Epidemiological surveillance of chikungunya fever in Mexico since its introduction in 2014-2016 and identification of circulating genotypes.

In 2014, the chikungunya virus (CHIKV) was detected for the first time in Mexico, the identified strain was the one corresponding to the Asian genotype which was phylogenetically grouped with the strains that circulated in the British Virgin Islands outbreak and was later classified with lineages of Caribbean strains. In three years, 13,569 cases of chikungunya were registered in Mexico. Although the transmission and spread of the virus are now considered a moderate risk, the danger that the virus reemerges is not ruled out due to the infestation of Aedes mosquitoes. In this study, we reviewed the chikungunya fever (CHIKF) cases reported between 2014 and 2016 to reanalyze the data. Seventeen cases were selected from different states where the circulation of the virus had been reported. Statistical data were analyzed and a retrospective analysis was carried out. Nucleic acid sequences were determined of these 17 samples. 2015 was the year with the highest number of cases (92.8%) and they were detected in 28 states of the country. There is a predominance of females, and the most affected age group was between 25 and 44 years. In 2016, CHIKV genotypes were not known, in this study the presence of the Asian genotype of Caribbean lineage was confirmed. The presence of the West African and ECSA genotypes was phylogenetically ruled out. The sequences obtained were deposited in GeneBank.

Evaluation of serological diagnostic tests of human brucellosis for prevention and control in Mexico.

Brucellosis is a zoonosis mainly present in developing countries. The WHO reports 500,000 new cases every year. From 2012 to 2016, 13,677 cases were reported in Mexico, with 2.00 to 2.64 rate per 100,000 inhabitants. To analyze the diagnostic algorithm of brucellosis in Mexico, we compared the commercial laboratory tests ELISA, Brucellacapt®, and lateral flow test (LFT) in a study of 473 individuals from two endemic Mexican populations. All patients were treated in first-level medical units for presenting brucellosis compatible symptoms and without a history of the disease. Clinical-epidemiological information was gathered and initial serum samples were obtained to react with anti-Brucella antibodies; subsequent samples were collected at follow-up treatment visits. Using the Rose Bengal screening, we found 165 negative samples and 308 positive reactive samples, of which 222 cases were confirmed and 234 were positive on at least one marker (IgG or IgM) or LFT. When Brucellacapt® was used, similar results to those observed with the conventional algorithm were found as judged by the Cohen's kappa coefficient (κ) (0.813, 95% CI 0.7788-0.8472). Similar κ indices between conventional algorithm and ELISA pair were found, 0.7038 (95% CI 0.6555-0.7521), representing high similarity between both groups of diagnosis. We conclude that conventional serodiagnoses, Brucellacapt® and LFT, presented inconclusive results and poor correlation between them. By contrast, ELISA test pair (IgG + IgM) presented high correlation with the conventional algorithm and greater capacity for correct positive and negative classification.

Complete genome sequence of a coxsackievirus type A24 variant causing an outbreak of acute haemorrhagic conjunctivitis in southeastern Mexico in 2017.

Cases of acute haemorrhagic conjunctivitis (AHC) caused by a coxsackie virus A24 variant (CV-A24v) in Mexico have been reported since 1987; however, no molecular data on the causative strains have been available. Here, we report the identification of the etiological agent responsible for the most recent AHC outbreak in southeastern Mexico (at the end of 2017) as well as the complete genome sequences of seven isolates, using next-generation sequencing (NGS). Phylogenomic analysis of the CV-A24v sequences reported here showed similarity to contemporary strains causing AHC outbreaks in French Guiana and Uganda, forming a novel clade related to genotype IV. Moreover, a specific mutational pattern in the non-structural proteins was identified in the 2017 isolates. This is the first report of genetic characterization of CV-A24v isolates obtained 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.

Desde el ISET al InDRE. I. Instituto de Salubridad y Enfermedades Tropicales: génesis y primeros años, 1934-1940.

