Probable Case of Vertical Transmission of SARS-CoV-2 in a Newborn in Mexico.

BACKGROUND: Much remains unknown about the transmission of the SARS-CoV-2 virus. Pregnant women are considered part of the risk population, and vertical transmission of other coronaviruses has been suggested; however, this type of transmission in SARS-CoV-2 is believed to be unlikely. CASE REPORT: A newborn delivered in term via cesarean section to an asymptomatic but COVID-19-positive 35-year-old woman started with respiratory distress in the first 30 min of life. A chest radiograph revealed pneumothorax and ground glass opacities. Ventilatory support with continuous positive airway pressure was needed. Given the respiratory failure and the positive test from the mother, the patient was sampled for SARS-CoV-2 (RT-PCR) at minute 30 of life, with a positive result reported at 36 h of life. No complications had been present during pregnancy, and cardiac screening and blood cultures revealed no other etiologies. CONCLUSION: Vertical transmission was highly likely in this case. Clinicians should be alert and report similar cases.

Simultaneous Detection of Major Drug Resistance Mutations of HIV-1 Subtype B Viruses from Dried Blood Spot Specimens by Multiplex Allele-Specific Assay.

A multiplex allele-specific (MAS) assay has been developed for the detection of HIV-1 subtype C drug resistance mutations (DRMs). We have optimized the MAS assay to determine subtype B DRMs in dried blood spots (DBS) collected from patients on antiretroviral therapy. The new assay accurately detected DRMs, including low-abundance mutations that were often missed by Sanger sequencing.

Evaluation of a dried blood and plasma collection device, SampleTanker(®), for HIV type 1 drug resistance genotyping in patients receiving antiretroviral therapy.

Whatman 903 filter paper is the only filter paper that has been used for HIV drug resistance (HIVDR) genotyping in resource-limited settings. In this study, we evaluated another dried blood specimen collection device, termed SampleTanker(®) (ST), for HIVDR genotyping. Blood specimens from 123 antiretroviral therapy (ART)-experienced patients were used to prepare ST whole blood and ST plasma specimens; they were then stored at ambient temperature for 2 or 4 weeks. The remaining plasma specimens were stored at -80°C and used as frozen plasma controls. Frozen plasma viral load (VL) was determined using the Roche Amplicor HIV-1 Monitor test, v.1.5 and 50 specimens with VL ≥3.00 log10 copies/ml were genotyped using the broadly sensitive genotyping assay. The medium VL for the 50 frozen plasma specimens with VL ≥3.00 log10 was 3.58 log10 copies/ml (IQR: 3.32-4.11) and 96.0% (48/50) of them were genotyped. Comparing to frozen plasma specimens, significantly lower genotyping rates were obtained from ST whole blood (48.98% and 42.85%) and ST plasma specimens (36.0% and 36.0%) stored at ambient temperature for 2 and 4 weeks, respectively (p<0.001). Nucleotide sequence identity and resistance profile analyses between the matched frozen plasma and ST whole blood or ST plasma specimens revealed high nucleotide sequence identities and concordant resistance profiles (98.1% and 99.0%, and 96.6% and 98.9%, respectively). Our results indicate that with the current design, the ST may not be the ideal dried blood specimen collection device for HIVDR monitoring for ART patients in resource-limited settings.

Human parainfluenza virus in patients with influenza-like illness from Central and South America during 2006-2010.

BACKGROUND: Human parainfluenza viruses (HPIVs) are common viral causes of community-acquired pneumonia, particularly in children. The four types of HPIV have world-wide distribution; however, limited information exists about the epidemiological profile of HPIV in Latin-America. OBJECTIVE: Provide epidemiologic and phylogenetic information about HPIVs that circulated in Latin America between 2006 and 2010 to better characterize the extent and variability of this respiratory virus in the region. METHODS: Oropharyngeal swabs, demographic data and clinical characteristics were obtained from individuals with influenza-like illness in 10 Latin-American countries between 2006-2010. Specimens were analyzed with culture and molecular methods. RESULTS: A total of 30 561 individuals were enrolled; 991 (3·2%) were HPIV positive. Most infected participants were male (53·7%) and under 5 years of age (68·7%). The HPIV type most frequently isolated was HPIV-3 (403, 40·7%). In 66/2007 (3·3%) hospitalized individuals, HPIV was identified. The most frequent symptoms at enrollment were cough and rhinorrhea. We identified certain patterns for HPIV-1, -2 and -3 in specific cities. Phylogenetic analysis revealed a homogeneous distribution in the region. CONCLUSIONS: In the current scenario, no vaccine or treatment is available for this pathogen. Our results contribute to the scarce epidemiologic and phylogenetic information of HPIV in the region that could support the development of specific management.

