Phylogenetic Analysis of Human Immunodeficiency Virus Type 1 Subtype C Env gp120 Sequences Among Four Drug-Naive Families Following Subsequent Heterosexual and Vertical Transmissions

Duri, Kerina; Gumbo, Felicity Zvanyadza; Kristiansen, Knut; Mapingure, Munyaradzi; Munjoma, Marshall; Chirenje, Mike; Rusakaniko, Simbarashe; Stray‐Pedersen, Babill; Müller, Fredrik

doi:10.1089/aid.2011.0217

Cited by 3 publications

(2 citation statements)

References 77 publications

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“…Conversely, a predominant variant may have been transmitted multiple times over the course of breastfeeding but our analysis did not attempt to resolve this dynamic. Our findings are in line with previous reports investigating early and late HIV transmission from a mother to her infant [ 32 , 33 ].…”

Section: Discussionsupporting

confidence: 93%

Evidence of Long-Lived Founder Virus in Mother-to-Child HIV Transmission

et al. 2015

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Exposure of the infant’s gut to cell-associated and cell-free HIV-1 trafficking in breast milk (BM) remains a primary cause of mother-to-child transmission (MTCT). The mammary gland represents a unique environment for HIV-1 replication and host-virus interplay. We aimed to explore the origin of the virus transmitted during breastfeeding, and the link with quasi-species found in acellular and cellular fractions of breast-milk (BM) and in maternal plasma. The C2–V5 region of the env gene was amplified, cloned and sequenced from the RNA and DNA of BM, the RNA from the mother’s plasma (PLA) and the DNA from infant’s dried blood spot (DBS) in 11 post-natal mother-infant pairs. Sequences were assembled in Geneious, aligned in ClustalX, manually edited in SeAL and phylogenetic reconstruction was undertaken in PhyML and MrBayes. We estimated the timing of transmission (ETT) and reconstructed the time for the most recent common ancestor (TMRCA) of the infant in BEAST. Transmission of single quasi-species was observed in 9 of 11 cases. Phylogenetic analysis illustrated a BM transmission event by cell-free virus in 4 cases, and by cell-associated virus in 2 cases but could not be identified in the remaining 5 cases. Molecular clock estimates, of the infant ETT and TMRCA, corresponded well with the timing of transmission estimated by sequential infant DNA PCR in 10 of 11 children. The TMRCA of BM variants were estimated to emerge during gestation in 8 cases. We hypothesize that in the remaining cases, the breast was seeded with a long-lived lineage latently infecting resting T-cells. Our analysis illustrated the role of DNA and RNA virus in MTCT. We postulate that DNA archived viruses stem from latently infected quiescent T-cells within breast tissue and MTCT can be expected to continue, albeit at low levels, should interventions not effectively target these cells.

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Section: Discussionsupporting

confidence: 93%

Evidence of Long-Lived Founder Virus in Mother-to-Child HIV Transmission

et al. 2015

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“…There is a paucity of data on the phylodynamics of HET non-B subtype epidemics, particularly in endemic Third World settings (Table 1) [57,152,153]. Single T/F viruses were observed in 68% of subtype C primary infections from Botswana, similar to that observed for MSM cohorts [153].…”

Section: Transmission Patterns Of Idu and Heterosexual Epidemicsmentioning

confidence: 79%

Phylogenetic inferences on HIV-1 transmission

Brenner¹,

Wainberg²,

Roger

2013

Aids

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Association of the OAS3 rs1859330 G/A genetic polymorphism with severity of enterovirus-71 infection in Chinese Han children

Tan

Yang

et al. 2017

Arch Virol

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The 2'5'-oligoadenylate synthetase (OAS) is an interferon (IFN)-induced protein that plays an important role in the antiviral action of IFN, with OAS3 being one of the four OAS classes (OAS1, OAS2, OAS3, OASL). The effect of OAS on several infectious viral diseases has been reported; however, a study of the effect of OAS3 on enterovirus 71 (EV71) is lacking. The purpose of this study was to evaluate the association of the OAS3 rs1859330 G/A genetic polymorphism with susceptibility and severity of EV71 infection. We investigated 370 Chinese Han children with hand-foot-mouth disease (HFMD) (214 of which were mild cases while 156 were severe). An improved multiplex ligation detection reaction (iMLDR) technique was carried out to examine the genotype. The AA genotype distribution (p = 0.002) and A allele frequency (OR = 1.83, 95% CI 1.32-2.52, p < 0.001) of OAS3 rs1859330 in severe cases were significantly higher than in mild cases. When comparing the different genotypes in EV71-infected patients, there were statistical differences in relation to rash (p = 0.03), oral ulcers (p = 0.005), pathologic reflex (p = 0.003), WBC counts (p = 0.032), CRP (p = 0.024), BG concentrations (p = 0.029), ALT (p = 0.02), and EEG (p = 0.019). However, there were no differences in relation to age, gender, AST, CK-MB, CT/ MRI, as well as some symptoms and signs (e.g. duration of fever (days), headache, convulsions, consciousness disturbance, paralysis, sign of meningeal irritation). In the cerebrospinal fluid (CSF) of severe cases, there were no differences in the levels of white cells, protein, glucose, chloride, lymphocytes and monocytes between the different genotypes. The plasma levels of IFN-γ in EV71-infected patients were significantly higher than in the control group (p < 0.01). IFN-γ concentrations in severe cases were lower in A allele carriers (AA+GA) (118.5 ± 12.6pg/mL) than in GG homozygotes (152.6 ± 56.3pg/mL p < 0.05). These findings suggest that the OAS3 rs1859330 G/A genetic polymorphism is associated with the severity of EV-71 infection, and that the A allele is a risk factor for the development of severe EV71 infection.

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Phylogenetic Analysis of Human Immunodeficiency Virus Type 1 Subtype C Env gp120 Sequences Among Four Drug-Naive Families Following Subsequent Heterosexual and Vertical Transmissions

Cited by 3 publications

References 77 publications

Evidence of Long-Lived Founder Virus in Mother-to-Child HIV Transmission

Evidence of Long-Lived Founder Virus in Mother-to-Child HIV Transmission

Phylogenetic inferences on HIV-1 transmission

Association of the OAS3 rs1859330 G/A genetic polymorphism with severity of enterovirus-71 infection in Chinese Han children

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