Flavio Augusto Pádua Milagres

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil. Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 2016) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 2016). Since the initial detection of ZIKV in Brazil, more than 45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting severe ZIKV-associated disease. However, the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly. Here we address this issue by generating 54 complete or partial ZIKV genomes, mostly from Brazil, and reporting data generated by a mobile genomics laboratory that travelled across northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Analyses of viral genomes with ecological and epidemiological data yield an estimate that ZIKV was present in northeast Brazil by February 2014 and is likely to have disseminated from there, nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates for the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. The role of northeast Brazil in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the basic reproduction number of the virus.

Performance of rapid hepatitis C virus antibody assays among high- and low-risk populations

BACKGROUND Rapid tests for the detection of antibodies to hepatitis C virus (anti-HCV) can facilitate access to diagnosis. OBJECTIVES This study aimed to evaluate the performance of rapid tests for anti-HCV detection in the sera, whole blood, and oral fluid samples from individuals with different endemicity profiles and risk behaviors. STUDY DESIGN Three groups donated biological samples that were tested using three anti-HCV rapid tests (WAMA, Bioeasy and OraSure): (I) suspected cases of hepatitis C, (II) individuals who were living in remote areas in Brazil and (III) crack users and beauty professionals. Reproducibility, repeatability and cross-reactivity to other infectious agents (dengue, HIV, malaria, and syphilis) were also evaluated. RESULTS In group I, specificities varied from 93.75% to 100% and sensitivities varied from 76.03% to 93.84% according to the EIA results. When anti-HCV/HCV RNA-reactive sera samples were considered true-positive HCV cases, the sensitivities and specificities varied from 86.3% to 99.09% and 93.75% to 100%, respectively. In group II, the OraSure rapid test presented the best performance. In group III, the Bioeasy assay performed best using saliva and whole blood and the OraSure assay performed best using oral fluid samples. The reproducibility and repeatability of the WAMA and Bioeasy tests were excellent. The level of concordance between the HCV EIAs and the rapid tests using samples that were reactive for other infectious agents varied from 82.35% to 100% for the WAMA assay and 94.11% to 100% for the Bioeasy assay. CONCLUSION All of the rapid tests could be used to identify active HCV infection among individuals with different endemicity profiles and risk behaviors.

Hepatitis C virus and human T-lymphotropic virus coinfection: epidemiological, clinical, laboratory and histopathological features

Twenty-four hepatitis C virus patients coinfected with human T-lymphotropic virus type 1 were compared with six coinfected with HTLV-2 and 55 with HCV alone, regarding clinical, epidemiological, laboratory and histopathological data. Fischers discriminant analysis was applied to define functions capable of differentiating between the study groups (HCV, HCV/HTLV-1 and HCV/HTLV-2). The discriminant accuracy was evaluated by cross-validation. Alcohol consumption, use of intravenous drugs or inhaled cocaine and sexual partnership with intravenous drug users were more frequent in the HCV/HTLV-2 group, whereas patients in the HCV group more often reported abdominal pain or a sexual partner with hepatitis. Coinfected patients presented higher platelet counts, but aminotransferase and gamma-glutamyl transpeptidase levels were higher among HCV-infected subjects. No significant difference between the groups was seen regarding liver histopathological findings. Through discriminant analysis, classification functions were defined, including sex, age group, intravenous drug use and sexual partner with hepatitis. Cross-validation revealed high discriminant accuracy for the HCV group.

Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas

Zika virus (ZIKV) transmission in the Americas was first confirmed in May 2015 in Northeast Brazil1. Brazil has the highest number of reported ZIKV cases worldwide (>200,000 by 24 Dec 20162) as well as the greatest number of cases associated with microcephaly and other birth defects (2,366 confirmed cases by 31 Dec 20162). Following the initial detection of ZIKV in Brazil, 47 countries and territories in the Americas have reported local ZIKV transmission, with 22 of these reporting ZIKV-associated severe disease3. Yet the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of such information for interpreting past trends in reported microcephaly. To address this we generated 53 complete or partial ZIKV genomes, mostly from Brazil, including data generated by the ZiBRA project – a mobile genomics lab that travelled across Northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Joint analyses of viral genomes with ecological and epidemiological data estimate that the ZIKV epidemic first became established in NE Brazil by March 2014 and likely disseminated from there, both nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates of the international spread of ZIKV from Brazil coincide with periods of high vector suitability in recipient regions and indicate the duration of pre-detection cryptic transmission in those regions. NE Brazil’s role in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the virus’ basic reproduction number. One Sentence Summary Virus genomes reveal the establishment of Zika virus in Northeast Brazil and the Americas, and provide an appropriate timeframe for baseline (pre-Zika) microcephaly in different regions.

Poor sensitivity of rapid tests for the detection of antibodies to the hepatitis B virus: implications for field studies

Rapid tests (RTs) can be used as an alternative method for the conventional diagnosis of hepatitis B virus (HBV). This study aims to evaluate antibodies to HBsAg (anti-HBs) and antibodies to HBeAg (anti-HBe) RTs under different Brazilian settings. The following three groups were included: GI: viral hepatitis outpatient services; GII: low resource areas; and GIII: crack users and beauticians. Imuno-rápido anti-HBsAg™ and Imuno-rápido anti-HBeAg™ RTs were evaluated and showed specificities greater than 95% in all groups. The sensitivity values to anti-HBs were 50.38%, 51.05% and 46.73% and the sensitivity values to anti-HBe were 76.99%, 10.34% and 11.76% in the GI, GII and GIII groups, respectively. The assays had a low sensitivity and high specificity, which indicated their use for screening in regions endemic for HBV.

