Genetic variability of human immunodeficiency virus‐1 in Bahia state,Northeast, Brazil: High diversity of HIV genotypes

The HIV‐1 genetic variability in Bahia state, Brazil, was investigated. DNA samples from 229 and 213 HIV‐1‐infected individuals were analyzed using the heteroduplex mobility assay (HMA) in gag and env fragments, respectively. One hundred seventy‐five samples were characterized in both genes. Thirty‐two subtype F and BF recombinant viruses were sequenced and analyzed by phylogenetic methods. The combination of HMA and sequencing results showed that seven different HIV‐1 genotypes comprised this sample: 147 (84%) B/B, 4 (2.3%) F/F, 3 (1.7%) B/F, 1 (0.6%) F/B, 1 (0.6%) F/D, 1 (0.6%) BF/F, and 18 (10.3%) BF/B. A significant divergence was observed between these two techniques results (84.4%). This is explained by the low accuracy of the HMA for detecting recombinant viruses. These recombinants were unrelated to CRF12, while two sequences were related to CRF28 and CRF29. Nineteen BF mosaics shared the same gag breakpoint. In conclusion, the use of HMA may be inappropriate in regions where different subtypes are co‐circulating. Subtype B is the most common genotype, however, an increased prevalence (13.1%) of different BF variants and a potentially new CRF suggest that recombination is occurring frequently in Bahia. These viruses were associated with women infected heterosexually. Finally, this study identified the presence of an F/D recombinant HIV‐1 in Brazil. J. Med. Virol. 81:391–399, 2009. © 2009 Wiley‐Liss, Inc.     

Polymorphism of the capsid L1 gene of human papillomavirus types 31, 33, and 35

The L1 gene encodes for the major capsid protein of human papillomaviruses (HPV). There is limited information on the polymorphism of L1 for types related to HPV‐16. This report explores the polymorphism of L1 in phylogenetically related types 31, 33, and 35 compared to HPV‐16. Genital specimens collected from 732 HIV‐seropositive and 323 HIV‐seronegative women were screened for HPV DNA with consensus L1 PCR. Cervical samples positive for HPV‐16 (n = 74), HPV‐31 (n = 78), HPV‐33 (n = 37), and HPV‐35 (n = 58) were further characterized by PCR‐sequencing of the complete L1 gene. The number of nucleotide substitutions within L1 ranged from 19 for HPV‐33 to 52 for HPV‐31. The ratio of the number of variants/number of isolates tested was higher for HPV‐31 (56.4%, P = 0.05) and HPV‐35 (60.3%, P = 0.04) compared to HPV‐16 (40.5%), while this ratio was lower for HPV‐33 (24.3%), although not significantly (P = 0.14). The maximal distance between HPV variants was greater in the five putative surface‐exposed loops of L1 than in sequences outside the loops (P < 0.01). Synonymous variations were encountered in 1.7% (95% CI 1.1–2.3) of nucleotides inside the L1 loops and 2.4% (95% CI1.2–3.7) of nucleotides outside the L1 loops. Non‐synonymous variations were encountered in 1.8% (95% CI 1.1–2.5) of nucleotides within the L1 loops and 0.2% (95% CI 0–0.4) of nucleotides outside the loops. dN/dS ratios were below 1.0 in extra‐loop and intra‐loop regions, but they were lower in extra‐loop regions. These results suggest that sequences within and outside the hypervariable loops of L1 were under selective constraint. J. Med. Virol. 82: 1168–1178, 2010. © 2010 Wiley‐Liss, Inc.     

A study of the genetic variability of human respiratory syncytial virus in Croatia, 2006–2008

Human respiratory syncytial virus (HRSV) is a common etiological agent of acute lower respiratory tract disease in infants. The molecular epidemiology of HRSV in Croatia over four consecutive seasons (from 2006 to 2008) was investigated. A total of 72 HRSV samples were chosen from 696 screened cases in a pediatric clinic in Zagreb. Molecular characterization of HRSV revealed the predominance of HRSV group B viruses in the first two epidemic seasons and HRSV group A viruses in the next two seasons. According to the phylogenetic analysis, NA1 and BA9 were the predominant circulating HRSV genotypes detected during the study. Overall, 82.9% of all HRSV A strains belonged to the NA1 genotype. The HRSV B genotype BA9, detected in two consecutive seasons (2006 and 2007), was the predominant circulating HRSV B genotype, accounting for 80.6% of all HRSV B strains. This study provides data on the circulation pattern of HRSV genotypes in Croatia and their molecular characterization. J. Med. Virol. 84:1985–1992, 2012. © 2012 Wiley Periodicals, Inc.     

