Evolution of genomes, host shifts and the geographic spread of SARS-CoV and related coronaviruses

Severe acute respiratory syndrome (SARS) is a novel human illness caused by a previously unrecognized coronavirus (CoV) termed SARS-CoV. There are conflicting reports on the animal reservoir of SARS-CoV. Many of the groups that argue carnivores are the original reservoir of SARS-CoV use a phylogeny to support their argument. However, the phylogenies in these studies often lack outgroup and rooting criteria necessary to determine the origins of SARS-CoV. Recently, SARS-CoV has been isolated from various species of Chiroptera from China (e.g., Rhinolophus sinicus) thus leading to reconsideration of the original reservoir of SARS-CoV. We evaluated the hypothesis that SARS-CoV isolated from Chiroptera are the original zoonotic source for SARS-CoV by sampling SARS-CoV and non-SARS-CoV from diverse hosts including Chiroptera, carnivores, artiodactyls and humans. Regardless of alignment parameters, optimality criteria, or isolate sampling, the resulting phylogenies clearly show that the SARS-CoV was transmitted to small carnivores well after the epidemic of SARS in humans that began in late 2002. The SARS-CoV isolates from small carnivores in Shenzhen markets form a terminal clade that emerged recently from within the radiation of human SARS-CoV. There is evidence of subsequent exchange of SARS-CoV between humans and carnivores. In addition SARS-CoV was transmitted independently from humans to farmed pigs (Sus scrofa). The position of SARS-CoV isolates from Chiroptera are basal to the SARS-CoV clade isolated from humans and carnivores. Although sequence data indicate that Chiroptera are a good candidate for the original reservoir of SARS-CoV, the structural biology of the spike protein of SARS-CoV isolated from Chiroptera suggests that these viruses are not able to interact with the human variant of the receptor of SARS-CoV, angiotensin-converting enzyme 2 (ACE2). In SARS-CoV study, both visually and statistically, labile genomic fragments and, putative key mutations of the spike protein that may be associated with host shifts. We display host shifts and candidate mutations on trees projected in virtual globes depicting the spread of SARS-CoV. These results suggest that more sampling of coronaviruses from diverse hosts, especially Chiroptera, carnivores and primates, will be required to understand the genomic and biochemical evolution of coronaviruses, including SARS-CoV.Fil: Janies, Daniel. Ohio State University; Estados UnidosFil: Habib, Farhat. Ohio State University; Estados UnidosFil: Alexandrov, Boyan. Ohio State University; Estados UnidosFil: Hill, Andrew. University of Colorado; Estados UnidosFil: Pol, Diego. Museo Paleontológico Egidio Feruglio; Argentina. Ohio State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Expectant management versus immediate treatment for low-grade cervical intraepithelial neoplasia

