conference and data exchange. In Brazil, more so than in the UK and USA, there is a need to develop non-PCR dependent rapid affordable SARS-CoV-2 infection screening tests, which also identify variant SARS-CoV-2 and other virus infections. Travel restrictions necessitated remote collaboration with validation on the available Clinical MALDI-TOF - the Bruker Biotyper (microflex LT/SH) - and on nasopharyngeal swab samples, as salivary gargle samples were not available. The Bruker Biotyper was shown to be almost log10^3 more sensitive at detection of high molecular weight spike proteins. A protocol for saline swab soaks out was developed and duplicate swab samples collected in Brazil were analysed by MALDI-TOF MS. The swab collected sample spectra varied from that of gargle-saliva in three additional mass peaks in the mass region expected for IgG heavy chains and human serum albumin. A subset of clinical samples with additional high mass, probably Spike-related proteins, were also found. Spectral data comparisons and analysis, subjected to machine learning algorithms in order to resolve RT-qPCR positive from RT-qPCR negative swab samples, showed a 78% agreement with RT-qPCR scoring for SARS-CoV-2 infection.

Advanced ventilatory support and mortality in hospitalized patients with COVID-19 caused by Gamma (P.1) variant of concern compared to other lineages: cohort study at a reference center in Brazil (preprint)

Background: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant of concern (VOC) Gamma (P.1) has increased transmissibility and resulted in elevated hospitalization, intensive care unit occupancy and mortality rates in Brazil. It is not known whether this VOC is also associated with more severe clinical course of disease. Methods This was a retrospective cohort study with non-elderly patients hospitalized for COVID-19 from June to December/2020 (first period) and February to May/2021 (second period) at a reference hospital in Brazil. Two cohorts were performed: the main cohort, composed by patients with SARS-CoV-2 lineages confirmed by whole genome sequencing; and the sensitivity cohort, composed by all eligible patients admitted before and after the emergence of Gamma. The primary outcome was the incidence rate of need of advanced ventilatory support. Results In the main cohort a total of 86 (43 Gamma and 43 non-Gamma) patients were included. Baseline characteristics were similar, except that Gamma patients had lower median Charlson’s comorbidity score. The crude and adjusted incidence rates of advanced respiratory support (adjusted Hazard Ratio [aHR], 1.78; 95% Confidence Interval [CI], 1.05–3.03), invasive respiratory support (aHR, 2.64; 95% CI, 1.34–5.19) and 28-day mortality from onset of symptoms (aHR, 4.73; 95% CI, 1.15–19.41) and adjusted 28-day mortality from hospital admission (aHR, 3.72; 95% CI, 1.19–11.65) were significantly higher in patients infected by Gamma. These patients had significantly lower days alive and free of supplemental oxygen support. The sensitivity cohort included 433 patients: 259 from the first and 174 from the second period (before and after the emergence of Gamma, respectively). Baseline characteristics were similar, except for a higher incidence of severe distress respiratory syndrome in patients from second group at admission. Patients from the second period had significantly higher incidence rates of advanced respiratory support (aHR, 2.04; 95% CI, 1.60–2.59), invasive ventilatory support (aHR, 2.72; 95%CI, 2.05–3.62), and 28-day mortality from the onset of symptoms (aHR, 2.62; 95%CI, 1.46–4.72). Conclusions Our study suggests that in non-elderly hospitalized patients, COVID-19 caused by Gamma VOC may present a more severe clinical course, with increased need of advanced respiratory support and higher 28-day mortality.

First identification of SARS-CoV-2 Lambda (C.37) variant in Southern Brazil (preprint)

In June 15, 2021, the lineage Lambda (C.37) of SARS-CoV-2 was considered a variant of interest (VOI) by the World Health Organization. This lineage has high prevalence in some South America countries but it was described only occasionally in Brazil. Here we describe the first report of the SARS-CoV-2 Lambda variant in Southern Brazil. The sequence described in this paper presented all the eight C.37 defining lineage mutations (ORF1a gene: del916;3675-3677; Spike gene: del16;246-252, G75V, T76I, L452Q, F490S, D614G, and T859N) in addition to other 19 mutations. Considering that this VOI has been associated with high rates of transmissibility, the possible spread in the Southern Brazilian community is a matter of concern.

Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalization rates in February 2021, Rio Grande do Sul, Southern Brazil (preprint)

The emergence SARS-CoV-2 P.1 lineage has been coincidental with a rapid growth in hospitalization in the northern region of Brazil. An exponential growth of severe COVID-19 occurred in Rio Grande do Sul state, Southern Brazil in February-2021. Whole-genome sequencing revealed that the previously undetected P.1 lineage accounted for 88.9% of specimens collected from patients at a referral COVID-19 hospital. These findings raise concerns regarding a possible association between lineage P.1 and rapid growth in cases and hospitalizations.