Human rhinoviruses and enteroviruses in influenza-like illness in Latin America.

BACKGROUND: Human rhinoviruses (HRVs) belong to the Picornaviridae family with high similarity to human enteroviruses (HEVs). Limited data is available from Latin America regarding the clinical presentation and strains of these viruses in respiratory disease. METHODS: We collected nasopharyngeal swabs at clinics located in eight Latin American countries from 3,375 subjects aged 25 years or younger who presented with influenza-like illness. RESULTS: Our subjects had a median age of 3 years and a 1.2:1.0 male:female ratio. HRV was identified in 16% and HEV was identified in 3%. HRVs accounted for a higher frequency of isolates in those of younger age, in particular children < 1 years old. HRV-C accounted for 38% of all HRVs detected. Phylogenetic analysis revealed a high proportion of recombinant strains between HRV-A/HRV-C and between HEV-A/HEV-B. In addition, both EV-D68 and EV-A71 were identified. CONCLUSIONS: In Latin America as in other regions, HRVs and HEVs account for a substantial proportion of respiratory viruses identified in young people with ILI, a finding that provides additional support for the development of pharmaceuticals and vaccines targeting these pathogens.

A single early introduction of HIV-1 subtype B into Central America accounts for most current cases.

Human immunodeficiency virus type 1 (HIV-1) variants show considerable geographical separation across the world, but there is limited information from Central America. We provide the first detailed investigation of the genetic diversity and molecular epidemiology of HIV-1 in six Central American countries. Phylogenetic analysis was performed on 625 HIV-1 pol gene sequences collected between 2002 and 2010 in Honduras, El Salvador, Nicaragua, Costa Rica, Panama, and Belize. Published sequences from neighboring countries (n = 57) and the rest of the world (n = 740) were included as controls. Maximum likelihood methods were used to explore phylogenetic relationships. Bayesian coalescence-based methods were used to time HIV-1 introductions. Nearly all (98.9%) Central American sequences were of subtype B. Phylogenetic analysis revealed that 437 (70%) sequences clustered within five significantly supported monophyletic clades formed essentially by Central American sequences. One clade contained 386 (62%) sequences from all six countries; the other four clades were smaller and more country specific, suggesting discrete subepidemics. The existence of one large well-supported Central American clade provides evidence that a single introduction of HIV-1 subtype B in Central America accounts for most current cases. An introduction during the early phase of the HIV-1 pandemic may explain its epidemiological success. Moreover, the smaller clades suggest a subsequent regional spread related to specific transmission networks within each country.

Social network-based recruitment successfully reveals HIV-1 transmission networks among high-risk individuals in El Salvador.

OBJECTIVE: HIV in Central America is concentrated among certain groups such as men who have sex with men (MSM) and female sex workers (FSWs). We compared social recruitment chains and HIV transmission clusters from 699 MSM and 787 FSWs to better understand factors contributing to ongoing HIV transmission in El Salvador. METHODS: Phylogenies were reconstructed using pol sequences from 119 HIV-positive individuals recruited by respondent-driven sampling (RDS) and compared with RDS chains in 3 cities in El Salvador. Transmission clusters with a mean pairwise genetic distance ≤ 0.015 and Bayesian posterior probabilities =1 were identified. Factors associated with cluster membership were evaluated among MSM. RESULTS: Sequences from 34 (43%) MSM and 4 (10%) FSW grouped in 14 transmission clusters. Clusters were defined by risk group (12 MSM clusters) and geographic residence (only 1 spanned separate cities). In 4 MSM clusters (all n = 2), individuals were also members of the same RDS chain, but only 2 had members directly linked through recruitment. All large clusters (n ≥ 3) spanned >1 RDS chain. Among MSM, factors independently associated with cluster membership included recent infection by BED assay (P = 0.02), sex with stable male partners (P = 0.02), and sex with ≥ 3 male partners in the past year (P = 0.04). CONCLUSIONS: We found few HIV transmissions corresponding directly with the social recruitment. However, we identified clustering in nearly one-half of MSM suggesting that RDS recruitment was indirectly but successfully uncovering transmission networks, particularly among recent infections. Interrogating RDS chains with phylogenetic analyses may help refine methods for identifying transmission clusters.

