Molecular characterisation of genital human papillomavirus among women in Southwestern, Nigeria.

BACKGROUND:Persistent infections with high-risk genital Human papillomavirus (HPV) especially types 16 and 18, are associated with cervical cancer. However, distribution of HPV types varies greatly across geographical regions and the available vaccines target only few types. This study was designed to determine the HPV types circulating in Southwestern Nigeria, thereby providing necessary information for effective control of the virus. METHODS:Endocervical swab samples were collected from a total of 295 consenting women attending routine cervical cancer screening, STI clinics and community-based outreach programme. Viral DNA was extracted from the samples and the consensus region of the HPV DNA was amplified by PCR using GP-E6/E7 primers. Type-specific nested multiplex PCR and Sanger sequencing were used to genotype the HPV isolates. RESULTS:In this study, 51 (17.3%) individuals were positive for HPV DNA using consensus primers that target the E6/E7 genes but only 48 (16.3%) were genotyped. A total of 15 HPV types (HPV-6, 16, 18, 31, 33, 35, 42, 43, 44, 52, 58, 66, 74, 81, 86) were detected, with HPV-31 being the most predominant (32.8%), followed by HPV-35 (17.2%) and HPV-16 (15.5%). Two rare HPV types; 74 and 86 were also detected. The HPV-74 isolate had three nucleotide (CCT) insertions at E7 gene that translated into amino acid proline. Highest nucleotide substitutions (n = 32) were found in HPV-44 genotype. Among positive individuals, 20.8% had dual infections and 86.2% had High-risk HPV types. CONCLUSIONS:Multiple Human papillomavirus types co-circulated in the study. Most of the circulating Human papillomavirus are high-risk type with type 31 being the most predominant. Although the implication of HPV-74 with proline insertion detected for the first time is unknown, it may have effect on the transformation potential of the virus. Polyvalent HPV vaccine will be more effective for the infection control in Nigeria

Genetic diversity of human respiratory syncytial virus circulating among children in Ibadan, Nigeria.

Human respiratory syncytial virus (HRSV) is the most common viral cause of acute lower respiratory tract infections (LRTIs) in infants and young children however, without an effective vaccine licensed for human use till date. Information on the circulating genotypes of HRSV from regions with high-burden of infection is vital in the global efforts towards the development of protective vaccine. We report here the genotypes of HRSV circulating among children in Ibadan, the first of such from Nigeria.Nasopharyngeal and oropharyngeal swabs collected from 231 children presenting with respiratory infections in some health facilities for care as well as those attending immunization centers for routine vaccination in Ibadan, Nigeria were used for the study. The 2nd hypervariable (HVR2) region of the glycoprotein (G) gene of HRSV was amplified and sequenced using HRSV group specific primers. HRSV was detected in 41 out of the 231 samples. Thirty-three of the isolates were successfully subtyped(22 subtype A and 11 subtype B). Fourteen of the subtype A and all the subtype B were successfully sequenced and genotyped. Phylogenetic analysis showed that genotype ON1 with 72 nucleotide (nt) duplication was the major subgroup A virus (11 of 14) detected together with genotype NA2. All the HRSV subtype B detected belong to the BA genotype with characteristic 60nt duplication. The ON1 genotypes vary considerably from the prototype strain due to amino acid substitutions including T292I which has not been reported elsewhere. The NA2 genotypes have mutations on four antigenic sites within the HVR2relative to the prototype A2. In conclusion, three genotypes of HRSV were found circulating in Ibadan, Nigeria. Additional study that will include isolates from other parts of the country will be done to determine the extent of genotype diversity of HRSV circulating in Nigeria

Correction: Phylogenetic analysis of hepatitis C virus among HIV/ HCV co-infected patients in Nigeria.

[This corrects the article DOI: 10.1371/journal.pone.0210724.]

Polymorphisms and drug resistance analysis of HIV-1 isolates from patients on first line antiretroviral therapy (ART) in South-eastern Nigeria.

Acquisition of resistance mutations by HIV-1 isolates causes treatment failure among infected patients receiving antiretroviral therapy (ART). This study determined patterns of drug-resistance mutations (DRMs) among HIV-1 isolates from patients receiving first-line ART in South-eastern Nigeria. Blood samples were collected from HIV-1 infected patients accessing antiretroviral treatment centers at General Hospital Awo-Omamma, Imo state, State Hospital Asaba, Delta state and St Joseph's Catholic Hospital Adazi, Anambra state and used for HIV-1 DNA sequencing and phylogenetic analysis. DRMs were scored using combination of Stanford algorithm and the 2015 International Antiviral Society-USA list while drug susceptibility was predicted using Stanford algorithm. Twenty eight of the HIV-1 isolates were sequenced and identified as subtypes G (35.7%), CRF02_AG (57.1%) and unclassifiable, UG (7.1%). Major PI resistance-associated mutations were identified at two sites including M46L (16.7% of subtype G/UG) and V82L (6.3% of CRF02_AG). Minor PI resistance-associated mutations identified among subtype G/UG are L10V/I (8.3%) and K20I (100%) while L10V/I (50%), K20I (100%), L33F (6.3%) and N88D (6.3%) were identified among CRF02_AG. Other polymorphisms found include; I13V/A, E35Q, M36I/L, N37D/S/E/H, R57K/G, L63T/P/S/Q, C67E/S, H69K/R, K70R, V82I and L89M in the range of 28.6% to 100% among the different subtypes. Interpretation based on Stanford algorithm showed that Darunavir/ritonavir is the only regimen whose potency was not compromised by the circulating mutations. Identification of major and minor PI resistance mutations in this study underscores the need for drug resistance testing prior to initiation of second line antiretroviral therapy in Nigeria

Alignment of deduced amino acid sequences of 2^nd hypervariable region of HRSV-A strains.

