Bats and humans during the SARS-CoV-2 outbreak: The case of bat-coronaviruses from Mexico.

The novel SARS-CoV-2 coronavirus has attracted attention due to the high number of human cases around the world. It has been proposed that this virus originated in bats, possibly transmitted to humans by an intermediate host, making bats a group of great interest during this outbreak. Almost 10% of the world's bat species inhabit Mexico, and 14 previous novel CoVs have been recorded in Mexican bats. However, the phylogenetic relationships between these viruses and the novel coronavirus are unknown. The aim of this communication was therefore to describe the phylogenetic relationships between Mexican bat-CoVs and SARS-CoV-2. We showed that Mexican bat-CoVs sequences are grouped into two genera, Alphacoronavirus and Betacoronavirus, and the new coronavirus is an independent clade within Betacoronavirus. Due to the diversity of CoVs in Mexican bats, the propensity of CoVs to shift hosts, the invasion mechanisms described for this new virus, and previous reports of animals infected by SARS-CoV-2, the risk of possible infection from humans to Mexican bats should not be discarded and warrants further analyses. To avoid future zoonotic infectious diseases and to limit persecution of bats, we urge researchers and the general population to take extreme precautions and avoid manipulation of bats during the current and future similar outbreaks.

Genetic diversity of Borrelia burgdorferi sensu stricto: Novel strains from Mexican wild rodents.

Borrelia burgdorferi s.s. is a Gram-negative spirochaete, the aetiological agent of Lyme disease, the most common vector-borne disease in the Northern hemisphere. Reports on the presence of B. burgdorferi in central Mexico have been strongly criticized, since these were based only on unspecific serological methods. Furthermore, the worldwide genetic diversity of B. burgdorferi s.s. has not been evaluated. For this reason, the aim of the present study was to confirm the presence of B. burgdorferi in the central area of Mexico and to evaluate its relationship with regard to the global genetic diversity of B. burgdorferi s.s. To achieve this, fragments of the flagellin and the outer surface protein A genes were amplified from ear biopsies of the arboreal wild endemic mice Habromys schmidlyi. With these sequences, a concatenated Bayesian analysis was performed to confirm the identity of B. burgdorferi s.s. Afterwards, the global genetic diversity of this bacterial species was evaluated using our sequences and those available in GenBank. A prevalence of 10.4% (5/48) of H. schmidlyi infected with Borrelia sp. was detected, and the phylogenetic analyses confirmed the identity of B. burgdorferi s.s. Using both genes, the genetic diversity was low. However, genetic structuring analyses revealed that populations of western United States and those from Mexico formed slightly different genetic groups, separated from the populations of the rest of the world. Our study not only confirms the presence of this bacterium in central Mexico, but also shows the most southern record of this bacterium so far. It also highlights the importance of H. schmidlyi as a new potential host of this bacterial species. Our study also provides first genetic data on an incipient process of divergence in B. burgdorferi s.s. populations of eastern United States and central Mexico.

Notes on Vampyressa thyone (Chiroptera: Phyllostomidae): distribution, genetics and hypopigmentation / Notas sobre Vampyressa thyone (Chiroptera: Phyllostomidae): distribución, genética e hipopigmentación

Abstract: The frugivorous bats of the genus Vampyressa include five neotropical species, and some of them are considered relatively rare and uncommonly encountered. The northernmost distribution of this genus is in Mexico where only one species, the monotypic Vampyressa thyone, is found. Here, we report the Northwesternmost record for this species, extending its distribution range to the state of Guerrero, Mexico. This record extends the limit of the species distribution by more than 153 km. We also compared this specimens with other V. thyone, and using mitochondrial cytochrome-b sequences we detected three geographic clades within the species. The new Mexican specimen represent the most divergent cytochrome-b sequence within V. thyone. We recommend a taxonomic revision to validate the taxonomic status of the three groups detected within V. thyone, particularly the differentiated Mexican clade. Additionally, we report a case of hypopigmentation in another V. thyone collected in a mature tropical rainforest in Chiapas, Mexico.

Resumen: Los murciélagos frugívoros del género Vampyressa agrupan a cinco especies neotropicales, algunas de ellas consideradas relativamente raras y poco comunes de encontrar. Este género alcanza su distribución más norteña en México en donde solo una especie monotípica, Vampyressa thyone, habita. Reportamos el registro al noroeste más alejado para esta especie, extendiendo su rango de distribución al estado de Guerrero, México. Este registro extiende el límite de distribución de la especie por más de 153 Km. También comparamos este espécimen con otros V. thyone, y utilizando secuencias mitocondriales de citocromo-b detectamos tres clados geográficos dentro de la especie. El nuevo espécimen mexicano representa la secuencia de citocromo-b más divergente dentro de V. thyone. Recomendamos una revisión taxonómica para validar el estatus taxonómico de los tres clados detectados dentro de V. thyone, y en particular para el clado mexicano más diferenciado. Adicionalmente, reportamos un caso de hipopigmentación en otro V. thyone colectado en una selva húmeda tropical en Chiapas, México.

