An emergence of a novel coronavirus, causative agent of COVID19, named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), occurred due to cross-species transmission. Coronaviruses are a large family of viruses able to infect a great number of hosts. Entrance of SARS-CoV-2 depends on the surface (S) protein interaction with host ACE2 protein and cleavage by TMPRSS2. ACE2 could be a species-specific barrier that interferes with bat-to-human coronavirus cross-species transmission. Molecular analysis supported bats as natural hosts for SARS-CoV and involved them in MERS-CoV origin. The genomic similarity between bat RaTG13 CoV strain and SARS-CoV-2 implicates bats in the origin of the new outbreak. Additionally, there is a hypothesis for the zoonotic transmission based on contact with Malayan pangolins by humans in Huanan seafood market in Wuhan, China. To investigate bats and pangolin as hosts in SARS-CoV-2 cross-species transmission, we perform an evolutionary analysis combining viral and host phylogenies and divergence of ACE2 and TMPRSS2 amino acid sequences between CoV hosts. Phylogeny showed SARS-like-CoV-2 strains that infected pangolin and bats are close to SARS-CoV-2. In contrast to TMPRSS2, pangolin ACE2 amino acid sequence has low evolutionary divergence compared with humans and is more divergent from bats. Comparing SARS-CoV with SARS-CoV-2 origins, pangolin has yet lower ACE2 evolutionary divergence with humans than civet-the main intermediary host of SARS-CoV. Thus, pangolin has become an opportune host to intermediates bat-to-human SARS-CoV-2 jump and entry.

Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two nonparametric tests of strict and relaxed molecular clocks built upon a framework that uses the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of Bayesian trees and well known non-parametric (one-sample and two-sample) KolmogorovSmirnov (KS) goodness-of-fit test. In the strict clock case, the method consists in using the one-sample Kolmogorov-Smirnov (KS) test to directly test if the phylogeny is clock-like, in other words, if it follows a Poisson law. The ECD is computed from the discretized branch lengths and the parameter λ of the expected Poisson distribution is calculated as the average branch length over the ensemble of trees. To compensate for the auto-correlation in the ensemble of trees and pseudo-replication we take advantage of thinning and effective sample size, two features provided by Bayesian inference MCMC samplers. Finally, it is observed that tree topologies with very long or very short branches lead to Poisson mixtures and in this case we propose the use of the two-sample KS test with samples from two continuous branch length distributions, one obtained from an ensemble of clock-constrained trees and the other from an ensemble of unconstrained trees. Moreover, in this second form the test can also be applied to test for relaxed clock models. The use of a statistically equivalent ensemble of phylogenies to obtain the branch lengths ECD, instead of one consensus tree, yields considerable reduction of the effects of small sample size and provides a gain of power.

Chagas disease, a zoonosis caused by the flagellate protozoan Trypanosoma cruzi , is a chronic and systemic parasitic infection that affects ~5–7 million people worldwide, mainly in Latin America. Chagas disease is an emerging public health problem due to the lack of vaccines and effective treatments. According to recent studies, several T. cruzi secreted proteins interact with the human host during cell invasion. Moreover, some comparative studies with T. rangeli , which is non-pathogenic in humans, have been performed to identify proteins directly involved in the pathogenesis of the disease. In this study, we present an integrated analysis of canonical putative secreted proteins (PSPs) from both species. Additionally, we propose an interactome with human host and gene family clusters, and a phylogenetic inference of a selected protein. In total, we identified 322 exclusively PSPs in T. cruzi and 202 in T. rangeli . Among the PSPs identified in T. cruzi , we found several trans-sialidases, mucins, MASPs, proteins with phospholipase 2 domains (PLA2-like), and proteins with Hsp70 domains (Hsp70-like) which have been previously characterized and demonstrated to be related to T. cruzi virulence. PSPs found in T. rangeli were related to protozoan metabolism, specifically carboxylases and phosphatases. Furthermore, we also identified PSPs that may interact with the human immune system, including heat shock and MASP proteins, but in a lower number compared to T. cruzi . Interestingly, we describe a hypothetical hybrid interactome of PSPs which reveals that T. cruzi secreted molecules may be down-regulating IL-17 whilst T. rangeli may enhance the production of IL-15. These results will pave the way for a better understanding of the pathophysiology of Chagas disease and may ultimately lead to the identification of molecular targets, such as key PSPs, that could be used to minimize the health outcomes of Chagas disease by modulating the immune response triggered by T. cruzi infection.

