Analysis of Rocky Mountain spotted fever cases in Northern Mexico reveals genetic variability of Rickettsia rickettsii and the different distribution of genotypes.

Rickettsioses have been reported in parts of Mexico since the last century, with Rocky Mountain spotted fever (RMSF) being one of the most prevalent in northern states. Unfortunately, fatality rates for RMSF in Mexico are higher than in other countries, like the USA. The reason for this difference in fatality rates is currently unknown and could be associated with a genotype of the bacterium, but no comparative molecular typing has been conducted in Mexico to date. The purpose of this study was to analyze 47 RMSF samples with different outcomes from several states in northern Mexico to know the genetic variability of Rickettsia rickettsii, as well as to reconstruct its phylogeny, for which the following intergenic regions were sequenced: RR0155-rpmB, cspA-ksgA, RR1240-tlc5, and Spo0J-abc T1, as well as the following partial genes: ompA, ompB, and gltA. We identified 8 genotypes with different distribution and prevalence among the states analyzed, as well as a different association with case outcome; these genotypes were clustered in 2 clades and 5 lineages were revealed, some of them probably exclusive from Mexico.

Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico.

The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.IMPORTANCE Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the initial virus strains introduced in Mexico came from Europe and the United States and that the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region.

Full genome sequence of the first SARS-CoV-2 detected in Mexico.

SARS-CoV-2 was first detected in the city of Wuhan, Hubei Province, China. In this report, we describe the complete genome sequence of the first imported SARS-CoV-2, detected in a Mexican patient who had traveled to Bergamo, Italy. Phylogenetic analysis showed that this isolate belongs to subclade A2a (lineage G) and is closely related to isolates from Finland, Germany and Brazil, all of which were from patients with a history of travel to Italy. This is the first report of the complete genome sequence of this virus in Mexico.

Mutational landscape and intra-host diversity of human papillomavirus type 16 long control region and E6 variants in cervical samples.

Human papillomavirus genotype 16 (HPV16) is the most frequent high-risk HPV (HR-HPV) identified in cervical precursor lesions and cervical cancer (CC) worldwide. The oncogenic potential of HPV16 is partly dependent on the lineage involved in the infection and the presence of clinically relevant mutations. In this report, we present the distribution of HR-HPV and the mutational profile and intra-host variability of HPV16 lineages, based on analysis of the long control region (LCR) and the E6 gene in samples with normal cytology (n = 39), squamous intraepithelial lesions (n = 25), and CC (n = 39). HR-HPV genotyping was performed using multiplex real-time PCR. HPV16 lineage assignments and mutation frequencies were determined by conventional PCR and Sanger DNA sequencing, and intra-patient viral populations were analyzed using next-generation sequencing (NGS). The most frequent HR-HPV type was HPV16, followed by HPV31 and HPV18. The frequency of HPV16 sublineages was A1/A2 > D2 > D3 and B1. Moreover, the most frequent mutations, both in samples from this study and in the available sequences from Mexican isolates in the GenBank database were LCR-G7518A, which is involved in carcinogenesis, and E6-T350G (producing L83V), associated with persistence of infection. Otherwise, deep sequencing revealed high conservation of viral lineages and mutations, independently of the stages studied. In conclusion, the high frequency and stability of these molecular markers, as well as the circulating viral lineages, could be related to the incidence of CC associated with HPV16. Hence, they deserve a broader analysis to determine the risk of specific populations for progression of the disease.

Draft genome sequence of first Vibrio diabolicus in Mexico strain InDRE-D1-M1, an emergent threat.

INTRODUCTION: The complete genome of the marine environmental bacterium Vibrio diabolicus isolated from raw shrimp in the city of Guadalajara in the state of Jalisco in Mexico is reported here. METHODOLOGY: Vibrio spp. it was isolated and identified using standard microbiological and molecular techniques. Whole genome sequencing was performed using the Miseq system (Illumina, USA). RESULTS: The Multi Locus Sequence Typing profile of the isolated Vibrio bacteria coincided only with 4 specific loci (atpA, gyrB, pyrH and recA) and with a total coverage of the species belonging to Vibrio spp. Analysis of the complete genome of the Vibrio isolate and other closely related species, using the genomic fingerprints of the Virtual Analysis Method for PHylogenomic fingerprint estimation (VAMPHyRe) software, revealed the clustering of this species among the clade Vibrio diabolicus. The antibiogram revealed that this strain of Vibrio diabolicus is resistant to ampicillin, which is consistent with the bioinformatic finding of the ß-lactamase enzyme that hydrolyzes carbenicillin class A. CONCLUSIONS: This study demonstrated that the environmental marine bacterium Vibrio diabolicus contains carrier genes associated with pathogenicity and ecological function, which could represent a threat to public health.