BACKGROUND: The optimal management strategy for women with low-grade biopsy-proven cervical intraepithelial neoplasia (CIN) is not clear. Our objective was to compare the effectiveness of regular colposcopic follow-up and treatment of progressive disease only versus immediate treatment. METHODS: Data were accrued between November 2000 and March 2006 for a noninferiority randomized clinical trial of 415 women with biopsy-proven grade 1 CIN from 8 Canadian and 2 Brazilian colposcopy clinics. Subjects were randomly assigned to either undergo immediate treatment with a loop electrical excision procedure (LEEP) or receive regular colposcopic follow-up for 18 months. The primary outcome was progression of disease to CIN 2 to 3 was based on histology obtained during 18 months of follow-up. Treatments were compared using differences of proportion with a 9% noninferiority margin. Analysis was conducted on the basis of intention-to-treat. RESULTS: An initial LEEP was performed on 179 women. Disease progression was found in 32. Easily controlled vaginal bleeding occurred in 16 (8.9%). During follow-up, disease progression was identified in 3 (1.7%) women in the immediate treatment arm and 9 (4.4%) in the colposcopic follow-up arm-a tolerable difference of 2.7% with 1-sided 95% confidence interval (CI) upper limit of 6.0%. Compliance with all 3 follow-up visits was 61% overall, but significantly worse in women ≥30 years of age (P <.05). CONCLUSIONS: The risk of progression to CIN grade 2 or 3 or cancer over 18 months was similar in the 2 treatment groups. In Canada and Brazil, follow-up for 18 months is a reasonable management strategy for women with persistent low-grade cytology who are found to have grade 1 CIN on referral for colposcopy and cervical biopsy. Cancer 2011. © 2010 American Cancer Society.The optimal management strategy for women with low-grade biopsy-proven cervical intraepithelial neoplasia (CIN) is not clear. Our objective was to compare the effectiveness of regular colposcopic follow-up and treatment of progressive disease only versus immediate treatment. METHODS: Data were accrued between November 2000 and March 2006 for a noninferiority randomized clinical trial of 415 women with biopsy-proven grade 1 CIN from 8 Canadian and 2 Brazilian colposcopy clinics. Subjects were randomly assigned to either undergo immediate treatment with a loop electrical excision procedure (LEEP) or receive regular colposcopic follow-up for 18 months. The primary outcome was progression of disease to CIN 2 to 3 was based on histology obtained during 18 months of follow-up. Treatments were compared using differences of proportion with a 9% noninferiority margin. Analysis was conducted on the basis of intention-to-treat. RESULTS: An initial LEEP was performed on 179 women. Disease progression was found in 32. Easily controlled vaginal bleeding occurred in 16 (8.9%). During follow-up, disease progression was identified in 3 (1.7%) women in the immediate treatment arm and 9 (4.4%) in the colposcopic follow-up arm-a tolerable difference of 2.7% with 1-sided 95% confidence interval (CI) upper limit of 6.0%. Compliance with all 3 follow-up visits was 61% overall, but significantly worse in women ≥30 years of age (P <.05). CONCLUSIONS: The risk of progression to CIN grade 2 or 3 or cancer over 18 months was similar in the 2 treatment groups. In Canada and Brazil, follow-up for 18 months is a reasonable management strategy for women with persistent low-grade cytology who are found to have grade 1 CIN on referral for colposcopy and cervical biopsy11771438144

Detection of Chlamydia trachomatis in genital swabs: comparison of commercial and in house amplification methods with culture

AIMS: To evaluate the sensitivity of the Roche Cobas, Roche Amplicor plate kit, ligase chain reaction (LCR), and an in house polymerase chain reaction (PCR) by titration of purified elementary bodies (EB) and also to test 245 urethral and endocervical specimens for Chlamydia trachomatis by the four assays as well as conventional culture. STUDY DESIGN: EB titrations were run in duplicate in each commercial assay and six times in the in house PCR. Clinical samples were aliquoted and tested by each assay and were considered positive if C trachomatis was detected by two or more separate tests or if the sample was either culture or immunofluorescence positive. Major outer membrane protein (MOMP) specific primers were used as a confirmatory assay for the in house PCR. RESULTS: The in house PCR, Roche Cobas Amplicor, LCR, and Amplicor plate kit gave detection limits of approximately 1, 1-2, 2, and 2-4 EBs respectively. By the criteria described above for definition of a C trachomatis positive result in clinical samples we identified 23 true positives among the 245 clinical specimens. The in house PCR detected all 23 giving a sensitivity of 100% and a specificity of 98%. The Roche Cobas Amplicor, Roche Amplicor plate kit, and LCR detected 21, 19, and 19 of these respectively giving sensitivities of 87.5%, 82%, and 82% respectively and specificities of 99.5%, 99%, and 100% respectively. The culture gave a sensitivity of 78% and specificity of 100%. CONCLUSION: All four amplification assays had a greater sensitivity than the culture used routinely in this laboratory. The in house plasmid PCR had the greatest sensitivity and when combined with confirmation by immunofluorescence detected the greatest number of positives. This increased sensitivity is likely to have been achieved by the use of a DNA purification step and of nested primers in the amplification stage and their combined use in routine diagnostic assays for chlamydia might increase the frequency of C trachomatis detections. However, this assay is much less user friendly than the two semiautomated commercial assays investigated in this study.