Parallel Evolution in the Emergence of Highly Pathogenic Avian Influenza A Viruses

Escalera-Zamudio, Marina; Gutierrez, Bernardo; Thézé, Julien; Keown, J.R.; Carrique, L.; Bowden, Thomas A.; Pybus, Oliver G.

doi:10.1101/370015

Cited by 6 publications

(11 citation statements)

References 86 publications

(90 reference statements)

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“…No evidence of episodic or directional positive selection was found for that site, as tested under local and global analyses to estimate dN/dS ratios (14,15). It would be relevant to explore if this change is associated with any biological properties of the virus, as has been shown previously for other virus populations (20). However, further structural biology analysis and experimental data would be needed to determine if this site has any functional impact or to determine its implications, if any, in local transmission dynamics.…”

Section: Resultsmentioning

confidence: 90%

“…To visualize details of the phylogenetic relatedness of the Mexican sequences, we then subsampled the previous large-scale WG alignment in a phylogenetically informed manner on the basis of the position of the Mexican variants within the large-scale trees and by selecting sequences using pairwise genetic distances (20,39). Briefly, all Mexican sequences were retained together with their immediate ancestors and descendants, and 184 sequences were further selected based on the minor pairwise genetic distance in relation to the Mexican genomes by the use of a threshold value of 99.5% (Table S3).…”

Section: Methodsmentioning

confidence: 99%

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

Taboada

Vázquez-Pérez

Muñoz-Medina

et al. 2020

J Virol

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The COVID-19 pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to implement 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, the SARS-CoV-2 lineage A/G, containing mostly sequences from North America, and the lineage B/S containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized fourteen independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represent 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 the H49Y amino acid change in the Spike protein. This mutation is a homoplasy occurring independently through time and space, and may function as a molecular marker to follow on any further spread of these viral variants throughout the country. Our results depict the 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 is crucial to implement effective control strategies as well as the evolution of the pandemics. In this work, we describe that the initial virus strains introduced in Mexico came from Europe and the United States and the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains having the mutation H49Y in the Spike protein, that could be further used as a molecular marker to follow viral spread within the country and the region.

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Section: Resultsmentioning

confidence: 90%

Section: Methodsmentioning

confidence: 99%

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

Taboada

Vázquez-Pérez

Muñoz-Medina

et al. 2020

J Virol

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“…2012 ). Moreover, no other nucleotide or protein motifs elsewhere on the viral genome have yet been associated with the pioneer step of HPAIV emergence ( Escalera-Zamudio et al. 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Phylodynamic study of the conserved RNA structure encompassing the hemagglutinin cleavage site encoding region of H5 and H7 low pathogenic avian influenza viruses

et al. 2021

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Highly Pathogenic Avian Influenza Viruses (HPAIV) evolve from Low Pathogenic Avian Influenza Viruses (LPAIV) of the H5 and H7 subtypes. This evolution is characterized by the acquisition of a multi-basic cleavage site (MBCS) motif in the hemagglutinin (HA) that leads to an extended viral tropism and severe disease in poultry. One key unanswered question is whether the risk of transition to HPAIV is similar for all LPAIV H5 or H7 strains, or whether specific determinants in the HA sequence of some H5 or H7 LPAIV strains correlate with a higher risk of transition to HPAIV. Here we determined if specific features of the conserved RNA stem loop located at the hemagglutinin cleavage site-encoding region could be detected along the LPAIV to HPAIV evolutionary pathway. Analysis of the thermodynamic stability of the predicted RNA structures showed no specific patterns common to HA sequences leading to HPAIV and distinct from those remaining LPAIV. However, RNA structure clustering analysis revealed that most of the American lineage ancestors leading to H7 emergences via recombination shared the same vRNA structure topology at the HA1/HA2 boundary region. Our study thus identified predicted secondary RNA structures present in the HA of H7 viruses, which could promote genetic recombination and acquisition of a MBCS.

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“…To visualize details on the phylogenetic relatedness of the Mexican sequences, we then 175 subsampled the previous large-scale WG alignment in a phylogenetically-informed manner, as based on 176 the position of the Mexican strains within the large-scale trees and by selecting sequences using pairwise 177 genetic distances 25,26 . Briefly, all Mexican sequences were retained together with their immediate 178 ancestors and descendants, and 184 sequences were further selected based on the minor pairwise 179 genetic distance in relation to the Mexican genomes under a threshold of 99.5% (SI Table 3).…”

mentioning

confidence: 99%

“…founder effect), but rather an independent occurrence. It would be important to follow up 292 the genomic surveillance of homoplasic mutations that keep emerging independently through time and 293 space, either to determine if these are sequencing errors 41 , or to know if these are real homoplasies that 294 may be associated with changes in biological properties or the virus, such as increased virulence as has 295 been shown for other viruses 25 . In addition, using H49Y as a molecular marker could be used to follow up 296 any further circulation and spread of these viral variants in Mexico.…”

mentioning

confidence: 99%

Genomic analysis of early SARS-CoV-2 strains introduced in Mexico

Taboada

Vázquez-Pérez

Medina

et al. 2020

Preprint

Self Cite

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The COVID-19 pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to implement 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, the SARS-CoV-2 lineage A/G, containing mostly sequences from North America, and the lineage B/S containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized fourteen independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represent local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described in the country. Within this Mexican cluster, we also identified an H49Y amino acid change in the spike protein. This mutation is a homoplasy occurring independently through time and space, and may function as a molecular marker to follow on any further spread of these viral variants throughout the country. Our results depict the general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.This work is the result of the collaboration of five institutions into one research consortium: three public health institutes and two universities. From the beginning of this work, it was agreed that the experimental leader of each institution would share the first authorship. Those were the criteria followed to assign first co-first authorship in this manuscript. The order of the other authors was randomly assigned.IMPORTANCEUnderstanding the introduction, spread and establishment of SARS-CoV-2 within distinct human populations is crucial to implement effective control strategies as well as the evolution of the pandemics. In this work, we describe that the initial virus strains introduced in Mexico came from Europe and the United States and the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains having the mutation H49Y in the Spike protein, that could be further used as a molecular marker to follow viral spread within the country and the region.

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Parallel Evolution in the Emergence of Highly Pathogenic Avian Influenza A Viruses

Abstract: 145 words)

Cited by 6 publications

References 86 publications

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

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

Phylodynamic study of the conserved RNA structure encompassing the hemagglutinin cleavage site encoding region of H5 and H7 low pathogenic avian influenza viruses

Genomic analysis of early SARS-CoV-2 strains introduced in Mexico

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