Lázaro Cárdenas government vision, and the process to create the Sanitary and Tropical Diseases Institute, which is considered strategic for public health, were consistent with the actions that were carried out: the Department of Public Sanitary asked the most relevant scientist of those days, Eliseo Ramírez, to design and follow-up the Institute's project. A commission of the Higher Education and Scientific Research Council reviewed and approved the project and conferred this institution its nature of research center with social and humanistic vocation since its foundation. Sanitary and Tropical Diseases Institute became the first post-revolutionary health institution that was born with well-remunerated job positions to conduct full-time research in Mexico, offering clinical services, teaching and supporting disease prevention and control campaigns. It was with no doubt a milestone in Mexican public health and crystalized the expectations of several generations of physicians and health researchers about having a high-level institution. It is the most significant public health institution of the country, with a new phase as Institute of Epidemiological Diagnosis and Reference. Without it, Mexican modern public health cannot be understood.

La visión del gobierno cardenista y el proceso para crear el Instituto de Salubridad y Enfermedades Tropicales, considerado estratégico para la salud pública, fueron congruentes con las acciones llevadas a cabo: el Departamento de Salubridad Pública encargó al científico más relevante de la época, Eliseo Ramírez, el diseño y seguimiento del Instituto, que una comisión del Consejo Nacional de Educación Superior y la Investigación Científica revisó, aprobó y desde su inicio le confirió el carácter de investigación con vocación social y humanística. El Instituto de Salubridad y Enfermedades Tropicales se convirtió en el primer organismo posrevolucionario que nació con plazas bien remuneradas para realizar investigación de tiempo completo en México, ofreciendo servicio clínico y enseñanza y apoyando las campañas sanitarias en la prevención y control de las enfermedades. Sin duda fue un parteaguas en la salud pública mexicana y cristalizó las expectativas de varias generaciones de médicos e investigadores en salud para tener una institución de alto nivel. Es la más significativa institución de salud pública del país, con una nueva etapa como Instituto de Diagnóstico y Referencia Epidemiológicos; sin ella no se entiende la moderna salud pública de México.

Desde el ISET al InDRE. II. Instituto de Salubridad y Enfermedades Tropicales: madurez y consolidación, 1940-1964.

The period that starts in 1940 is crucial for the creation of Mexico's modern health system. The Institute of Sanitary and Tropical Diseases is the pioneer institution in health research and on its first two decades it achieved maturity and consolidated lines of research expressed in almost 1700 publications. It also obtained notorious international visibility and was selected as a regional reference for epidemiological surveillance of influenza, streptococcus and salmonella. Its evolution took place with an innovation rhythm that would be decreasing by the end of this period. It faced limitations to renew lines of research, researchers and laboratory equipment. However, its role in public health decisions of the country remained central.

El periodo que comienza en 1940 es crucial para la creación del moderno sistema de salud de México. El Instituto de Salubridad y Enfermedades Tropicales es la institución pionera en investigación en salud y en sus primeras dos décadas logra madurez y consolida líneas de investigación expresadas en casi 1700 publicaciones. También obtiene notoria visibilidad internacional y fue seleccionado como referencia regional para la vigilancia epidemiológica de influenza, estreptococo y salmonela. Su evolución se produjo con ritmo de innovación que iría disminuyendo para el final de ese periodo. Enfrentó limitaciones para renovar líneas de trabajo, investigadores y equipo de laboratorio, sin embargo, su papel en las decisiones de la salud pública del país siguió siendo central.

Desde el ISET al InDRE. III. Instituto de Salubridad y Enfermedades Tropicales: crisis y renovación, 1965-1989.

This paper analyzes the situation and the changes made in the Institute of Sanitary and Tropical Diseases between 1965 and 1989 to become the National Institute of Epidemiological Diagnosis and Reference. Three major stages are identified during this period: crisis, transition and renewal. The factors that led to the crisis, the decisions made to overcome it and to harmonize the work of laboratories with epidemiological and public health criteria are discussed. The recognition obtained by researchers of the Institute despite the crisis is described, as well as the way the institution managed to continue with projects despite the changing global situation. The transition included the arrival of a new generation of professionals with modern computer-based and conceptual tools and the remarkably well met challenge of participating in national surveys with rigorous criteria. All this moved the institution to define its profile towards diagnosis and reference.

