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13 results on '"Oramisi, Violet"'

1. The COVID-19 pandemic and disruptions to essential health services in Kenya: a retrospective time-series analysis

Author

Cosmas, Leonard, Gatheca, Gladwell, Kiarie, James, Soe, Khaing, Munyao, Oliver, Gathiti, Zipporah, Maina, Lucy, Godana, Adano, Muthee, Rose, Onyango, Brian, Langat, Chirchir, Wangari, Claudine, Sadia, Christine, Onyango, Joyce, Kimanga, Davies, Nyangasi, Mary, Otieno, David, Kamau, Peter, Cheburet, Samuel, Kibet, Sergon, Gitau, Shikoh, Kiarie, Helen, Temmerman, Marleen, Nyamai, Mutono, Liku, Nzisa, Thuo, Wangari, Oramisi, Violet, Nyaga, Lilly, Karimi, Janette, Wamalwa, Phidelis, Mwenda, Valerian, Ombajo, Loice Achieng, and Thumbi, S M

Published
2022
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4. Uptake and effect of universal test-and-treat on twelve months retention and initial virologic suppression in routine HIV program in Kenya

Author

Kimanga, Davies O., primary, Oramisi, Violet A., additional, Hassan, Amin S., additional, Mugambi, Mary K., additional, Miruka, Frederick O., additional, Muthoka, Kennedy J., additional, Odhiambo, Jacob O., additional, Yegon, Peter K., additional, Omoro, Gonza O., additional, Mbaire, Catherine, additional, Masamaro, Kenneth M., additional, Njogo, Susan M., additional, Barker, Joseph L, additional, and Ngugi, Catherine N., additional

Published
2022
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5. The COVID-19 pandemic and disruptions to essential health services in Kenya: a retrospective time-series analysis

Author

Kiarie, Helen, primary, Temmerman, Marleen, additional, Nyamai, Mutono, additional, Liku, Nzisa, additional, Thuo, Wangari, additional, Oramisi, Violet, additional, Nyaga, Lilly, additional, Karimi, Janette, additional, Wamalwa, Phidelis, additional, Gatheca, Gladwell, additional, Mwenda, Valerian, additional, Ombajo, Loice Achieng, additional, Thumbi, S M, additional, Cosmas, Leonard, additional, Kiarie, James, additional, Soe, Khaing, additional, Munyao, Oliver, additional, Gathiti, Zipporah, additional, Maina, Lucy, additional, Godana, Adano, additional, Muthee, Rose, additional, Onyango, Brian, additional, Langat, Chirchir, additional, Wangari, Claudine, additional, Sadia, Christine, additional, Onyango, Joyce, additional, Kimanga, Davies, additional, Nyangasi, Mary, additional, Otieno, David, additional, Kamau, Peter, additional, Cheburet, Samuel, additional, Kibet, Sergon, additional, and Gitau, Shikoh, additional

Published
2022
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6. Prevalence of Hepatitis B Virus Infection in Kenya: A Study Nested in the Kenya Population-Based HIV Impact Assessment 2018

Author

Ondondo, Rahael, primary, Muthusi, Jacques, additional, Oramisi, Violet, additional, Kimani, Daniel, additional, Ochwoto, Missiani, additional, Young, Peter Wesley, additional, Ngugi, Catherine, additional, Waruru, Anthony, additional, Mwangi, Jane, additional, Chao, Ann, additional, Bronson, Megan A., additional, Dobbs, Trudy, additional, Ng’ang’a, Lucy, additional, Bowen, Nancy, additional, Aoko, Appolonia, additional, Armstrong, Paige A., additional, Aman, Rashid, additional, and Bulterys, Marc, additional

Published
2022
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9. COVID-19 Pandemic and Disruptions in Essential Health Services in Kenya

Author

Kiarie, Helen, primary, Temmerman, Marleen, additional, Mutono, Nyamai, additional, Liku, Nzisa, additional, Thuo, Wangari, additional, Oramisi, Violet, additional, Nyaga, Lillian, additional, Karimi, Janette, additional, Wamalwa, Phidelis, additional, Gatheca, Gladwell, additional, Mwenda, Valerian, additional, Group, MEHS Data & M&E Sub Working, additional, Ombajo, Loice Achieng, additional, and Thumbi, SM, additional