Short communication: HIV incidence among vulnerable populations in Honduras: results from an integrated behavioral and biological survey among female sex workers, men who have sex with men, and Garifuna in Honduras, 2006.

Honduras has one of the highest HIV prevalence rates in Central America. Data on HIV incidence are needed to identify groups at greatest need of prevention interventions to inform the national HIV response. We applied a test for recent infection to HIV-positive specimens from a biological and behavioral survey to estimate assay-derived incidence among men who have sex with men (MSM), female sex workers (FSW), and the Garifuna population in Honduras. Assay-derived estimates were compared to the mathematically modeled estimates in the same populations to assess plausibility of the assay-based estimates. Assay-derived incidence was 1.1% (95% CI 0.2-2.0) among MSM, 0.4% (95% CI 0.1-0.8) among the Garifuna, and 0% (95% CI 0-0.01) among FSWs. The modeled incidence estimates were similar at 1.03% among MSM, 0.30% among the Garifuna, and 0.23% among FSWs. HIV incidence based on the assay was highest among MSM in Honduras, lowest among FSWs, and similar to modeled incidence in these groups. Targeted programs on HIV prevention, care, and treatment are urgently needed for the MSM population. Continued support for existing prevention programs for FSWs and Garifuna are recommended.

Prevalence of transmitted HIV-1 drug resistance among female sex workers and men who have sex with men in El Salvador, Central America.

Transmitted drug resistance has important implications for the successful use and management of therapy among persons infected with HIV. We estimated the prevalence of transmitted drug resistance in 145 samples from female sex workers (n = 47) and men who have sex with men (n = 98) in El Salvador. Samples were collected during March to September 2008, using a respondent driven sampling. The HIV-1 pol gene was sequenced to identify drug resistance mutations and transmitted drug resistance was scored as recommended by World Health Organization. Specimens were classified as recent or established infections using the Immunoglobulin G-Capture BED-Enzyme Immunoassay. The overall prevalence of transmitted drug resistance was 9.4% (95% CI: 4.7-16.1%), and was 5.9% for non-nucleoside reverse transcriptase inhibitors, 4.2% for nucleoside reverse transcriptase inhibitors, and 0.8% for protease inhibitors. Transmitted drug resistance prevalence was 10.3% (95% CI: 2.8-24.2%) among female sex workers, and 9.0% (95% CI: 3.6-17.6%) among men who have sex with men. Nineteen patients were classified as having recent infection (16.2%, 95% CI: 10.1-24.2%), while 98 patients (83.8%, 95% CI: 75.8-89.9%) were classified as having established infections. Transmitted drug resistance among recent and established infections was similar at 10.5% and 9.2%, respectively. This study shows that the prevalence of transmitted drug resistance is moderate among female sex workers and men who have sex with men in El Salvador. These results highlight the importance of transmitted drug resistance surveillance in a representative sample of recently infected patients following the World Health Organization guidelines.

Comparison of HIV-1 resistance profiles in plasma RNA versus PBMC DNA in heavily treated patients in Honduras, a resource-limited country.

