WITHDRAWN: The evolutionary rate dynamically tracks changes in HIV-1 epidemics: Application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) genetic diversity, due to its high evolutionary rate, has long been identified as a main cause of problems in the development of an efficient HIV-1 vaccine. However, little is known about differences in evolutionary rate between different subtypes. In this study, we collected representative samples of the main epidemic subtypes and circulating recombinant forms (CRFs), namely, sub-subtype A1, subtypes B, C, D, and G, and CRFs 01_AE and 02_AG. We analyzed separate data sets for pol and env. We performed a Bayesian Markov chain Monte Carlo relaxed-clock phylogenetic analysis and applied a codon model to the resulting phylogenetic trees to estimate nonsynonymous (dN) and synonymous (dS) rates along each and every branch. We found important differences in the evolutionary rates of the different subtypes. These are due to differences not only in the dN rate but also in the dS rate, varying in roughly similar ways, indicating that these differences are caused by both different selective pressures (for dN rate) and the replication dynamics (for dS rate) (i.e., mutation rate or generation time) of the strains. CRF02_AG and subtype G had higher rates, while subtype D had lower dN and dS rates than the other subtypes. The dN/dS ratio estimates were also different, especially for the env gene, with subtype G showing the lowest dN/dS ratio of all subtypes.

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The identification of a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) among men who have sex with men in Jiangsu, China

Current HIV Research ◽

10.2174/1570162x18666201026143200 ◽

2020 ◽

Vol 18 ◽

Author(s):

Yin Yueqi ◽

Zhou Ying ◽

Lu Jing ◽

Guo Hongxiong ◽

Chen Jianshuang ◽

...

Keyword(s):

Maximum Likelihood ◽

Phylogenetic Trees ◽

Second Generation ◽

Emergency Situation ◽

The World ◽

Break Points ◽

Sex With Men ◽

Full Length Genome ◽

Virus Strains ◽

Hiv 1

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recently years. Objective: This study aimed to report on novel HIV-1 recombinants. Method: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints inner virus, which differed from any previously identified CRF and URF around the world. Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

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High intrapatient HIV-1 evolutionary rate is associated with CCR5-to-CXCR4 coreceptor switch

Infection Genetics and Evolution ◽

10.1016/j.meegid.2013.05.004 ◽

2013 ◽

Vol 19 ◽

pp. 369-377 ◽

Cited By ~ 12

Author(s):

Mattias Mild ◽

Rebecca R. Gray ◽

Anders Kvist ◽

Philippe Lemey ◽

Maureen M. Goodenow ◽

...

Keyword(s):

Evolutionary Rate ◽

Coreceptor Switch ◽

Cxcr4 Coreceptor ◽

Hiv 1

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Analysis of evolutionary rate of HIV-1 subtype B using blood donor samples in Japan

Virus Genes ◽

10.1007/s11262-018-1548-1 ◽

2018 ◽

Vol 54 (3) ◽

pp. 457-460 ◽

Cited By ~ 1

Author(s):

Naoya Shinohara ◽

Chieko Matsumoto ◽

Keiji Matsubayashi ◽

Tadashi Nagai ◽

Masahiro Satake

Keyword(s):

Blood Donor ◽

Evolutionary Rate ◽

Subtype B ◽

Hiv 1

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Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1

Infection Genetics and Evolution ◽

10.1016/j.meegid.2018.09.008 ◽

2018 ◽

Vol 66 ◽

pp. 43-47 ◽

Cited By ~ 1

Author(s):

Juan Á. Patiño-Galindo ◽

Francisco Domínguez ◽

María T. Cuevas ◽

Elena Delgado ◽

Mónica Sánchez ◽

...