El artículo analiza la situación y los cambios efectuados en el Instituto de Salubridad y Enfermedades Tropicales entre 1965 y 1989 para transformarse en el Instituto Nacional de Diagnóstico y Referencia Epidemiológicos. Se identifican tres grandes etapas en el periodo: crisis, transición y renovación. Se señalan los elementos que llevaron a la crisis, las decisiones que se tomaron para salir de ella y armonizar el trabajo de los laboratorios con criterios epidemiológicos y de salud pública. Se citan las distinciones obtenidas por investigadores del Instituto a pesar de la crisis y se describe cómo la institución logró seguir con proyectos a pesar de la cambiante situación mundial. La transición incluyó la llegada de una nueva generación de profesionales con modernas herramientas informáticas y conceptuales y el desafío de participar en encuestas nacionales con criterios rigurosos. Todo ello movió a la institución a definir su perfil hacia el diagnóstico y la referencia.

Diagnostic algorithm for the confirmation of cases of measles and rubella in Mexico.

Due to the successful implementation of measles and rubella elimination strategies, Mexico announced the interruption of endemic transmission of measles in 1996 and that of rubella in 2008. After a verification process, the region of the Americas was declared free of rubella and congenital rubella syndrome in 2015 and of measles in 2016. In order to maintain the elimination status in Mexico, it is essential to continue laboratory surveillance within the framework of the Global Measles and Rubella Laboratory Network. The Institute of Epidemiological Diagnosis and Reference, through the National Network of Public Health Laboratories, guarantees timely and reliable results in view of the possible reintroduction of these and other emerging pathogens.

Algoritmo diagnóstico para la confirmación de casos de sarampión y rubéola en México.

Due to the successful implementation of measles and rubella elimination strategies, Mexico announced the interruption of endemic transmission of measles in 1996 and that of rubella in 2008. After a verification process, the region of the Americas was declared free of rubella and congenital rubella syndrome in 2015 and of measles in 2016. In order to maintain the elimination status in Mexico, it is essential to continue laboratory surveillance within the framework of the Global Measles and Rubella Laboratory Network. The Institute of Epidemiological Diagnosis and Reference, through the National Network of Public Health Laboratories, guarantees timely and reliable results in view of the possible reintroduction of these and other emerging pathogens.

Debido a la implementación exitosa de las estrategias de eliminación del sarampión y la rubéola, México enunció la interrupción de la transmisión endémica del sarampión en 1996 y de la rubéola en 2008. Después de un proceso de verificación, la región de las Américas fue declarada libre de rubéola y del síndrome de rubéola congénita en 2015 y del sarampión en 2016. Para mantener el estatus de eliminación en México es esencial continuar con la vigilancia por laboratorio en el marco de la Red Mundial de Laboratorios de Sarampión y Rubéola. El Instituto de Diagnóstico y Referencia Epidemiológicos, a través de la Red Nacional de Laboratorios de Salud Pública, garantiza resultados oportunos y confiables ante la posible reintroducción de estos y otros patógenos emergentes.

Seroprevalence of Poliomyelitis Antibodies Among Children Aged 1 to 4 Years Old and Factors Associated With Poliovirus Susceptibility; Mexican Health and Nutrition Survey, 2012.

Background: An essential component of the "Polio Eradication and Endgame Strategic Plan 2013-2018" is the evaluation of population immunity. Mexico introduced the inactivated polio vaccine (IPV) into its routine immunization schedule in 2007 but continued to give trivalent oral polio vaccine OPV twice a year during National Health Weeks through 2016. Methods: To describe the seroprevalence of poliomyelitis among children one to four years old in Mexico and analyze risk factors for susceptibility. We detected antibodies to poliovirus type 1 by microneutralization test in 966 serum samples randomly selected from the National Health and Nutrition Survey, 2012. We assessed variables associated with susceptibility using multivariable logistic regression. Results: The overall weighted seroprevalence of the general population was 98.39% (95% confidence interval [CI] 96.76-99.21). We found significant differences of prevalence according to age (94.39%, 95% CI 87.56-97.58; 99.02%, 95% CI 95.68-99.79; 99.82%, 95% CI 98.77-99.98; and 100% among children 1, 2, 3, and 4 years old respectively) and number of IPV doses (96.91%, 95% CI 90.55-99.44; 100%; 97.85%, 95% CI 94.46-99.18; and 99.92%, 95% CI 99.45-99.98 for 1 2, 3, and 4 number of doses, respectively). Multivariate analyses showed that susceptibility was associated with younger age, fewer doses of IPV, and certain socioeconomic levels. Conclusions: Overall seroprevalence was high. However, we found susceptible children among younger ages and children with fewer or unknown IPV doses belonging to certain socioeconomic strata. Results are relevant for countries transitioning from OPV to IPV and underline the importance of achieving high coverage with IPV.

