Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal

Funding This study is co-funded by Fundação para a Ciência e a Tecnologia and Agência de Investigação Clínica e Inovação Biomédica [grant number 234_596874175] on behalf of the Research 4 COVID-19 call. This work is also a result of the GenomePT project [grant number POCI-01-0145- FEDER-022184], supported by COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. Based on our high sequencing sampling during the early epidemics [15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases until the end of March and April, respectively], we estimate that, between 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%–18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8–29.7%, CI 95%; 3177–4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.publishersversionpublishe

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

© The Author(s) 2022.BACKGROUND: Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. METHODS: By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal. RESULTS: We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. CONCLUSIONS: Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.publishersversionpublishe

Longitudinal Monitoring of SARS-CoV-2 IgM and IgG Seropositivity to Detect COVID-19.

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a novel beta-coronavirus that has recently emerged as the cause of the 2019 coronavirus pandemic (COVID-19). Polymerase chain reaction (PCR) based tests are optimal and recommended for the diagnosis of an acute SARS-CoV-2 infection. Serology tests for viral antibodies provide an important tool to diagnose previous exposure to the virus. Here we evaluate the analytical performance parameters of the Diazyme SARS-CoV-2 IgM/IgG serology assays and describe the kinetics of IgM and IgG seroconversion observed in patients with PCR-confirmed COVID-19 who were admitted to our hospital.MethodsWe validated the performance of the Diazyme assay in 235 presumed SARS-CoV-2 negative subjects to determine specificity. Subsequently, we evaluated the SARS-CoV-2 IgM and IgG seroconversion of 54 PCR-confirmed COVID-19 patients and determined sensitivity of the assay at three different timeframes.ResultSensitivity and specificity for detecting seropositivity at ≥15 days following a positive SARS-CoV-2 PCR result, was 100.0% and 98.7% when assaying for the panel of IgM and IgG. The median time to seropositivity observed for a reactive IgM and IgG result from the date of a positive PCR was 5 days (IQR: 2.75-9 days) and 4 days (IQR: 2.75-6.75 days), respectively.ConclusionsOur data demonstrate that the Diazyme IgM/IgG assays are suited for the purpose of detecting SARS-CoV-2 IgG and IgM in patients with suspected SARS-CoV-2 infections. For the first time, we report longitudinal data showing the evolution of seroconversion for both IgG and IgM in a cohort of acutely ill patients in the United States. We also demonstrate a low false positive rate in patients who were presumed to be disease free

Pathophysiology, histopathology and therapeutic of SARS-CoV-2

The rapid transmission of SARS-CoV-2 through the world has induced the scientist to understand the histopathology of the virus and then to find an effective drug. However, many of the point associated with the virus pathogenicity still unknown and need more studies. In this chapter the pathophysiology, histopathology and therapeutic of SARS-CoV-2 has been reviewed. It was appeared that pathogenicity of SARS-CoV-2 is belonging to the viral with genome structure which acting by blocking the host innate immune response. Both chloroquine and hydroxyl-chloroquine have similar structure and mechanism action and they are among the most effective antiviral for treating the patents with the SARS-CoV-2. Chloroquine works by inhibition the intracellular organism by increasing the pH

Multicentre Performance Evaluation of the Elecsys Anti-SARS-CoV-2 Immunoassay as an Aid in Determining Previous Exposure to SARS-CoV-2