Keyword(s):

Evolutionary Rate ◽

Scale Analysis ◽

Genome Scale ◽

Hiv 1

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Monitoring of HIV Drug Resistance Mutations in Newly Diagnosed Patients in Cyprus (2010–2012)

Open Forum Infectious Diseases ◽

10.1093/ofid/ofx163.1066 ◽

2017 ◽

Vol 4 (suppl_1) ◽

pp. S424-S424

Author(s):

Ioannis Demetriades

Keyword(s):

Drug Resistance ◽

Phylogenetic Trees ◽

Resistance Mutation ◽

Drug Resistance Mutation ◽

High Rate ◽

Resistance Testing ◽

Newly Diagnosed ◽

Resistance Mutations ◽

Subtype B ◽

Hiv 1

Abstract Background A molecular epidemiology study of HIV-1 infection was conducted in 100 HIV-1 diagnosed and untreated patients in Cyprus representing 65.4 percent of all the reported HIV-1 infections in Cyprus between 2010 and 2012. Methods Eighty-two patients were newly diagnosed (genotypic drug resistance testing within six months from diagnosis), and 18 patients were HIV-1 diagnosed for a longer period or the diagnosis date was unknown. Results Phylogenetic trees of the pol sequences obtained in this study with reference sequences indicated that subtypes B and A1 were the most common subtypes present and accounted for 41.0 and 19.0% respectively, followed by subtype C (7.0%), F1 (8.0%), CRF02_AG (4.0%), A2 (2.0%), other CRFs (7.0%) and unknown recombinant forms, URFs (12%). Most of newly-diagnosed study subjects were Cypriots (63%), males (78%) with median age 39 (Interquartile Range, IQR 33–48) reporting having sex with other men, MSM (51%). Conclusion A high rate of clustered transmission of subtype B drug-sensitive strains to reverse transcriptase and protease inhibitors was observed among MSM. Twenty-eight out of forty-one MSM study subjects (68.0%) infected were implicated in five transmission clusters, two of which are subtype A1 and three subtype B strains. The two largest MSM subtype B clusters included nine and eight Cypriot men, respectively, living in all major cities in Cyprus. There were only three newly diagnosed patients with transmitted drug resistant HIV-1 strains, one study subject from the United Kingdom infected with subtype B strain and one from Romania with subtype A2 strain, both with the PI drug resistance mutation M46L and one patient from Greece with subtype A1 strain with the NNRTI drug resistance mutation K103N. Disclosures All authors: No reported disclosures.

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P20-21 LB. Gene-to-gene differences in evolutionary rate between HIV-1 and natural SIV from sooty mangabeys: implications for vaccine tests in non-human primates

Retrovirology ◽

10.1186/1742-4690-6-s3-p425 ◽

2009 ◽

Vol 6 (S3) ◽

Author(s):

W Fischer ◽

C Apetrei ◽

BH Hahn ◽

NL Letvin ◽

GJ Nabel ◽

...

Keyword(s):

Evolutionary Rate ◽

Sooty Mangabeys ◽

Hiv 1

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Bayesian inference from incomplete longitudinal data: A simple method to quantify sensitivity to nonignorable dropout

Statistics in Medicine ◽

10.1002/sim.3655 ◽

2009 ◽

Vol 28 (22) ◽

pp. 2725-2747 ◽

Cited By ~ 12

Author(s):

Hui Xie

Keyword(s):

Bayesian Inference ◽

Longitudinal Data ◽

Simple Method ◽

Nonignorable Dropout

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Revealing the history of infectious disease epidemics through phylogenetic trees

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.1995.0088 ◽

1995 ◽

Vol 349 (1327) ◽

pp. 33-40 ◽

Cited By ~ 54

Keyword(s):

Phylogenetic Trees ◽

Viral Transmission ◽

Human Populations ◽

Viral Sequence ◽

Immunodeficiency Virus ◽

History Of ◽

The Difference ◽

Disease Epidemics ◽

Hiv 1

Phylogenetic trees play an increasing role in molecular epidemiology, where they have been used to understand the forces that shape patterns of viral sequence diversity. Phylogenetic trees can also be used to trace the dynamics of viral transmission within populations. Case studies document the worldwide spread of Human Immunodeficiency Virus type 1 (HIV -1) and hepatitis C virus (HCV). Despite similarities between these viruses, especially in their transmission routes, they are shown to have very different epidemiological histories. A possible reason for the difference is that HCV has coexisted longer with human populations.

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