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1. Neutralizing antibody correlate of protection against severe-critical COVID-19 in the ENSEMBLE single-dose Ad26.COV2.S vaccine efficacy trial

Author

Carpp, Lindsay N., Hyrien, Ollivier, Fong, Youyi, Benkeser, David, Roels, Sanne, Stieh, Daniel J., Van Dromme, Ilse, Van Roey, Griet A., Kenny, Avi, Huang, Ying, Carone, Marco, McDermott, Adrian B., Houchens, Christopher R., Martins, Karen, Jayashankar, Lakshmi, Castellino, Flora, Amoa-Awua, Obrimpong, Basappa, Manjula, Flach, Britta, Lin, Bob C., Moore, Christopher, Naisan, Mursal, Naqvi, Muhammed, Narpala, Sandeep, O’Connell, Sarah, Mueller, Allen, Serebryannyy, Leo, Castro, Mike, Wang, Jennifer, Petropoulos, Christos J., Luedtke, Alex, Lu, Yiwen, Yu, Chenchen, Juraska, Michal, Hejazi, Nima S., Wolfe, Daniel N., Sadoff, Jerald, Gray, Glenda E., Grinsztejn, Beatriz, Goepfert, Paul A., Bekker, Linda-Gail, Gaur, Aditya H., Veloso, Valdilea G., Randhawa, April K., Andrasik, Michele P., Hendriks, Jenny, Truyers, Carla, Vandebosch, An, Struyf, Frank, Schuitemaker, Hanneke, Douoguih, Macaya, Kublin, James G., Corey, Lawrence, Neuzil, Kathleen M., Follmann, Dean, Koup, Richard A., Donis, Ruben O., and Gilbert, Peter B.

Published
2024
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3. Human immunoglobulin gene allelic variation impacts germline-targeting vaccine priming

Author

deCamp, Allan C., Corcoran, Martin M., Fulp, William J., Willis, Jordan R., Cottrell, Christopher A., Bader, