Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Garces-Ayala F

PROVIDER: S-EPMC7300367 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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

Garcés-Ayala Fabiola F Araiza-Rodríguez Adnan A Mendieta-Condado Edgar E Rodríguez-Maldonado Abril Paulina AP Wong-Arámbula Claudia C Landa-Flores Magaly M Del Mazo-López Juan Carlos JC González-Villa Maribel M Escobar-Escamilla Noé N Fragoso-Fonseca David Esaú DE Esteban-Valencia María Del Carmen MDC Lloret-Sánchez Lourdes L Arellano-Suarez Dayanira Sarith DS Nuñez-García Tatiana Ernestina TE Contreras-González Nervain Benjamin NB Cruz-Ortiz Natividad N Ruiz-López Adriana A Fierro-Valdez Miguel Ángel MÁ Regalado-Santiago Daniel D Martínez-Velázquez Nancy N Mederos-Michel Mireya M Vázquez-Pérez Joel J Martínez-Orozco José Arturo JA Becerril-Vargas Eduardo E Salas Jorge J Hernández-Rivas Lucía L López-Martínez Irma I Alomía-Zegarra José Luis JL López-Gatell Hugo H Barrera-Badillo Gisela G Ramírez-González José Ernesto JE

Archives of virology 20200618 9

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 s ...[more]

PMID: 32556599

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Project description:Background & objectivesSince December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.MethodsThroat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing. Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken.ResultsThree cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2. Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512). Phylogenetic analysis showed that the Indian sequences belonged to different clusters. Predicted linear B-cell epitopes were found to be concentrated in the S1 domain of spike protein, and a conformational epitope was identified in the receptor-binding domain. The predicted T-cell epitopes showed broad human leucocyte antigen allele coverage of A and B supertypes predominant in the Indian population.Interpretation & conclusionsThe two SARS-CoV-2 sequences obtained from India represent two different introductions into the country. The genetic heterogeneity is as noted globally. The identified B- and T-cell epitopes may be considered suitable for future experiments towards the design of vaccines and diagnostics. Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2.

Project description:BackgroundEstimates of SARS-CoV-2 infection fatality rates (IFRs) in developing countries remain poorly characterized. Mexico has one of the highest reported COVID-19 case-fatality rates worldwide, although available estimates do not consider serologic assessment of prior exposure nor all SARS-CoV-2-related deaths. We aimed to estimate sex- and age-specific IFRs for SARS-CoV-2 in Mexico.MethodsThe total number of people in Mexico with evidence of prior SARS-CoV-2 infection was derived from National Survey of Health and Nutrition-COVID-19 (ENSANUT 2020 Covid-19)-a nationally representative serosurvey conducted from August to November 2020. COVID-19 mortality data matched to ENSANUT's dates were retrieved from the death-certificate registry, which captures the majority of COVID-19 deaths in Mexico, and from the national surveillance system, which covers the subset of COVID-19 deaths that were identified by the health system and were confirmed through a positive polymerase chain reaction test. We analysed differences in IFRs by urbanization and region.ResultsThe national SARS-CoV-2 IFR was 0.47% (95% CI 0.44, 0.50) using death certificates and 0.30% (95% CI 0.28, 0.33) using surveillance-based deaths. The IFR increased with age, being close to zero at age <30 years, but increasing to 1% at ages 50-59 years in men and 60-69 years in women, and being the highest at ≥80 years for men (5.88%) and women (6.23%). Across Mexico's nine regions, Mexico City (0.99%) had the highest and the Peninsula (0.26%) the lowest certificate-based IFRs. Metropolitan areas had higher certificate-based IFR (0.63%) than rural areas (0.17%).ConclusionAfter the first wave of the COVID-19 pandemic, the overall IFR in Mexico was comparable with those of European countries. The IFR in Mexico increased with age and was higher in men than in women. The variations in IFRs across regions and places of residence within the country suggest that structural factors related to population characteristics, pandemic containment and healthcare capabilities could have influenced lethality at the local level.

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

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

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