Recombination Located over 2A-2B Junction Ribosome Frameshifting Region of Saffold Cardiovirus

Here we report the nearly full-length genome of a recombinant Saffold virus strain (SAFV-BR-193) isolated from a child with acute gastroenteritis. Evolutionary analysis performed using all available near-full length Saffold picornavirus genomes showed that the breakpoint found in the Brazilian strain (SAFV-BR-193) is indeed a recombination hotspot. Notably, this hotspot is located just one nucleotide after the ribosomal frameshift GGUUUUU motif in the SAFV genome. Empirical studies will be necessary to determine if this motif also affects the binding affinity of RNA-dependent RNA-polymerase (RdRp) and therefore increases the changes of RdRp swap between molecules during the synthesis of viral genomes.

Wuhan large pig roundworm virus identified in human feces in Brazil

We report here the complete genome sequence of a bipartite virus, herein denoted WLPRV/human/BRA/TO-34/201, from a sample collected in 2015 from a two-year-old child in Brazil presenting acute gastroenteritis. The virus has 98–99% identity (segments 2 and 1, respectively) with the Wuhan large pig roundworm virus (unclassified RNA virus) that was recently discovered in the stomachs of pigs from China. This is the first report of a Wuhan large pig roundworm virus detected in human specimens, and the second genome described worldwide. However, the generation of more sequence data and further functional studies are required to fully understand the ecology, epidemiology, and evolution of this new unclassified virus.

Near full length genome of a recombinant (E/D) cosavirus strain from a rural area in the central region of Brazil

In the present article we report the nearly full length genome of a Cosavirus strain (BRTO-83) isolated from a child with acute gastroenteritis, and who is an inhabitant of a rural area in the central region of Brazil. The sample was previously screened and negative for both: common enteric viruses (i.e. rotavirus and norovirus), bacteria, endoparasites and helminthes. Evolutionary analysis and phylogenetic inferences indicated that the Brazilian BRTO-83 Cosavirus strain was a recombinant virus highly related to the E/D recombinant NG385 strain (Genbank JN867757), which was isolated in Nigeria from an acute flaccid paralysis patient. This is the first report of a recombinant E/D Cosavirus strain detected in Brazil, and the second genome described worldwide. Further surveillance and molecular studies are required to fully understand the epidemiology, distribution and evolution of the Cosavirus.

Rapid diagnosis of Zika virus through saliva and urine by Loop-mediated isothermal amplification (LAMP)

ABSTRACT Background: Zika virus (ZIKV) is a single-stranded RNA virus and member of the Flaviviridae family. Recent studies have reported that saliva can be an important alternative to detect ZIKV. Saliva requires less processing than blood greatly simplifying the assay. Loop-mediated Isothermal Amplification (LAMP) is a rapid assay that detects nucleic acids, including ZIKV RNA. Aim: The aim of this study was to evaluate the efficacy of saliva and urine to diagnose ZIKV infection in subjects during the acute phase, through ZIKV RNA detection by LAMP. Method: A total of 131 samples (68 saliva and 63 urine samples) from 69 subjects in the acute phase of ZIKV infection, and confirmed positive for ZIKV by blood analysis through real time-PCR, were collected and analyzed by Reverse Transcriptase Loop-mediated Isothermal Amplification (RT-LAMP). Results: From the 68 saliva samples, 45 (66.2%) were positive for ZIKV with an average time to positivity (Tp) of 13.5 min, and from the 63 urine samples, 25 (39.7%) were positive with the average Tp of 15.8 min. Saliva detected more samples (p = 0.0042) and had faster Tp (p = 0.0176) as compared with urine. Conclusion: Saliva proved to be a feasible alternative to diagnose ZIKV infection during the acute phase by LAMP.

Determination of hepatitis B, C and D prevalence among urban and Amerindian populations from the Eastern Brazilian Amazon: a cross sectional study

BackgroundThis study was conducted to determine the prevalence of HBV, HCV, and HDV in urban populations and Amerindians living in the state of Tocantins (Eastern Amazon).MethodsA total of 948 individuals were recruited in Tocantinopolis city (Tocantins state) of whom 603 were Amerindians (from 6 tribes) and 345 were non-Amerindians (6 urban areas of Tocantinópolis city). Anti-HCV, HBsAg, anti-HBc, anti-HBs, anti-HBc IgM, anti-HBe, HBeAg, and anti-delta antibodies were determined using enzyme immunoassay.ResultsHBV cleared infection (both anti-HBc/anti-HBs+), chronic inactive/immune controlled HBV infection (anti-HBc + only), previous HBV vaccination (anti-HBs + only), active HBV infection (HBsAg+), individuals susceptible to HBV, and anti-HCV reactivity were found in 12.9, 1.8, 27.2, 0.5, 57.7, 1.2% in Amerindians and 12.1, 2.0, 37.1, 0.3, 55.4, 0.3% in non-Amerindians respectively. Out of 139 anti-HBc reactive individuals, 70 were anti-HBe reactive and none presented HBeAg or anti-HBc IgM. Anti-HBc prevalence was associated to older age (p < 0.0001). Overall anti-Delta prevalence was 0.3% and regarding anti-HBc reactive individuals, anti-delta prevalence was 3.4 and 0% in Amerindians and non-Amerindians respectively.ConclusionsOverall low prevalence of HBV and HCV infection was found in the populations studied, but high HBV and HCV prevalence was observed in Amerindians compared to non-Amerindians suggesting that these individuals have a higher likelihood of acquiring to these infections. Anti-delta antibodies were found among Amerindians from Eastern Amazon suggesting a risk for this population. Of note is that nearly half of Amerindians had no anti-HBs, indicating a need for HBV vaccination campaigns in this population.