The World Health Organization currently does not recommend the use of dried blood spot specimens for drug resistance testing in patients undergoing antiretroviral therapy (ART). Therefore, HIV-1 resistance testing using peripheral blood mononuclear cells (PBMCs) may be of value in resource-limited settings. We compared genotypic resistance profiles in plasma and PBMCs from patients failing ART in two cities of Honduras (Tegucigalpa and San Pedro Sula), a resource-limited country. One hundred patients failing ART were randomly selected from a longitudinal patient monitoring cohort. Plasma and PBMC samples without patient identifier were used for genotypic resistance testing. Sequence data were analyzed, resistance profiles were determined and compared using Stanford HIV Drug Resistance Database algorithm. Specimens with concordant resistance profiles between the two compartments were 88% (95% CI: 80.3% - 94.5 %). Nine specimens (12%, 95% CI: 6.5% - 21.3%) had discordant resistance profiles of clinical significance. Logistic regression analyses indicated that patients on triple therapy were 17.24 times more likely to have concordant drug resistance profile than those on non-triple therapies (OR=17.24, 95% CI: 3.48, 83.33), while patients with increasing number of regimens and years on ART have a decreased rate of concordance (OR = 0.59, 95% CI: 0.32, 1.09 and OR = 0.62, 95% CI: 0.43, 0.88), respectively, than those with less number of regimens and years on ART. Our results show high level of concordance between plasma and PBMC resistance profiles, indicating the possibility of using PBMCs for drug resistance testing in resources-limited settings.

Circulating strains of human respiratory syncytial virus in central and south America.

Human respiratory syncytial virus (HRSV) is a major cause of viral lower respiratory tract infections among infants and young children. HRSV strains vary genetically and antigenically and have been classified into two broad subgroups, A and B (HRSV-A and HRSV-B, respectively). To date, little is known about the circulating strains of HRSV in Latin America. We have evaluated the genetic diversity of 96 HRSV strains by sequencing a variable region of the G protein gene of isolates collected from 2007 to 2009 in Central and South America. Our results show the presence of the two antigenic subgroups of HRSV during this period with the majority belonging to the genotype HRSV-A2.

Short communication: high prevalence of drug resistance in HIV type 1-infected children born in Honduras and Belize 2001 to 2004.

Antiretroviral therapy has had a great impact on the prevention of mother-to-child transmission (MTCT) of HIV-1. However, development of drug resistance, which could be subsequently transmitted to the child, is a major concern. In Honduras and Belize the prevalence of drug resistance among HIV-1-infected children remains unknown. A total of 95 dried blood spot samples was obtained from HIV-1-infected, untreated children in Honduras and Belize born during 2001 to 2004, when preventive antiretroviral therapy was often suboptimal and consisted of monotherapy with nevirapine or zidovudine. Partial HIV-1 pol gene sequences were successfully obtained from 66 children (Honduras n=55; Belize n=11). Mutations associated with drug resistance were detected in 13% of the Honduran and 27% of the Belizean children. Most of the mutations detected in Honduras (43%) and all mutations detected in Belize were associated with resistance to nonnucleoside reverse transcriptase inhibitors, which was expected from the wide use of nevirapine to prevent MTCT during the study period. In addition, although several mothers reported that they had not received antiretroviral therapy, mutations associated with resistance to nucleoside reverse transcriptase inhibitors and protease inhibitors were found in Honduras. This suggests prior and unreported use of these drugs, or that these women had been infected with resistant virus. The present study demonstrates, for the first time, the presence of drug resistance-associated mutations in HIV-1-infected Honduran and Belizean children.

Genetic analysis of influenza A/H1N1 of swine origin virus (SOIV) circulating in Central and South America.

Since the first detection of swine origin virus (SOIV) on March 28, 2009, the virus has spread worldwide and oseltamivir-resistant strains have already been identified in the past months. Here, we show the phylogenetic analysis of 63 SOIV isolates from eight countries in Central and South America, and their sensitivity to oseltamivir.

Molecular characterization of adenovirus circulating in Central and South America during the 2006-2008 period.

BACKGROUND: Human Adenoviruses are recognized pathogens, causing a broad spectrum of diseases. Serotype identification is critical for epidemiological surveillance, detection of new strains and understanding of HAdvs pathogenesis. Little data is available about HAdvs subtypes in Latin America. METHODS: In this study, we have molecularly characterized 213 adenoviruses collected from ILI presenting patients, during 2006-08, in Central and South America. RESULTS: Our results indicate that 161(76%) adenoviruses belong to subgroup C, 45 (21%) to subgroup B and 7 (3%) to subtype E4.

Antiviral resistance in influenza viruses circulating in Central and South America based on the detection of established genetic markers.

