Phylogenetic analysis of the emergence of main hepatitis C virus subtypes in São Paulo, Brazil

Nishiya, Anna S.; Almeida‐Neto, Cesar de; Romano, Camila Malta; Alencar, Cecília Salete; Ferreira, Suzete Cleusa; Di-Lorenzo-Oliveira, Claudia; Levi, José Eduardo; Salles, Nanci Alves; Mendrone‐Júnior, Alfredo; Sabino, Éster Cerdeira

doi:10.1016/j.bjid.2015.06.010

Cited by 7 publications

(7 citation statements)

References 46 publications

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“…The current data also corroborates a prior study that used a phylogenetic model to infer the timing for the introduction of specific HCV genotypes in Brazil [28]. According to the Time to Most Recent Common Ancestor (TMRCA) as inferred by Bayesian analysis, G1B entered in Brazil around the year 1923 (1844-1967), whereas G3 entered in 1967 (1955-1980), and G1A in 1979 (1967-1987).…”

Section: Discussionsupporting

confidence: 85%

HCV genotype profile in Brazil of mono-infected and HIV co-infected individuals: A survey representative of an entire country

et al. 2020

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Introduction To be eligible for government-provided treatment in Brazil, all HCV-infected individuals are required to be genotyped shortly after diagnosis. We describe the HCV genotype (G) profiles by geographic region, gender, age and HIV co-infection. Methods We assessed 29,071 genotypes collected from HCV-infected individuals from March 2016 to March 2018 (Abbott Real-Time HCV Genotype). We randomly selected 12,336 samples for HIV co-infection testing using an EIA rapid test kit (TR DPP HIV 1/2 Bio-Manguinhos). Descriptive statistical analyses were performed using R. Results Overall, HCV genotype distribution was 40.9% G1A, 30.2% G1B, 23.8% G3, 3.8% G2, 0.7% G4, 0.1% G5 and 0.6% with multiples genotypes. G1A prevalence was 44.4% among males and 35.8% among females. G1B and G2 were more prevalent in older individuals than G1A and G3. G3 was more prevalent in the South region. Of samples tested for HIV co-infection, 15% were HIV+. Median age among HCV/HIV co-infected individuals was 50 years old compared to 57 years old among mono-infected individuals. Distinct HCV genotype prevalence between HCV/HIV co-infected and HCV mono-infected individuals were respectively: G1A 60.6% versus 37.8%, G1B 15.2% versus 32.9%, and G3 18.9% versus 24.7%. G4 was detected among co-infected young men (3.5% versus 0.2% among monoinfected).

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Section: Discussionsupporting

confidence: 85%

HCV genotype profile in Brazil of mono-infected and HIV co-infected individuals: A survey representative of an entire country

et al. 2020

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“…In the latter study, the only sequence from Australia, and 3 sequences from United States, all branched out at about 1950, as did other sequences from Denmark, Italy, China and New Zealand. Two other studies from South America that used partial 3a sequences from Brazil, placed the tMRCA around 1967-1979, which is considerably more recent [4,28].…”

Section: Discussionmentioning

confidence: 99%

“…The epidemic of genotype 3a has also been examined in previous studies [4,15,28,29], including 2 that used full-length genomes [15,29]. However, for both of these previous studies, <50 full-length 3a sequences were available from across the globe with very few or no sequences from United States and Australia.…”

Section: Discussionmentioning

confidence: 99%

Historical Trends in the Hepatitis C Virus Epidemics in North America and Australia

Rodrigo¹,

Eltahla²,

Bull³

et al. 2016

J Infect Dis.

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Background. Bayesian evolutionary analysis (coalescent analysis) based on genetic sequences has been used to describe the origins and spread of rapidly mutating RNA viruses, such as influenza, Ebola, human immunodeficiency virus (HIV), and hepatitis C virus (HCV).Methods. Full-length subtype 1a and 3a sequences from early HCV infections from the International Collaborative of Incident HIV and Hepatitis C in Injecting Cohorts (InC3), as well as from public databases from a time window of 1977-2012, were used in a coalescent analysis with BEAST software to estimate the origin and progression of the HCV epidemics in Australia and North America. Convergent temporal trends were sought via independent epidemiological modeling.Results. The epidemic of subtype 3a had more recent origins (around 1950) than subtype 1a (around 1920) in both continents. In both modeling approaches and in both continents, the epidemics underwent exponential growth between 1955 and 1975, which then stabilized in the late 20th century.Conclusions. Historical events that fuelled the emergence and spread of injecting drug use, such as the advent of intravenous medical therapies and devices, and growth in the heroin trade, as well as population mixing during armed conflicts, were likely drivers for the cross-continental spread of the HCV epidemics.

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“…Genotype 1b seems to be the first to entry in this country, resulting from multiple introductions in different geographic areas over the years. 13 Local HCV 1b lineages comprises a total of seven highly supported clades (BR1b_I to BR1b_VII), endorsing its greater variation compared with other genotypes such as 1a and 3. 14 In this study, a substantial heterogeneity in genotype 1b was seen in both analysis of nucleotide diversity and amino acid substitutions in predefined residues of NS3 region.…”

Section: Discussionmentioning

confidence: 96%

“…In Brazil, HCV genotype dissemination followed a dynamic and complex pattern. Genotype 1b seems to be the first to entry in this country, resulting from multiple introductions in different geographic areas over the years . Local HCV 1b lineages comprises a total of seven highly supported clades (BR1b_I to BR1b_VII), endorsing its greater variation compared with other genotypes such as 1a and 3 .…”

Section: Discussionmentioning

confidence: 98%

Characterization of clinical predictors of naturally occurring NS3/NS4A protease polymorphism in genotype 1 hepatitis C virus mono and HIV co‐infected patients

Neto

Malta

Gomes‐Gouvêa

et al. 2017

Journal of Medical Virology

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Spontaneously occurring resistance may impair the success of protease inhibitors based regimens in HCV treatment. This study aimed to evaluate associations between amino acid substitutions in NS3/NS4A domain and clinical features of 247 HCV mono or HCV/HIV co-infected patients. Fourteen samples (5.7%) harbored at least one resistance-associated substitution (RAS). The following RASs were detected in NS3 region: T54S (6-2.4%), V55A (7-2.8%), and Q80R (2-0.8%). S122G occurred in 86.9% of HCV genotype 1b samples with either natural polymorphisms or RASs. Advanced liver fibrosis and HIV co-infection were not related to NS3/NS4A amino acid substitutions.

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Phylogenetic analysis of the emergence of main hepatitis C virus subtypes in São Paulo, Brazil

Cited by 7 publications

References 46 publications

HCV genotype profile in Brazil of mono-infected and HIV co-infected individuals: A survey representative of an entire country

HCV genotype profile in Brazil of mono-infected and HIV co-infected individuals: A survey representative of an entire country

Historical Trends in the Hepatitis C Virus Epidemics in North America and Australia

Characterization of clinical predictors of naturally occurring NS3/NS4A protease polymorphism in genotype 1 hepatitis C virus mono and HIV co‐infected patients

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