Introduction:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spilled over to humans via wild mammals, entering the host cell using angiotensin-converting enzyme 2 (ACE2) as receptor through Spike (S) protein binding. While SARS-CoV-2 became fully adapted to humans and globally spread, some mammal species were infected back. The present study evaluated the potential risk of mammals becoming hosts for SARS-CoV-2 through bioinformatics prediction based on ACE2 receptors. Methods: We used evolutionary bioinformatic approaches and comparative analysis of ACE2 critical residues that bind SARS-CoV-2 S-protein and predicted potential SARS-CoV-2 hosts among mammals and assessed their risk. Results: ACE2 phylogenetic tree placed primates close to rodents and rabbits. Felines, rodents, and rabbits had higher ACE2 similarities than human ACE2 (hACE2). Farmed animals, such as bovids, swine, and equids, had similar ACE2 compared to hACE2; however, these animals showed low SARS-CoV-2 susceptibility. Some cetaceans also presented high similarities in ACE2 key residues with hACE2. Conclusion: Here, we showed wild and domestic mammals with a low divergence of ACE2 compared to humans, discussing their possible chance of being infected, especially those animals kept as livestock or pets. Regarding the feasible transmission through contaminated water, cetaceans can be at risk of SARS-CoV-2 infection. Extensive surveillance of SARS-CoV-2 should be applied to prevent new coronavirus outbreaks and preserve mammals from infectious threats.

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Chronic myeloid leukemia (CML) is a stem cell disease where t(9;22) translocation is considered the primary molecular event leading to the appearance of the bcr-abl fusion gene and consequent cellular transformation. Bcr-Abl tyrosine-kinase inhibitors have been developed and are fairly successful in the treatment of CML. Despite their outstanding clinical activity in CML, they are not a definitive cure: the efficacy of imatinib mesylate (Gleevec®), for instance, in CML-blastic phase is reduced and reports of resistance and intolerance to it have been published. Since Bcr-abl initiates cellular modifications leading to an extreme resistance to apoptosis, we decided to investigate possible secondary targets for CML therapy. We evaluate the expression of known anti and pro-apoptotic genes in terms of CML progression and response to Gleevec. We studied 10 health controls and 71 CML patients in different phases (20 chronic phase, 20 accelerated phase, 10 blastic phase, 15 cytogenetic remission post-Gleevec® and 6 Gleevec® refractory patients). CML group was constituted by 26 men and 35 women, median age of 51.7 years (range 23–73 years), 5 men and 5 women, median age of 49.3 (range 25–72 years), were healthy controls. Peripheral blood mononuclear cells were isolated and expression of bax, bcl-w, mcl-1, bcl-2, a1 and bcl-xL was analyzed by real-time RT-PCR. Protein expression of Bcl-2 and Bcl-xL were analyzed by western-blot. The results of real-time RT-PCR and western-blot are expressed by relative expression, e.g. ratio of investigated genes or protein to the reference GAPDH gene and protein, respectively. We observed an increase of bcl-w (p<0.001), mcl-1 (p< 0.001), a1 (p<0.01) and bcl-xL (p<0.001) gene expression and a remarkable reduction of bcl-2 (p<0.001) in CML-BP patients (table 1). Patients in remission post-Gleevec® presented an anti-apoptotic gene expression profile similar to controls (p>0.05) and refractory patients profile seem to be analogous to blastic crisis (p>0.05). bax levels did not show significant changes in CML patients in different phases (p>0.05). Bcl-2 and Bcl-xL protein data support real-time RT-PCR findings. Taken together these results suggest that mcl-1, bcl-w, bcl-xL and a1 contribute to disease progression and resistance to treatment in CML patients. Further investigations on the state of the apototic machinery in CML patients should provide new approaches for drug design and consequently new efficient treatment for AP, BC and refractory CML patients. Table 1. Ratio of amplicons of the investigated genes to housekeeping (GAPDH). Gene C CP-CML AP-CML BP-CML CCR-CML R-CML C: control; CP: chronic phase; AP: accelerated phase; BP: blastic crisis; CCR: complete cytogenetic remission; R: refractory patients. Results expressed by mean /SD. mcl-1 3.6/0.9 4.4/1.0 8.5/5.0 12.6/2.7 2.4/0.7 13.7/3.6 a1 329.9/153.3 564.1/349.1 1,7000/564.4 972.4/564.0 434.2/98.1 968.8/2.4 bcl-w 4.2/1.1 12.8/3.2 3.4/0.6 17.2/8.6 3.5/0.8 19.8/3.2 bcl-xL 2.9/1.3 5.4/1.1 10.6/3.5 39.4/6.2 3.0/2.1 42.0/3.5 bcl-2 21.1/5.2 13.8/7.0 6.1/3.1 3.1/1.3 21.7/6.4 3.6/2.2 bax 3.2/1.3 4.2/0.8 3.7/1.3 5.2/2.5 4.5/2.7 4.2/2.7

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Canine distemper virus (CDV) is a pathogen which affects dogs and causes severe disease leading to death. Dogs infected with CDV can be diagnosed by RNA detection by Nested PCR technique. The following study proposed to evaluate CDV RNA in blood, urine and saliva samples. The Nested-PCR technique was able to detect CDV RNA in different types of biologic samples. The higher number of positive results was obtained in urine samples.