<p><b>A)</b> Alignment of HRSV-A genotype ON1 sequences from different parts of the world. Alignments are shown and residues numbered relative to sequences of prototype ON1 strain ON67-1210A (GenBank accession no. JN257693). The strains from this study are highlighted. The country of isolation of other strains used in the alignment are also highlighted. Identical residues are indicated by dots and stop codons by asterisks. Potential N-glycosylation sites (N-X-T/S, where X is not a proline) are indicated by gray-shaded rectangles. Potential O-glycosylation sites of the prototype ON1 strain are indicated by unfilled circles, while black circles indicated the predicted O-glycosylation sites common in all Nigeria strains. Other predicted O- glycosylation sites, not found in all the strains in Nigeria are underlined. The two copies of the 23 amino acids duplicated sequences are framed by rectangles. <b>B)</b> Alignment of HRSV-A subtype NA2 from this study. Alignments are shown relative to the sequence of prototype strain A2 (GenBank accession number M11486). The identifier of strains from this study are highlighted. Residues are numbered relative to the amino acid sequences of prototype ON1 strain ON67-1210A (GenBank accession no. JN257693). Identical residues are indicated by dots, alignment gaps by dashes and stop codons by asterisks. Potential N-glycosylation sites (N-X-T/S, where X is not a proline) are indicated by shaded rectangles. Potential O-glycosylation sites of the prototype A2 strain were indicated by unfilled circles, while black circles indicated the predicted O-glycosylation sites in the Nigeria NA2 strains.</p

Phylogenetic tree of the second hypervariable region of the G gene of HRSV A.

<p>The genotypes represented by the reference strains are indicated before the strain ID with the country of isolation of the ON1 reference strains indicated next to the strain names. The genotypes circulating in Ibadan, Nigeria are indicated by solid triangles. Multiple sequences alignment and phylogenetic tree were constructed using Muscle and neighbor-joining algorithm in MEGA 5.05 software. Statistical significance of the tree topology was tested by 1000 bootstrap replication. Only bootstrap values above 70% are displayed at the nodes. Scale bar indicates nucleotide substitutions per site.</p

Amino acid alignments of the 2nd hypervariable region of the G protein from HRSV-B.

<p>Residues are numbered relative to the sequences of prototype BA4128/99B (GenBank accession number AY333364). Identical residues are indicated by dots; gaps are indicated by dash and stop codons by asterisks. The two copies of the duplicated 20-amino acids are framed by rectangles. Potential N-glycosylation sites (NXT/S, where X is not a proline) are indicated by shaded rectangles. Potential O-glycosylation sites of the prototype BA strain are indicated by unfilled circles, while black circles indicated the predicted O-glycosylation sites common to all Nigeria strains. Other predicted O–glycosylation sites that are not found in all the strains from Nigeria are underlined. The genotypes are shown on the right by brackets.</p

Original Article Occult HBV infection among a cohort of Nigerian adults

Objective: To determine markers of HBV infection and detect the presence of its occult infection in serum of a cohort of adult Nigerians. Methodology: The study involved 28 adult Nigerians with viral hepatitis (Group 1) and 28 apparently healthy adult Nigerians as controls (Group 2). Their sera were assayed for HBsAg, HBeAg, anti-HBe, anti-HBc, anti-HBs, and anti-HCV, while HBV DNA was determined in 15 patients with chronic hepatitis. Significance of differences between the patients and control subjects was assessed using Chi-square test at a 95 % confidence level. Results: Sero-detection of HBsAg, HBeAg, anti-HBe and anti-HBc was higher among the patients compared to the controls. HBV infection was diagnosed by HBsAg (89%) and a duo of HBsAg and anti-HBc (100%) among the patients. Similarly, eleven and four types of different patterns of HBV markers were observed among the respective groups. Anti-HBe (9.5%), anti-HBc (14.3%), and anti-HBs (9.5%) were detected among all the subjects who were sero-negative for HBsAg. HBV DNA was also detected in 86.7 % of the 15 patients with chronic hepatitis, while occult HBV infection was observed in 7.2 % of the patients and none (0%) of the controls, p &lt; 0.05. Furthermore, HCV infection occurred among subjects with all the different patterns of HBV markers, except those with occult HBV infection and natural immunity to HBV. Conclusion: This study shows that occult HBV infection is present among Nigerian adults and determination of HBsAg, anti-HBc, anti-HBe, and HBV DNA will assist in its detection