BACKGROUND: Recent influenza antiviral resistance studies reveal an alarming increase in both adamantanes and neuraminidase inhibitors (NAIs) resistant viral strains worldwide, particularly in Asia, Europe and the United States. OBJECTIVES: In this study, we have evaluated influenza virus resistance in Central and South America. METHODS: Influenza viruses, isolated from symptomatic patients throughout Central and South America in 2005-2008 were analyzed for inhibitor resistance. The M2 and NA genes of influenza viruses were sequenced and resistance was inferred by comparison with published sequences and known resistant mutations. RESULTS: Our results indicate that: (i) resistance to adamantanes was seen in the majority (95.5%) of the influenza A/H3N2 isolates but only in one isolate of the influenza A/H1N1 viruses; (ii) resistance to NAIs began to be detected in A/H1N1 isolates from Central America in 2008; and (iii) none of the influenza B viruses analyzed were resistant to NAIs. CONCLUSIONS: These findings suggest a limited effectiveness of influenza inhibitors due to the detection of resistance among A/H1 and A/H3 viruses.

Humoral immune response of dengue hemorrhagic fever cases in children from Tegucigalpa, Honduras.

The humoral immune response in Honduran dengue hemorrhagic fever (DHF) hospitalized pediatric cases from the epidemics of 2004 and 2005 was studied in sera collected from 5 to 7 days of fever onset. A total of 145 cases were included in the study: 40 classified as primary with DHF Grade I or II and 86 classified as secondary; from them, 73 were DHF Grade I or II and 13 were dengue shock syndrome (DSS) Grade III or IV. The highest number of primary cases was found in children < 1 year of age. The highest number of secondary cases was observed in children between 5 and 10 years of age. The IgA values showed a statistically significant difference between primary and secondary groups. The relationship between antibody responses and severity grade is discussed. This is the first study related to the humoral immune response and severity grade in DHF cases in Honduran children.

Optimization of the oligonucleotide ligation assay, a rapid and inexpensive test for detection of HIV-1 drug resistance mutations, for non-North American variants.

OBJECTIVE: We evaluated the feasibility of the oligonucleotide ligation assay (OLA), a specific, sensitive, and economical ligase-based point mutation assay designed to detect HIV-1 drug-resistance mutations at 12 codons of HIV-1 subtype B pol, for potential use in resource-poor settings. METHODS: Specimens from HIV-1-infected individuals collected by 7 international laboratories, including subtypes A, B, C, D, F, G, J, and recombinants AE and AG, were tested by the OLA developed for HIV-1 subtype B. Common polymorphisms that interfered with reactivity of the OLA were identified and modified probes designed and evaluated. RESULTS: 92.5% (2,410) of 2,604 codons in specimens from 217 individuals were successfully genotyped by the subtype B OLA. A high rate (range 8.3%-31.2%) of indeterminate results (negative OLA reaction for both mutant and wild type) was observed for 5 codons. Modified probes at reverse transcriptase codons 151 and 184 and protease codon 90 increased the rate of valid OLA to 96.1%. CONCLUSIONS: The OLA designed for HIV-1 subtype B genotyped most pol codons in non-B subtypes from Asia and Africa but was improved by addition of several modified probes. International laboratories experienced in molecular techniques were able to perform the OLA.

Sampling designs for HIV molecular epidemiology with application to Honduras.

Proper sampling is essential to characterize the molecular epidemiology of human immunodeficiency virus (HIV). HIV sampling frames are difficult to identify, so most studies use convenience samples. We discuss statistically valid and feasible sampling techniques that overcome some of the potential for bias due to convenience sampling and ensure better representation of the study population. We employ a sampling design called stratified cluster sampling. This first divides the population into geographical and/or social strata. Within each stratum, a population of clusters is chosen from groups, locations, or facilities where HIV-positive individuals might be found. Some clusters are randomly selected within strata and individuals are randomly selected within clusters. Variation and cost help determine the number of clusters and the number of individuals within clusters that are to be sampled. We illustrate the approach through a study designed to survey the heterogeneity of subtype B strains in Honduras.

