Molecular characteristic of HIV-1 CRF01_AE in Nanjing from 2015 to 2017

Li, Wei; Chu, Jinjin; Fan, Wei; He, Yan; Dong, Xiang; Ge, You; Ji, Yu; Musa, Taha Hussein; Cao, Shang; Ni, Qian; Wei, Ping; Li, Xiaoshan

doi:10.1016/j.meegid.2019.104038

Cited by 10 publications

(16 citation statements)

References 24 publications

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“…In addition, the number of new infections among those younger than 35 years had increased. Multiple sex partners and low rates of active HIV test were common among individuals infected with HIV‐1 CRF07_BC in Nanjing, consistent with our previous study 27 . These HIV risk behaviors continue to pose a great challenge to public health programs designed to reduce HIV incidence 28 …”

Section: Discussionsupporting

confidence: 86%

“…Multiple sex partners and low rates of active HIV test were common among individuals infected with HIV-1 CRF07_BC in Nanjing, consistent with our previous study. 27 These HIV risk behaviors continue to pose a great challenge to public health programs designed to reduce HIV incidence. 28 In this study, we performed a comprehensive phylodynamic analysis of CRF07_BC sequences from Nanjing.…”

Section: Discussionmentioning

confidence: 99%

“…HIV‐1 subtypes were determined based on branching topology, clustering and split the support of the analyzed sequences and their phylogenetic relationships with HIV‐1 reference sequences as described elsewhere 19 . The reference sequences were downloaded from Los Alamos HIV Databases based on the HIV‐BLAST online tools (http://www.hiv.lanl.gov/content/sequence/BASCI_BLAST/basic_blast.html), duplicate sequences were removed based on the sequence identifiers and accession numbers, and sequences with more than equal to 5% ambiguous nucleotides were excluded, as described in our previous work 20 . A total of 424 reference sequences were identified.…”

Section: Methodsmentioning

confidence: 99%

“…19 The reference sequences were downloaded from Los Alamos HIV Databases based on the HIV-BLAST online tools (www.hiv.lanl.gov/content/sequence/BASCI_BLAST/ basic_blast.html), duplicate sequences were removed based on the sequence identifiers and accession numbers, and sequences with more than equal to 5% ambiguous nucleotides were excluded, as described in our previous work. 20 A total of 424 reference sequences were identified. Nanjing sequences and reference sequences were aligned and manually edited using the CLUSTAL X 21 and BioEdit software version 7.2, 22 and the best substitution model was the general time-reversible substitution model with γ distributed rate variation among sites, which was estimated by MEGA X software package.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

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The evolutionary and transmission characteristic of HIV‐1 CRF07_BC in Nanjing, Jiangsu

et al. 2020

Journal of Medical Virology

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To understand the epidemiology, evolutionary and transmission characteristics of HIV‐1 CRF07_BC in Nanjing, China. One hundred and fifty‐nine patients with HIV‐1 CRF07_BC were recruited. DNA sequencing, phylogenetic analysis, and molecular transmission cluster analysis were conducted to determine the molecular epidemiology and evolutionary characteristics. Of these HIV‐1‐infected patients, 95.6% were male, and men who sex with men (76.7%) were the main transmission route. Only 34.0% of these cases were born in Nanjing, and most of them (64.8%) reported having multiple sex partners in the last 6 months. The maximum likelihood phylogenetic analyses of HIV‐1 CRF07_BC revealed two lineages. Overall, 67.3% of Nanjing sequences were connected to at least one other individual distributed in 11 clusters, and the average degree was 21.2 with range (1‐178). The clustered patients were more likely to be male. The time to a most recent common ancestor for the early HIV‐1 CRF07_BC circulating in Nanjing was estimated to be 1998.71[1997.36‐2001.07]. The mean estimated evolutionary rate for the epidemic cluster was slightly lower at 2.38[2.12‐2.65] × 10−3 per site per year with the relaxed exponential clock model. HIV‐1 CRF07_BC was transmitted into Nanjing more than 20 years ago from Yunnan and has become one of the most predominant subtypes with a higher evolutionary rate than before.