E6 and E7 variants of human papillomavirus‐16 and ‐52 in Japan,the Philippines,and Vietnam

Human papillomavirus (HPV) has several intragenotypic variants with different geographical and ethnic distributions. This study aimed to elucidate the distribution patterns of E6 and E7 (E6/E7) intragenotypic variants of HPV type 16 (HPV‐16), which is most common worldwide, and HPV‐52, which is common in Asian countries such as Japan, the Philippines, and Vietnam. In previous studies, genomic DNA samples extracted from cervical swabs were collected from female sex workers in these three countries and found to be positive for HPV‐16 or HPV‐52. Samples were amplified further for their E6/E7 genes using type‐specific primers and analyzed genetically. Seventy‐nine HPV‐16 E6/E7 genes were analyzed successfully and grouped into three lineages: European (Prototype), European (Asian), and African‐2. The prevalences of HPV‐16 European (Prototype)/European (Asian) lineages were 19.4%/80.6% (n = 31) in Japan, 75.0%/20.8% (n = 24) in the Philippines, and 0%/95.8% (n = 24) in Vietnam. The 109 HPV‐52 E6/E7 genes analyzed successfully were grouped into four lineages, A–D; the prevalences of lineages A/B/C/D were, respectively, 5.1%/92.3%/0%/2.6% in Japan (n = 39), 34.4%/62.5%/0%/3.1% in the Philippines (n = 32), and 15.8%/73.7%/7.9%/2.6% in Vietnam (n = 38). The distribution patterns of HPV‐16 and HPV‐52 lineages in these countries differed significantly (P < 0.000001 and P = 0.0048, respectively). There was no significant relationship between abnormal cervical cytology and either HPV‐16 E6/E7 lineages or specific amino acid mutations, such as E6 D25E, E6 L83V, and E7 N29S. Analysis of HPV‐16 and HPV‐52 E6/E7 genes can be a useful molecular‐epidemiological tool to distinguish geographical diffusion routes of these HPV types in Asia. J. Med. Virol. 85: 1069–1076, 2013. © 2013 Wiley Periodicals, Inc.     

Genetic analysis of human immunodeficiency virus type 1 nef in Portugal: subtyping, identification of mosaic genes, and amino acid sequence variability

Extending our previous genetic characterization of human immunodeficiency virus type 1 (HIV-1) strains circulating in Portugal, we here report the first phylogenetic and putative amino acid sequence variability analyses of nef accessory gene. Viral sequences (n = 53) were amplified by nested PCR from proviral DNA purified from peripheral blood mononuclear cells of HIV-1 infected individuals (n = 49). Phylogenetic inference analysis demonstrated a distribution of the viral sequences between subtypes A (sub-subtype A1), B, D, F (sub-subtype F1), G, H, and J, with subtypes G and B accounting altogether for more than half of the genotypes found. A significant number of the proviral DNA sequences analyzed (18.4%) were shown to correspond to intragenic nef recombinants, with the majority having the typical CRF02_AG nef structure. In addition, three novel intragenic recombinant structures were found (B/G/B, CRF02_AG/H, and D/G). From phylogenetic analysis, it was concluded that part of the non-recombinant nef genes might have actually been amplified from mosaic viruses: CRF06_cpx, CRF14_BG, and a new envA/nefJ recombinant. While comparing all the putative Nef sequences, significant amino acid sequence variability was observed. However, most of the described nef functional motifs were relatively well conserved in the majority of the sequences analyzed and numerous amino acid changes fell outside these regions. The results presented unambiguously endorse the high level of complexity of HIV-1 epidemics in Portugal.     

Clinical variability and genetic homogeneity of the camptodactyly‐arthropathy‐coxa vara‐pericarditis syndrome

The camptodactyly‐arthropathy‐coxa vara‐pericarditis syndrome (CACP) is an autosomal recessive condition characterized by the association of congenital or early onset camptodactyly and noninflammatory arthropathy with synovial hyperplasia. Progressive coxa vara deformity and/or noninflammatory pericardial or pleural effusions have been observed in some patients. Recently, the disease gene has been assigned to human chromosome region 1q25‐q31, and truncating mutations have been identified in the megakaryocyte stimulating factor gene. Studying 12 patients from 8 unrelated families, we emphasized hip and spine involvement, particularly in the course of the disease as shown in a 58‐year‐old patient. Despite clinical variability, linkage studies support genetic homogeneity of the disease. Am. J. Med. Genet. 95:233–236, 2000.     

Genetic heterogeneity and clinical variability in the Sanfilippo syndrome (types A, B, and C)

A study of 73 patients with the Sanfilippo syndrome (36 patients with Sanfilippo A disease, 23 with Sanfilippo B disease and 14 with Sanfilippo C disease) revealed both intertype and intratype variability. The course of the disease was relatively mild in Sanfilippo B disease and dementia was less severe. Type A showed earlier onset with more severe clinical manifestations and an earlier age at death. Sanfilippo C disease was slightly less severe than Sanfilippo A disease. The intratype variability may be explained in part by differences in genetic and environmental background. In Sanfilippo B disease, genetic heterogeneity is suggested by the observation of a more severe and a mild variant, and this variation may be due to the involvement of different allelic mutations. The intra-familial variability of the different types was small, but in three families with Sanfilippo B disease intrafamilial variability was evident.     