Aplicación del PCR-ADN en el diagnóstico de la infección por VIH-1 en infantes / PCR for diagnosis of HIV-1 infection in infants

ANTECEDENTES. Ante la necesidad de establecer el diagnóstico temprano de la infección por VIH-1 en niños nacidos de madres VIH-1 seropositivas del Proyecto Piloto de Prevención de la Transmisión Perinatal y pacientes pediátricos que lo requieran, se implementa la técnica de Reacción en cadena de la Polimerasa en ADN del VIH-1. METODOS. La población de estudio fueron niño(as) nacidos de madres VIH-1 serpositivas de varios centros asistenciales de Honduras y Belice. Las muestras tomadas en papel filtro fueron procesadas para la extracción del ADN; la amplificación del ADN se hizo por medio de un PCR anidado, utilizando primers dirigidos a la regón POL del VIH-1, los amplicones fueron detectados por electroforesis en gel de agarosa. RESULTADOS. En el período de febrero del 2001 a noviembre del 2002, se analizaron 109 muestras de niños, en los cuales se desconocía su estado de infección, 25 (23.8 por ciento)resultaron positivos y 83(76.2 por ciento)negatios por PCR. Es importante mencionar que 10/25 (40 por ciento)niños cuyas madres optaron por darle lactancia materna resultaron positivos, 1/4 (25 por ciento)niños en quienes se desconocía si habían recibido lactancia materna estaban positivos. Nueve de 57 (15.7 por ciento)niños cuyas madres recibieron terapia antiretroviral ( curso corto de zidovudina o nevirapina) fueron positivos; 15/42 (35.7 por ciento)niños cuyas madres no recibieron terapia antiretroviral, resultaron positivos. CONCLUSIONES. Este método constituye un simple ensayo para detección de ADN-VIH-1 en muestras de sangre colectadas en papel filtro, lo cual elimina largos pasos de extracción y purificación del ADN y facilita el transporte y manejo de las muestras. La implementación de esta técnica en el pais implica desarrollo tecnológico, ya que de no ser así el diagnóstico de infección con VIH-1 en los infantes no sería posible hasta la edad de 15-18 meses através de pruebas serológicas

Aplicación del PCR-ADN en el diagnóstico de la infección por VIH-1 en infantes / PCR for diagnosis of HIV-1 infection in infants

ANTECEDENTES. Ante la necesidad de establecer el diagnóstico temprano de la infección por VIH-1 en niños nacidos de madres VIH-1 seropositivas del Proyecto Piloto de Prevención de la Transmisión Perinatal y pacientes pediátricos que lo requieran, se implementa la técnica de Reacción en cadena de la Polimerasa en ADN del VIH-1. METODOS. La población de estudio fueron niño(as) nacidos de madres VIH-1 serpositivas de varios centros asistenciales de Honduras y Belice. Las muestras tomadas en papel filtro fueron procesadas para la extracción del ADN; la amplificación del ADN se hizo por medio de un PCR anidado, utilizando primers dirigidos a la regón POL del VIH-1, los amplicones fueron detectados por electroforesis en gel de agarosa. RESULTADOS. En el período de febrero del 2001 a noviembre del 2002, se analizaron 109 muestras de niños, en los cuales se desconocía su estado de infección, 25 (23.8 por ciento)resultaron positivos y 83(76.2 por ciento)negatios por PCR. Es importante mencionar que 10/25 (40 por ciento)niños cuyas madres optaron por darle lactancia materna resultaron positivos, 1/4 (25 por ciento)niños en quienes se desconocía si habían recibido lactancia materna estaban positivos. Nueve de 57 (15.7 por ciento)niños cuyas madres recibieron terapia antiretroviral ( curso corto de zidovudina o nevirapina) fueron positivos; 15/42 (35.7 por ciento)niños cuyas madres no recibieron terapia antiretroviral, resultaron positivos. CONCLUSIONES. Este método constituye un simple ensayo para detección de ADN-VIH-1 en muestras de sangre colectadas en papel filtro, lo cual elimina largos pasos de extracción y purificación del ADN y facilita el transporte y manejo de las muestras. La implementación de esta técnica en el pais implica desarrollo tecnológico, ya que de no ser así el diagnóstico de infección con VIH-1 en los infantes no sería posible hasta la edad de 15-18 meses através de pruebas serológicas