Bayesian phylodynamic inference on the temporal evolution and global transmission of SARS-CoV-2

Abstract

Coronavirus, uses the Angiotensin Converting Enzyme-2 Receptor to enter airway cells. Viral endocytosis is mediated by several factors, including clathrin, the adaptor protein-2 complex (AP2) and the adaptor-associated kinase-1 (AAK1). 2 According to a recent report, 3 COVID-19, the disease caused by SARS-CoV-2, is characterized by three clinical patterns: no symptoms, mild to moderate disease, severe pneumonia requiring admission to Intensive Care Unit (ICU) in up to 31% of the patients. 3 Thus far, there is no specific therapy for COVID-19 infection. No benefit of lopinavir-ritonavir treatment resulted in a recent trial. 4 Hydroxychloroquine, currently used in view of its "in vitro" observed effect of reduction of viral replication, seems unsatisfactory. 5 Elevated proinflammatory cytokine/chemokine responses seem associated with respiratory failure. 3 Recently, tocilizumab, an interleukin-6 inhibitor, was reported as effective in patients with severe COVID-19 pneumonia. 6 Baricitinib, another inhibitor of cytokine-release, seems an interesting anti-inflammatory drug. It is a Janus kinase inhibitor (anti-JAK) licensed for the treatment of rheumatoid arthritis (RA) with good efficacy and safety records. 7 Moreover it seems to have anti-viral effects by its affinity for AP2-associated protein AAK1, reducing SARS-CoV-2 endocytosis. 8 On this basis, we assessed the safety of baricitinib therapy combined with lopinavir-ritonavir in moderate COVID-19 pneumonia patients and we evaluated its clinical impact.All consecutive hospitalized patients (March 16th −30th) with moderate COVID-19 pneumonia, older than 18 years, were treated for 2 weeks with baricitinib tablets 4 mg/day added to ritonavir-lopinavir therapy. The last consecutive patients with moderate COVID-19 pneumonia receiving standard of care therapy (lopinavir/ritonavir tablets 250 mg/bid and hydroxychloroquine 400 mg/day/orally for 2 weeks) admitted before the date of the first baricitinib-treated patient served as controls. Antibiotics were scheduled only in the case of suspected bacterial infection.Inclusion criteria were: a. SARS-Co-V2 positivity in the nasal/oral swabs; b. presence of at least 3 of the following symptoms: fever, cough, myalgia, fatigue; c. evidence of radiological pneumonia . After discharge, patients treated with baricitinib were planned to be followed for additional 6 weeks. Exclusion criteria: history of thrombophlebitis (TP), latent tuberculosis infection (QuantiFERON Plus-test positivity, Qiagen, Germany 9 ), pregnancy and lactation.Mild to moderate COVID-19 disease definition: presence of bilateral pneumonia with or without ground glass opacity and in absence of consolidation, not requiring intubation at enrollment; arterial oxygen saturation (SpO2) > 92% at room-air, and ratio arterial oxygen partial pressure/fractional inspired oxygen (PaO2/FiO2) 10 0-30 0 mmHg. Parameters daily accessed were: fever, pulmonary function, Modified Early Warning Score (MEWS), 10 pulse rate, blood pressure. After the initial execution, r...

Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru

“…ML phylodynamic analysis revealed that the time to the most recent common ancestor (tMRCA) of the analyzed full genomic data was 28 November 2019 (20 November 2019 to 14 December 2020, CI 90%) being the inferred ancestral root Asia. These observations are in line with the known epidemiology of the pandemic (5). Furthermore, the analysis of genomic data has shown that Peruvian isolates were widely distributed across the phylogenetic tree suggesting multiple, independent introductions, designed as nodes (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18) with over 70% of statistical support from ML ( Figure 1A and Table 1).…”

“…As consequence, Peru has become one of the countries with the highest mortality rate from the current pandemic, although it is likely because of increase of diagnostic capacity and reported cases compared to other countries. Whole-genome sequencing (WGS) data of SARS-CoV-2 has rapidly become publicly available to have revealed insights about the genome structure as well as the temporal evolution and global transmission of the virus (5). However, the sources of epidemic transmission and genomic diversity of SARS-CoV-2 strains circulating in Peru to have led to the rapid spread of the virus remains poorly investigated.…”

Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America

“…Reads were mapped to the Wuhan-Hu-1 reference genome (NC_045512.2) using BWA ( Li et al, 2020 ) and BBmap ( brian-jgi, 2020 ); then, assembled consensus sequences were submitted to GISAID. Substitution matrices of nucleotides and amino acids of S and N proteins were generated from a multiple sequence alignment with the reference genome against the 43 assembled Colombian SARS-CoV-2 genomes ( Table 1 ) using the Muscle algorithm ( Edgar, 2004 ) in MEGA X ( Kumar et al, 2016 ).…”

Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia

“…In both strategies, SARS-CoV-2 specific oligonucleotides were used for the generation of amplicons by means of a Q5® high fidelity DNA polymerase (New England Biolabs Inc., UK), in order to avoid the introduction of artificial mutations. The genomes were assembled by mapping to the reference genome (NC_045512.2) using the BWA (Li et al, 2020) and BBmap (brian-jgi, 2020) software to generate a consensus genome by the two assembly tools.…”

“…Since then, refinements of these protocols are not known in the context of more than 31,000 sequences reported on May 24, 2020, worldwide, including Latin America, which provide a more complete perspective of the accumulated genetic variability and sequence particularities of viruses circulating in specific regions that could affect the efficiency and sensitivity of the rRT-PCR protocols currently shared by WHO. The mutation rate of SARS-CoV-2 as a virus with an RNA genome is higher than that of viruses with a DNA genome (Tang et al, 2020), with an estimated mean evolutionary rate of 2.24 × 10 −3 substitutions/site/year (Li et al, 2020); therefore, changes in the sequence could occur over time that compromise the operational performance of diagnostic tests (PAHO, 2020). The objective of this study was to describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main in-house methods for SARS-CoV-2 detection.…”