Published
2021
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10. From sequence data to patient result: a solution for HIV drug resistance genotyping with Exatype, end to end software for Pol-HIV-1 Sanger based Sequence analysis and patient HIV drug resistance result generation

Author

Kingwara, Leonard, primary, Karanja, Muthoni, additional, Ngugi, Catherine, additional, Kangogo, Geoffrey, additional, Bera, Kipkerich, additional, Kimani, Maureen, additional, Bowen, Nancy, additional, Abuya, Dorcus, additional, Oramisi, Violet, additional, and Mukui, Irene, additional

Published
2020
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11. From sequence data to patient result: a solution for HIV drug resistance genotyping with Exatype, end to end software for Pol-HIV-1 Sequence analysis and patient HIV drug resistance result generation

Author

King’wara, Leonard, primary, Karanja, Muthoni, additional, Ngugi, Catherine, additional, Kangogo, Geoffrey, additional, Bera, Kipkerich, additional, Kimani, Maureen, additional, Bowen, Nancy, additional, Abuya, Dorcas, additional, Oramisi, Violet, additional, and Mukui, Irene, additional

Published
2020
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13. From Sequence Data to Patient Result: A Solution for HIV Drug Resistance Genotyping With Exatype, End to End Software for Pol-HIV-1 Sanger Based Sequence Analysis and Patient HIV Drug Resistance Result Generation.

Author

Kingwara, Leonard, Karanja, Muthoni, Ngugi, Catherine, Kangogo, Geoffrey, Bera, Kipkerich, Kimani, Maureen, Bowen, Nancy, Abuya, Dorcus, Oramisi, Violet, and Mukui, Irene

Abstract

Introduction: With the rapid scale-up of antiretroviral therapy (ART) to treat HIV infection, there are ongoing concerns regarding probable emergence and transmission of HIV drug resistance (HIVDR) mutations. This scale-up has to lead to an increased need for routine HIVDR testing to inform the clinical decision on a regimen switch. Although the majority of wet laboratory processes are standardized, slow, labor-intensive data transfer and subjective manual sequence interpretation steps are still required to finalize and release patient results. We thus set out to validate the applicability of a software package to generate HIVDR patient results from raw sequence data independently.Methods: We assessed the performance characteristics of Hyrax Bioscience's Exatype (a sequence data to patient result, fully automated sequence analysis software, which consolidates RECall, MEGA X and the Stanford HIV database) against the standard method (RECall and Stanford database). Exatype is a web-based HIV Drug resistance bioinformatic pipeline available at sanger.exatype.com. To validate the exatype, we used a test set of 135 remnant HIV viral load samples at the National HIV Reference Laboratory (NHRL).Result: We analyzed, and successfully generated results of 126 sequences out of 135 specimens by both Standard and Exatype software. Result production using Exatype required minimal hands-on time in comparison to the Standard (6 computation-hours using the standard method versus 1.5 Exatype computation-hours). Concordance between the 2 systems was 99.8% for 311,227 bases compared. 99.7% of the 0.2% discordant bases, were attributed to nucleotide mixtures as a result of the sequence editing in Recall. Both methods identified similar (99.1%) critical antiretroviral resistance-associated mutations resulting in a 99.2% concordance of resistance susceptibility interpretations. The Base-calling comparison between the 2 methods had Cohen's kappa (0.97 to 0.99), implying an almost perfect agreement with minimal base calling variation. On a predefined dataset, RECall editing displayed the highest probability to score mixtures accurately 1 vs. 0.71 and the lowest chance to inaccurately assign mixtures to pure nucleotides (0.002-0.0008). This advantage is attributable to the manual sequence editing in RECall.Conclusion: The reduction in hands-on time needed is a benefit when using the Exatype HIV DR sequence analysis platform and result generation tool. There is a minimal difference in base calling between Exatype and standard methods. Although the discrepancy has minimal impact on drug resistance interpretation, allowance of sequence editing in Exatype as RECall can significantly improve its performance. [ABSTRACT FROM AUTHOR]

Published
2020
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