Epidemiology and genetic variability of human metapneumovirus during a 4‐year‐long study in Southeastern Brazil

Epidemiological and molecular characteristics of human metapneumovirus (hMPV) were compared with human respiratory syncytial virus (hRSV) in infants and young children admitted for acute lower respiratory tract infections in a prospective study during four consecutive years in subtropical Brazil. GeneScan polymerase chain assays (GeneScan RT‐PCR) were used to detect hMPV and hRSV in nasopharyngeal aspirates of 1,670 children during January 2003 to December 2006. hMPV and hRSV were detected, respectively, in 191 (11.4%) and in 702 (42%) of the children admitted with acute lower respiratory tract infections at the Sao Paulo University Hospital. Sequencing data of the hMPV F gene revealed that two groups of the virus, each divided into two subgroups, co‐circulated during three consecutive years. It was also shown that a clear dominance of genotype B1 occurred during the years 2004 and 2005, followed by genotype A2 during 2006. J. Med. Virol. 81:915–921, 2009. © 2009 Wiley‐Liss, Inc.     

Performance of the Abbott RealTime high‐risk HPV test in women with abnormal cervical cytology smears

HPV DNA testing is known to be much more sensitive than cytology, but less specific. A range of HPV and related tests in 858 women referred for colposcopy because of an abnormal smear were evaluated to compare the performances of these tests. This article compared the Abbott test to other tests which had been previously evaluated. This test was a real true test for 14 high‐risk HPV types. The Abbott test was found to be highly sensitive for cervical intraepithelial neoplasia grade 3 or worse (CIN3+) (98.9%) with a specificity of 31.5%. These numbers were comparable with the Qiagen HC2 test, the Roche Linear Array and Amplicor tests, and the Gen‐Probe APTIMA test. Differences between these tests appeared to be related mostly to the choice of cutoff level. An added feature of the Abbott test was the provision of type specific results for HPV 16 and 18. J. Med. Virol. 82: 1186–1191, 2010. © 2010 Wiley‐Liss, Inc.     

Prevalence of low‐risk and high‐risk types of human papillomavirus and other risk factors for HPV infection in Germany within different age groups in women up to 30 years of age: An epidemiological observational study

Human papillomavirus (HPV) infection is frequent in young women and persistent infection may lead to cervical cancer. Therefore, vaccination against HPV is recommended for young women in the age group from 12–17 years in Germany. However, epidemiological data on the prevalence of HPV types and risk factors for infection for younger women in Germany is scarce. To address this, an observational study was performed in Germany including 1,692 women aged 10–30 years. After a routine Pap smear, cervical swabs were tested for high‐risk and low‐risk HPV, respectively, using the Hybrid Capture 2 (HC2) test, and genotyped using the PCR‐based tests SPF₁₀/LiPA₂₅ and PapilloCheck®. In addition, the women were interviewed regarding their medical history and lifestyle factors. Three hundred seventy‐seven (22.28%) women had positive HC2 results. The proportion of HPV positive women was highest in the 20–22 age group with 28.3%. Predominant HPV types were HPV 16, 42, 51 and HPV 16, 51, 31 as defined by PapilloCheck® and SPF₁₀/LiPA₂₅, respectively. 95.8% of women did not show signs of any cervical lesion. Adjusted analysis identified number of sexual partners (OR:1.105; 95% CI:[1.069–1.142]), smoking (OR:1.508; [1.155–1.968]), and vaccination against HPV (OR:0.589; [0.398–0.872]) rather than increasing age as risk associated with HPV infection. Comparison of the genotyping assays showed that they correspond well regarding the high‐risk HPV types but less well for low‐risk HPV types. This epidemiological study shows that high‐risk HPV infection is common in young women in Germany. According to our data, vaccination of young women could have a potential impact on the prevention of HPV infection and cervical disease. J. Med. Virol. 82:1928–1939, 2010. © 2010 Wiley‐Liss, Inc.     

Genetic analysis of hepatitis A virus outbreak in France confirms the co-circulation of subgenotypes Ia, Ib and reveals a new genetic lineage

Genetic analysis of selected genome regions of hepatitis A Virus (HAV) suggested that distinct genotype could be defined in different geographic locations. In order to study the degree of genetic variability among HAV isolated during a single epidemic outbreak, sequences from a 148 base pair segment within the VP1 amino terminal region were obtained for eight distinct HAV isolates from an outbreak that occurred in North Bretagne (France). These sequences were compared among themselves and with published sequences from 30 different strains that represented different HAV sub-genotypes that were isolated all over the world. Phylogenetic analysis revealed an extensive genetic heterogeneity among strains belonging to the same outbreak and revealed co-circulation of sub-genotype IA, IB, and the presence of IIIA sub-genotype for the first time in a Mediterranean country.