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Section: Discussionsupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Phylogenetic Analysismentioning

confidence: 99%

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The evolutionary and transmission characteristic of HIV‐1 CRF07_BC in Nanjing, Jiangsu

et al. 2020

Journal of Medical Virology

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“…Nanjing, the provincial capital city of Jiangsu Province, ranks in the top three of the cumulative number of reported HIV-infected patients in the whole province. Our previous study has indicated that CRF01_AE was the most prevalent strain in Nanjing (Li et al, 2019). However, a few studies have systematically investigated the molecular epidemiology features of CRF01_AE/B recombinants in Nanjing.…”

Section: Introductionmentioning

confidence: 99%

The Molecular Epidemiological and Immunological Characteristics of HIV-1 CRF01_AE/B Recombinants in Nanjing, China

Liu

et al. 2022

Front. Microbiol.

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Human immunodeficiency virus-type 1 (HIV-1) CRF01_AE/B recombinants are newly emerging strains that are spreading rapidly in Southern and Eastern China. This study aimed to elucidate the molecular epidemiological characteristics of HIV-1 CRF01_AE/B recombinants in Nanjing and to explore the impact of these novel strains on the immunological status. A total of 1,013 blood samples from newly diagnosed HIV-1-infected patients were collected in Nanjing from 2015 to 2019, among which 958 partial Pol sequences were sequenced successfully. We depicted the molecular epidemiological characteristics of CRF01_AE/B recombinants by the molecular evolutionary analysis, Bayesian system evolution analysis, and transmission network analysis. The generalized additive mixed model was applied to evaluate the CD4+ T-cell count change of CRF01_AE/B recombinants. The Kaplan–Meier analysis was performed to assess the time from combined antiretroviral therapy (cART) initiation to immune reconstruction. We have identified 102 CRF01_AE/B recombinants (102/958, 10.65%) in Nanjing, including CRF67_01B (45/102, 44.12%), CRF68_01B (35/102, 34.31%), and CRF55_01B (22/102, 12.57%). According to the Bayesian phylogenetic inference, CRF55_01B had a rapid decline stage during 2017–2019, while CRF67_01B and CRF68_01B have experienced a fast growth phase during 2014–2015 and then remained stable. We have constructed 83 transmission networks, in which three larger clusters were composed of CRF67_01B and CRF68_01B. CRF01_AE/B recombinants manifested a faster decrease rate of CD4+ T-cell count than CRF_07BC but similar to CRF01_AE. The probability of achieving immune reconstruction in CRF01_AE/B recombinants was lower than CRF07_BC in the subgroup of baseline CD4+ T-cell count at cART initiation <300 cells/μl. In summary, CRF67_01B and CRF68_01B were the major strains of CRF01_AE/B recombinants in Nanjing, which have formed large transmission clusters between Nanjing and other provinces. CRF01_AE/B recombinants might be associated with rapid disease progression and poor immune reconstruction. The continuous epidemiological monitoring of CRF01_AE/B recombinants should be highly emphasized.

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Characteristics of the different HIV-1 risk populations based on the genetic transmission network of the newly diagnosed HIV cases in Jiangsu, Eastern China

Zhou,

Lu,

Zhang

et al. 2023

Heliyon

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Molecular characteristic of HIV-1 CRF01_AE in Nanjing from 2015 to 2017

Cited by 10 publications

References 24 publications

The evolutionary and transmission characteristic of HIV‐1 CRF07_BC in Nanjing, Jiangsu

The evolutionary and transmission characteristic of HIV‐1 CRF07_BC in Nanjing, Jiangsu

The Molecular Epidemiological and Immunological Characteristics of HIV-1 CRF01_AE/B Recombinants in Nanjing, China

Characteristics of the different HIV-1 risk populations based on the genetic transmission network of the newly diagnosed HIV cases in Jiangsu, Eastern China

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