Introduction We performed a multicentre evaluation of the Elecsys® Anti-SARS-CoV-2 immunoassay (Roche Diagnostics), an assay utilising a recombinant protein representing the nucleocapsid (N) antigen, for the in vitro qualitative detection of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods Specificity was evaluated using serum/plasma samples from blood donors and routine diagnostic specimens collected before September 2019 (i.e., presumed negative for SARS-CoV-2-specific antibodies); sensitivity was evaluated using samples from patients with polymerase chain reaction (PCR)-confirmed SARS-CoV-2 infection. Point estimates and 95% confidence intervals (CIs) were calculated. Method comparison was performed versus commercially available assays. Results Overall specificity for the Elecsys Anti-SARS-CoV-2 immunoassay (n = 9575) was 99.85% (95% CI 99.75–99.92): blood donors (n = 6714; 99.82%), routine diagnostic specimens (n = 2861; 99.93%), pregnant women (n = 2256; 99.91%), paediatric samples (n = 205; 100.00%). The Elecsys Anti-SARS-CoV-2 immunoassay demonstrated significantly higher specificity versus LIAISON SARS-CoV-2 S1/S2 IgG (99.71% vs. 98.48%), EUROIMMUN Anti-SARS-CoV-2 IgG (100.00% vs. 94.87%), ADVIA Centaur SARS-CoV-2 Total (100.00% vs. 87.32%) and iFlash SARS-CoV-2 IgM (100.00% vs. 99.58%) assays, and comparable specificity to ARCHITECT SARS-CoV-2 IgG (99.75% vs. 99.65%) and iFlash SARS-CoV-2 IgG (100.00% vs. 100.00%) assays. Overall sensitivity for Elecsys Anti-SARS-CoV-2 immunoassay samples drawn at least 14 days post-PCR confirmation (n = 219) was 93.61% (95% CI 89.51–96.46). No statistically significant differences in sensitivity were observed between the Elecsys Anti-SARS-CoV-2 immunoassay versus EUROIMMUN Anti-SARS-CoV-2 IgG (90.32% vs. 95.16%) and ARCHITECT SARS-CoV-2 IgG (84.81% vs. 87.34%) assays. The Elecsys Anti-SARS-CoV-2 immunoassay showed significantly lower sensitivity versus ADVIA Centaur SARS-CoV-2 Total (85.19% vs. 95.06%) and iFlash SARS-CoV-2 IgG (86.25% vs. 93.75%) assays, but significantly higher sensitivity versus the iFlash SARS-CoV-2 IgM assay (86.25% vs. 33.75%). Conclusion The Elecsys Anti-SARS-CoV-2 immunoassay demonstrated very high specificity and high sensitivity in samples collected at least 14 days post-PCR confirmation of SARS-CoV-2 infection, supporting its use to aid in determination of previous exposure to SARS-CoV-2

SARS-CoV-2 aberrantly elevates mitochondrial bioenergetics to induce robust virus propagation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 'highly transmissible respiratory pathogen, leading to severe multi-organ damage. However, knowledge regarding SARS-CoV-2-induced cellular alterations is limited. In this study, we report that SARS-CoV-2 aberrantly elevates mitochondrial bioenergetics and activates the EGFR-mediated cell survival signal cascade during the early stage of viral infection. SARS-CoV-2 causes an increase in mitochondrial transmembrane potential via the SARS-CoV-2 RNA-nucleocapsid cluster, thereby abnormally promoting mitochondrial elongation and the OXPHOS process, followed by enhancing ATP production. Furthermore, SARS-CoV-2 activates the EGFR signal cascade and subsequently induces mitochondrial EGFR trafficking, contributing to abnormal OXPHOS process and viral propagation. Approved EGFR inhibitors remarkably reduce SARS-CoV-2 propagation, among which vandetanib exhibits the highest antiviral efficacy. Treatment of SARS-CoV-2-infected cells with vandetanib decreases SARS-CoV-2-induced EGFR trafficking to the mitochondria and restores SARS-CoV-2-induced aberrant elevation in OXPHOS process and ATP generation, thereby resulting in the reduction of SARS-CoV-2 propagation. Furthermore, oral administration of vandetanib to SARS-CoV-2-infected hACE2 transgenic mice reduces SARS-CoV-2 propagation in lung tissue and mitigates SARS-CoV-2-induced lung inflammation. Vandetanib also exhibits potent antiviral activity against various SARS-CoV-2 variants of concern, including alpha, beta, delta and omicron, in in vitro cell culture experiments. Taken together, our findings provide novel insight into SARS-CoV-2-induced alterations in mitochondrial dynamics and EGFR trafficking during the early stage of viral infection and their roles in robust SARS-CoV-2 propagation, suggesting that EGFR is an attractive host target for combating COVID-19