Molecular systematics and phylogeography of the endemic Osgood's deermouse Osgoodomys banderanus (Rodentia: Cricetidae) in the lowlands of western Mexico.

Osgoodomys banderanus is a recognized and endemic rodent species of western Mexico, an area known for its high biodiversity and number of endemisms. Phylogeographical relationships within this taxon were analyzed based on mitochondrial (ND3, tRNA-Arginine, ND4L and partial ND4) and nuclear (GHR) nucleotide sequences. We obtained a total of 112 samples from 22 localities, covering the complete distribution of the species. Phylogenetic analyses using Maximum Likelihood and Bayesian inference confirmed that Osgoodomys is a monophyletic group. In addition, phylogenetic and phylogeographic analyses detected three major clades, which do not coincide with the recognized subspecies of O. banderanus. The genetic lineages detected are the western clade (Nayarit, Jalisco and northern Colima), the central clade (Colima, Michoacán, and northern Guerrero) and the eastern clade (central and southern Guerrero). Genetic distances among clades (5-9%) and nucleotide substitutions (30-88) among haplogroups were high, especially in the southern group. Mountain ranges such as the Transmexican Volcanic Belt and the Sierra Madre del Sur, as well as the Balsas River act as geographical barriers for Osgoodomys. Our results suggest the presence of three independent species, which need to be characterized morphologically to confirm our hypothesis.

Genetic and ecological processes promoting early diversification in the lowland Mesoamerican bat Sturnira parvidens (Chiroptera: Phyllostomidae).

With 22 species, Sturnira is the most speciose genus of frugivorous Neotropical bats. Sturnira parvidens inhabits lowland tropical areas from Mexico to Central America. The elevation of this taxon to species level was recent, and discrepancies with respect to its geographic limits and phylogenetic position continue to exist. In order to identify genetic and ecological processes likely involved in the diversification and current distribution of S. parvidens, we evaluated relationships, researched phylogeographic and demographic history, and tested the divergence/conservatism of the climatic niche of this bat. We used data from mitochondrial loci (cytochrome b and the hypervariable D-loop region I) and the nuclear recombination activating gene 1, in 173 samples of S. parvidens and 77 samples of related species. We performed Bayesian analyses to infer phylogenetic relationships and analyzed phylogeographic structure, genetic diversity, divergence times and historical demography. Sturnira bakeri is the sister group of S. parvidens, and inhabits Western Ecuador. The two species diverged c. 1.84Ma, and their distributions are disjunct and separated by Sturnira luisi. Within S. parvidens there are two haplogroups with nearly allopatric distributions that are limited to the Sierra Madre del Sur, on the Mexican Pacific Slope. The divergence time between haplogroups was c. 0.423Ma and we detected signals of demographic expansion. We also analyzed 526 occurrence data of S. parvidens to test for changes in environmental niche of this species. We detected signals of divergence of climatic niche, mainly in temperature and seasonality variables. Likely, both genetic and ecological processes have shaped the evolutionary history of S. parvidens. Despite many climatic fluctuations during the Pleistocene, only the most intense oscillations had an impact on these bats. In addition, ecological differentiation prevents admixture of genetic lineages that are in contact and lack apparent geographical barriers at the southern Sierra Madre del Sur. We concluded that speciation in Sturnira was promoted by this taxon's ability to colonize new geographical and environmental spaces and form genetically structured groups when populations become isolated.

Isolation and characterization of microsatellite markers for Sturnira parvidens and cross-species amplification in Sturnira species.

BACKGROUND: Sturnira is one of the most species-rich genera in the Neotropics, and it is found from Mexico and the Lesser Antilles to Argentina. This genus forms a well-supported monophyletic clade with at least twenty-one recognized species, as well as several others under taxonomic review. Sturnira parvidens is a widespread frugivorous bat of the deciduous forests of the Neotropics, is highly abundant, and is a major component in fruit dispersal to regenerate ecosystems. METHODS: We used a technique based on Illumina paired-end sequencing of a library highly enriched for microsatellite repeats to develop loci for S. parvidens. We analyzed millions of resulting reads with specialized software to extract those reads that contained di-, tri-, tetra-, penta-, and hexanucleotide microsatellites. RESULTS: We selected and tested 14 polymorphic (di, tri, and tetra) microsatellites. All markers were genotyped on 26 different individuals from distinct locations of the distributional area of S. parvidens. We observed medium-high genetic variation across most loci, but only 12 were functionally polymorphic. Levels of expected heterozygosity across all markers were high to medium (mean HE  = 0.79, mean HO  = 0.72). We examined ascertainment bias in twelve bats of the genus, obtaining null/monomorphic/polymorphic amplifications. DISCUSSION: The Illumina paired-end sequencing system is capable of identifying massive numbers of microsatellite loci, while expending little time, reducing costs, and providing a large amount of data. The described polymorphic loci for S. parvidens in particular, and for the genus in general, could be suitable for further genetic analysis, including taxonomic inconsistencies, parentage/relatedness analysis, and population genetics assessments.