Full genome and phylogenetic analysis of hepatitis B virus genotype F in Mexican isolates.

Hepatitis B virus genotype F (HBV/F) is endemic in Central and South America with a minor proportion in Mexico and North America. HBV/F is divided into subgenotypes and subtypes with particular geographic circulation patterns. Here, we report the complete genome sequence and molecular characterization of HBV/F from three isolates. Phylogenetic analysis with all available HBV/F sequences showed that our sequences belonged to the F1b subtype and, in addition, the absence of the previously reported F1a subtype in Mexican isolates. Our findings suggest the circulation of HBV/F1b, the first phylogenomic study of HBV/F in Mexico.

Genotypic variability analysis of DENV-1 in Mexico reveals the presence of a novel Mexican lineage.

Here, we report for the first time the circulation of dengue virus type 1 (DENV-1) belonging to the lineage IV of genotype V (African American genotype) based on phylogenetic analysis of nucleotide sequences from 10 DENV-1-positive samples obtained in Mexico between 2012 and 2014. Our data revealed that the lineages III and IV of DENV-1 genotype V were found circulating during the same period, probably explaining the rise in the number of cases of severe dengue during that period.

Utility of high-throughput DNA sequencing in the study of the human papillomaviruses.

The Papillomaviridae family is probably the most diverse group of viruses that affect vertebrates. The study of the relationship between infection by certain types of human papillomavirus (HPV) and the development of neoplastic epithelial lesions is of particular interest because of the high prevalence of HPV-related carcinomas in populations of developing countries. To understand the mechanisms of infection and their association with different clinical manifestations, molecular tools play an important role in the description of new types of HPV, the characterization of effector properties of the viral factors, the specific diagnosis and monitoring of HPV types, and the alteration patterns at genetic level in the host. Technological advances in the field of DNA sequencing have led to the development of different next-generation sequencing systems, allowing obtaining a large amount of data and broadening the applications to study viral diseases. In this review, we summarize the main approaches and their perspectives where the use of massively parallel sequencing has been proved as a useful tool in the research of the HPV infection.

Differential Detection of Enterovirus and Herpes Simplex Virus in Cerebrospinal Fluid by Real-Time RT-PCR.

BACKGROUND: Enterovirus (EV) and herpes simplex virus 1 and 2 (HSV1 and HSV2) are the main etiologic agents of central nervous system infections. Early laboratory confirmation of these infections is performed by viral culture of the cerebrospinal fluid (CSF), or the detection of specific antibodies in serum (e.g., HSV). The sensitivity of viral culture ranges from 65 to 75%, with a recovery time varying from 3 to 10 days. Serological tests are faster and easy to carry out, but they exhibit cross-reactivity between HSV1 and HSV2. Although molecular techniques are more sensitive (sensitivity >95%), they are more expensive and highly susceptible to cross-contamination. METHODS: A real-time RT-PCR for the detection of EV, HSV1, and HSV2 was compared with end-point nested PCR. RESULTS: We tested 87 CSF samples of patients with a clinical diagnosis of viral meningitis or encephalitis. Fourteen samples were found to be positive by RT-PCR, but only 8 were positive by end-point PCR. The RT-PCR showed a specificity range of 94-100%, the negative predictive value was 100%, and the positive predictive value was 62, 100, and 28% for HSV1, HSV2, and EV, respectively. CONCLUSION: Real-time RT-PCR detected EV, HSV1, and HSV2 with a higher sensitivity and specificity than end-point nested RT-PCR.

