Influenza virus A (H1 and H3) and B co-circulation among patient presenting with acute respiratory tract infection in Ibadan, Nigeria

Background: Influenza is an acute respiratory disease that continues to cause global epidemics and pandemics in human with significant mortality and morbidity. Objectives: This study was designed to identify the circulating influenza virus in Ibadan, Nigeria during the 2006/2007 season. Methods: Throat swab samples were collected from patients presenting with acute respiratory tract infection at the Out-Patient Departments of major hospitals in Ibadan over a period of seven months from November 2006 to May 2007. Isolation of influenza virus was performed using Madin-Darby Canine Kidney cell line and 10 days old chicken embryonated egg. Isolates was identified by haemagglutination and haemagglutination-inhibition assays using selected CDC Influenza reference antisera (A, B, subtype H1 and H3). Results: Out of 128 patients tested, 21(16.4%) yielded positive for virus isolation. Identification of the isolates showed that 19(14.8%) were positive for influenza virus out of which 11(8.6%) and 8(6.2%) were influenza A and B viruses respectively. Influenza A virus 6(4.7%) were subtype H1; 4(3.1%) were co-subtype H1 and H3; and 1(0.8%) was not inhibited by subtype H1 and H3. Conclusion: The circulation of influenza virus A and B in this study is important to contributing knowledge and data to influenza epidemiology and surveillance in Nigeria

Technology in Massachusetts Schools, 2004-2005

BACKGROUND:ATCC HIV-1 drug resistance test kit was designed to detect HIV-1 drug resistance (HIVDR) mutations in the protease and reverse transcriptase genes for all HIV-1 group M subtypes and circulating recombinant forms. The test has been validated for both plasma and dried blood spot specimen types with viral load (VL) of ≥1000 copies/ml. We performed an in-country assessment on the kit to determine the genotyping sensitivity and its accuracy in detecting HIVDR mutations using plasma samples stored under suboptimal conditions. METHODS:Among 572 samples with VL ≥1000 copies/ml that had been genotyped by ViroSeq assay, 183 were randomly selected, including 85 successful genotyped and 98 unsuccessful genotyped samples. They were tested with ATCC kits following the manufacturer's instructions. Sequence identity and HIVDR patterns were analysed with Stanford University HIV Drug Resistance HIVdb program. RESULTS:Of the 183 samples, 127 (69.4%) were successfully genotyped by either method. While ViroSeq system genotyped 85/183 (46.5%) with median VL of 32,971 (IQR: 11,150-96,506) copies/ml, ATCC genotyped 115/183 (62.8%) samples with median VL of 23,068 (IQR: 7,397-86,086) copies/ml. Of the 98 unsuccessful genotyped samples with ViroSeq assay, 42 (42.9%) samples with lower median VL of 13,906 (IQR: 6,122-72,329) copies/ml were successfully genotyped using ATCC. Sequence identity analysis revealed that the sequences generated by both methods were >98% identical and yielded similar HIVDR profiles at individual patient level. CONCLUSION:This study confirms that ATCC kit showed greater sensitivity in genotyping plasma samples stored in suboptimal conditions experiencing frequent and prolonged power outage. Thus, it is more sensitive particularly for subtypes A and A/G HIV-1 in resource-limited settings

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

Determinants of knowledge associated with occupational hazards and perceived health problems among dye workers in Abeokuta, Nigeria

Background. Identification of potential hazards, their adverse health effects and predisposing factors in the workplace are critical to improving safety. The objective of the study was to assess the knowledge of occupational hazards, prevalence of perceived health problems and their predictors among textile dye workers in Abeokuta Nigeria who work in unsupervised settings. Methods. In this cross-sectional study, data was collected from 199 participants using a validated semi-structured interviewer-administered questionnaire. Multiple linear regression analysis was used to determine the predictors of knowledge while Pearson Chi-square was employed to test association between perceived health problems, sociodemographic and work environment characteristics. Results. The mean age of the respondents was 40 (SD=12) years with average work experience of 19 years. Majority of respondents 139 (69.8%) had lower than average scores on knowledge of 25 questions on chemical hazards. There was no correlation between knowledge score and work experience (p= 0.492) or age (p=0.462) but knowledge was significantly associated with exposure score (p=0.004), gender (p=0.002) and adherence to instructions on chemicals usage (p=0.041) after adjusting for safe practice. The most frequent health problems among the dye workers were respiratory disorder (53.8%), allergies (51.8%) and skin disorders (24.1%). Airborne gaseous pollutants from mixing of chemicals was associated with allergies (p=0.045), circulatory (p=0.02) and skin disorders (p=0.049) while air-borne textile fibre /dye particles could predict allergies (p=0.028). Conclusion. Findings revealed that exposure, gender and adherence to instruction labels on dye/chemical containers could determine knowledge of chemical hazards while physical work environment characteristics could determine health problems

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