Effect of SARS-CoV-2 infection in pregnancy on CD147, ACE2 and HLA-G expression

Introduction: Recent studies reported a differential expression of both ACE2 and CD147 in pregnant women associated to SARS-CoV-2 placental infection. The aim of this study is to further investigate the placental SARS-CoV-2 infection and the potential effect on protein expression (ACE2, CD147, HLA-G and CD56). Methods: The study was on three subgroups: i) 18 subjects positive for SARS-CoV-2 swab at delivery; ii) 9 subjects that had a positive SARS-CoV-2 swab during pregnancy but resulted negative at delivery; iii) 11 control subjects with physiological pregnancy and with no previous or concomitant SARS-CoV-2 swab positivity. None of the subjects were vaccinated for SARS-CoV-2 infection. The placenta samples were analyzed for SARS-CoV-2 NP (Nucleocapsid protein) positivity and the expression of ACE2, CD147, HLA-G and CD56. Results: We observed a higher percentage of SARS-CoV-2 NP positive placenta samples in the group of SARS-CoV-2 PCR positive at delivery in comparison with SARS-CoV-2 PCR negative at delivery. The localization of SARS-CoV-2 NP positivity in placenta samples was mainly in syncytiotrophoblast (ST) of SARS-CoV-2 PCR positive at delivery group and in extra-villous trophoblast (EVT) of SARS-CoV-2 PCR negative at delivery group. CD147, HLA-G positivity was higher in ST of SARS-CoV-2 PCR positive at delivery group, while CD56-expressing immune cells were decreased in comparison with control subjects. Discussion: We confirmed the ability of SARS-CoV-2 to infect placenta tissues. The simultaneous SARS-CoV-2 swab positivity at delivery and the positivity of the placenta tissue for SARS-CoV-2 NP seems to create an environment that modifies the expression of specific molecules, as CD147 and HLA-G. These data suggest a possible impact of SARS-CoV-2 infection during pregnancy, that might be worthy to be monitored also in vaccinated subjects

Gastrointestinal SARS CoV-2 Infection and The Dynamic of Its Detection in Stool

Introduction: SARS-CoV-2 has been strongly associated with respiratory illnesses however the SARS-CoV-2 infection of the gastrointestinal tract is not fully clear. We examined the frequency of positive stool SARS-CoV-2 RT-PCR in COVID-19 patients, duration of the stool viral shedding after the viral clearance of the respiratory samples and its association with gastrointestinal symptoms Methods: We did a search in PubMed and Google Scholar of studies published in the English language before June 30th, 2020. Search queries included: “COVID-19”, “SARS-CoV-2”, and “stool SARS-CoV-2 RT-PCR”. We excluded studies with less than 8 patients from our review. Results: Among the 707 patients who had respiratory samples positive for SARS-CoV-2, 361 (51%) patients tested positive through stool SARS CoV-2 RT-PCR. From the 198 patients who tested positive for SARS-CoV-2 in stool, 101 (51%) patients continued testing positive after respiratory samples were negative through SARS-CoV-2 RT-PCR. The longest duration of positive SARS-CoV-2 in stool was 48 days and 33 days after the negative upper respiratory samples. Out of 200 patients who had positive fecal PCR for SARS-CoV-2, 95 patients (47.5%) had at least one gastrointestinal manifestation. Conclusions: About a half of COVID-19 patients had positive stool SARS-CoV-2 RT-PCR and 51% of patients had positive stool SARS CoV-2 RT-PCR after the respiratory samples became negative for SARS-CoV-2 RT-PCR. At least one GI symptom was reported in 47.5% of patients with a positive stool SARS-CoV-2 RT-PCR