Molecular characterization of atypical antigenic variants of canine rabies virus reveals its reintroduction by wildlife vectors in southeastern Mexico.

Rabies is an infectious viral disease that is practically always fatal following the onset of clinical signs. In Mexico, the last case of human rabies transmitted by dogs was reported in 2006 and canine rabies has declined significantly due to vaccination campaigns implemented in the country. Here we report on the molecular characterization of six rabies virus strains found in Yucatan and Chiapas, remarkably, four of them showed an atypical reaction pattern when antigenic characterization with a reduced panel of eight monoclonal antibodies was performed. Phylogenetic analyses on the RNA sequences unveiled that the three atypical strains from Yucatan are associated with skunks. Analysis using the virus entire genome showed that they belong to a different lineage distinct from the variants described for this animal species in Mexico. The Chiapas atypical strain was grouped in a lineage that was considered extinct, while the others are clustered within classic dog variants.

[Clinical and epidemiological characterization of chikungunya fever in Mexico]. / Caracterización clínica y epidemiológica de fiebre chikungunya en México.

On 6 December 2013, the Pan American Health Organization (PAHO) and the World Health Organization (WHO) reported confirmation of the first two cases of indigenous transmission of chikungunya fever (CHIK) in the Region of the Americas on the island of Sint Maarten (Netherlands Antilles). For the period 2013-2014, a total of 25 627 confirmed autochthonous cases were distributed in 43 countries, with Mexico reporting 155 cases in five states. Information on cases of CHIK in Mexico was obtained from the database of the General Directorate of Epidemiology (Ministry of Health of Mexico). The distribution of confirmed autochthonous cases of CHIK for 2015, by sex, was 64% female (5 583) and 36% male (3 085). The most frequent symptoms were fever in 98% of cases (8 564), followed by headache in 91.6% (7 941), myalgia in 89.9% (7 792), mild arthralgias in 73.5% (6 367), severe polyarthralgia in 72.6% (6 295), and exanthema in 58% (5 032). The clinical presentation of autochthonous cases of CHIK in Mexico has shown several clinical manifestations different from those seen in outbreaks in African and Asian countries and other regions in the Americas; for example, a greater percentage of cases with headache and myalgia and a smaller percentage of cases with arthralgia.

Genome Sequence Analysis of Vibrio cholerae clinical isolates from 2013 in Mexico reveals the presence of the strain responsible for the 2010 Haiti outbreak. / El análisis molecular de la secuencia del genoma completo de aislados clínicos de Vibrio cholerae en México en 2013 revela la presencia de la cepa causante de la epidemia de Haití en 2010.

The first week of September 2013, the National Epidemiological Surveillance System identified two cases of cholera in Mexico City. The cultures of both samples were confirmed as Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Initial analyses by pulsed-field gel electrophoresis and by polymerase chain reaction-amplification of the virulence genes, suggested that both strains were similar, but different from those previously reported in Mexico. The following week, four more cases were identified in a community in the state of Hidalgo, located 121 km northeast of Mexico City. Thereafter a cholera outbreak started in the region of La Huasteca. Genomic analyses of the strains obtained in this study confirmed the presence of pathogenicity islands VPI-1 and VPI-2, VSP-1 and VSP-2, and of the integrative element SXT. The genomic structure of the 4 isolates was similar to that of V. cholerae strain 2010 EL-1786, identified during the epidemic in Haiti in 2010. This study shows that molecular epidemiology is a very powerful tool to monitor, prevent and control diseases of public health importance in Mexico.

