Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes

<p>Abstract</p> <p>Background</p> <p>Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are related human tumor viruses that cause primary effusion lymphomas (PEL) and Burkitt's lymphomas (BL), respectively. Viral genes expressed in naturally-infected cancer cells contribute to disease pathogenesis; knowing which viral genes are expressed is critical in understanding how these viruses cause cancer. To evaluate the expression of viral genes, we used high-resolution separation and mass spectrometry coupled with custom tiling arrays to align the viral proteomes and transcriptomes of three PEL and two BL cell lines under latent and lytic culture conditions.</p> <p>Results</p> <p>The majority of viral genes were efficiently detected at the transcript and/or protein level on manipulating the viral life cycle. Overall the correlation of expressed viral proteins and transcripts was highly complementary in both validating and providing orthogonal data with latent/lytic viral gene expression. Our approach also identified novel viral genes in both KSHV and EBV, and extends viral genome annotation. Several previously uncharacterized genes were validated at both transcript and protein levels.</p> <p>Conclusions</p> <p>This systems biology approach coupling proteome and transcriptome measurements provides a comprehensive view of viral gene expression that could not have been attained using each methodology independently. Detection of viral proteins in combination with viral transcripts is a potentially powerful method for establishing virus-disease relationships.</p

High human cytomegalovirus loads and diverse linked variable genotypes in both HIV-1 infected and exposed, but uninfected, children in Africa.

Human cytomegalovirus, HCMV, was analysed using real-time quantitative PCR in symptomatic or asymptomatic pediatric cohorts from HIV-1 infected, exposed (HIV-1+ mothers), or uninfected groups in Zambia, an HIV-1/AIDS endemic region of Africa. HCMV infections were identified in 94% samples from HIV-1+ respiratory pediatric mortalities, 50% with high DNA loads of 10(3)-10(8) copies/10(6) cells. In comparison, HCMV viremia with high DNA loads, indicative of acute infections, were in 10% hospitalised febrile infants, with 50% HIV-1+. Whereas high sera loads were in 1% of asymptomatic infants, with 2% HIV-1+, and higher levels in both HIV-1 infected or exposed, but negative infants. All 8 linked-hypervariable glycoprotein gN-gO genotypes were shown, including identification of a new gN4d group with gO5 linkage (previously only Merlin reference strain), and samples with multiple infections. Overall, this shows global genotypes in Africa (unlike some herpesviruses) and acute pediatric HCMV infections in both HIV-1+ plus exposed, but uninfected infants, an emerging group

Improving influenza surveillance in sub-Saharan Africa

PROBLEM: Little is known about the burden of influenza in sub-Saharan Africa. Routine influenza surveillance is key to getting a better understanding of the impact of acute respiratory infections on sub-Saharan African populations. APPROACH: A project known as Strengthening Influenza Sentinel Surveillance in Africa (SISA) was launched in Angola, Cameroon, Ghana, Nigeria, Rwanda, Senegal, Sierra Leone and Zambia to help improve influenza sentinel surveillance, including both epidemiological and virological data collection, and to develop routine national, regional and international reporting mechanisms. These countries received technical support through remote supervision and onsite visits. Consultants worked closely with health ministries, the World Health Organization, national influenza laboratories and other stakeholders involved in influenza surveillance LOCAL SETTING: Influenza surveillance systems in the target countries were in different stages of development when SISA was launched. Senegal, for instance, had conducted virological surveillance for years, whereas Sierra Leone had no surveillance activity at all. RELEVANT CHANGES: Working documents such as national surveillance protocols and procedures were developed or updated and training for sentinel site staff and data managers was organized. LESSONS LEARNT: Targeted support to countries can help them strengthen national influenza surveillance, but long-term sustainability can only be achieved with external funding and strong national government leadership