La primera semana de septiembre de 2013, el Sistema Nacional de Vigilancia Epidemiológica identificó dos casos de cólera en Ciudad de México. Los cultivos de ambas muestras se confirmaron como Vibrio cholerae serogrupo O1, serotipo Ogawa, biotipo El Tor. Los análisis iniciales por electroforesis por campos pulsados y por reacción en cadena de la polimerasa indicaron que ambas cepas eran similares, pero diferentes de las previamente reportadas en México. La semana siguiente se identificaron cuatro casos más en una comunidad del Estado de Hidalgo, ubicada a 121 kilómetros al noreste de Ciudad de México. Posteriormente se inició un brote de cólera en la región de La Huasteca. Los análisis genómicos de cuatro cepas obtenidas en este estudio confirmaron la presencia de las islas de patogenicidad VPI -1 y VPI-2, VSP-1 y VSP-2, y del elemento integrador SXT. La estructura genómica de los cuatro aislamientos fue similar a la de V. cholerae cepa 2010 EL-1786, identificada durante la epidemia en Haití en 2010. Este estudio pone de manifiesto que la epidemiología molecular es una herramienta muy poderosa para vigilar, prevenir y controlar enfermedades de importancia en salud pública en México.

Fatal Psychrobacter sp. infection in a pediatric patient with meningitis identified by metagenomic next-generation sequencing in cerebrospinal fluid.

The genus Psychrobacter contains environmental, psychrophilic and halotolerant gram-negative bacteria considered rare opportunistic pathogens in humans. Metagenomics was performed on the cerebrospinal fluid (CSF) of a pediatric patient with meningitis. Nucleic acids were extracted, randomly amplified, and sequenced with the 454 GS FLX Titanium next-generation sequencing (NGS) system. Sequencing reads were assembled, and potential virulence genes were predicted. Phylogenomic and phylogenetic studies were performed. Psychrobacter sp. 310 was identified, and several virulence genes characteristic of pathogenic bacteria were found. The phylogenomic study and 16S rRNA gene phylogenetic analysis showed that the closest relative of Psychrobacter sp. 310 was Psychrobacter sanguinis. To our knowledge, this is the first report of a meningitis case associated with Psychrobacter sp. identified by NGS metagenomics in CSF from a pediatric patient. The metagenomic strategy based on NGS was a powerful tool to identify a rare unknown pathogen in a clinical case.

Evidence of the presence of the Zika virus in Mexico since early 2015.

To assess the possible circulation of Zika virus (ZIKV) prior to the first documented case in Mexico, we reanalyzed the stored samples from the states of Veracruz and Yucatán, which were originally collected to test for dengue (DENV) and chikungunya (CHIKV) but were negative for these viruses despite the symptomatology. The samples were originally collected between the 30 and 46 epidemiological weeks (EW) when the ZIKV was not yet declared as a Public Health Emergency of International Concern (PHEIC). From the total 4016 negative samples, a total of one hundred samples, 50 from Veracruz (CHIK- DENV-) and 50 from Yucatán (4 CHIK- DENV- and 46 CHIK- or DENV-), were tested for Zika virus by using RT-PCR. Results showed that in Veracruz and Yucatán, 20 % (10/50) and 70 % (35/50) were, respectively, ZIKV positive, indicating unequivocally the presence of ZIKV at least since July 2015. We also tested non-confirmed suspect measles cases from early 2015 for ZIKV by RT-PCR. Remarkably in 11 Mexican states, 86 % (18/21) were positive with the earlier symptoms onset as early as May 2015. Finally, RT-PCR analyses on RNA extracted from Aedes aegypti mosquitoes captured from January to March 2015 showed the presence of ZIKV, strongly suggesting that the vector was already carrying the virus at the start of 2015.

Identification of Asian genotype of chikungunya virus isolated in Mexico.

We identified 25 autochthonous chikungunya virus cases in Mexico, initially detected by RT-PCR targeting the E1 gene and propagated in C6/36 Aedes albopictus cells, in 2014. To determine the type of virus found, in a previous report, the genomes of 2 CHIKV strains were fully sequenced. Genome sequence analysis revealed that these isolates from Mexico belonged to the Asian genotype, and a phylogenetic association with the circulating strain in the British Virgin Islands was also established in the same year. This was further supported by changes in specific amino acids, E2-V368A and 6K-L20M. For these reasons, it can be inferred that the route of virus entry to Mexico was held across the countries in the Caribbean and Central America. The presence of E1-A226V mutation associated with more efficient replication in the salivary gland of the A. albopictus mosquito was not observed. Interestingly, a newly acquired NSP4-S399C mutation was observed; however, the significance of changes in amino acid found in non-structural proteins in autochthonous strains remains to be elucidated.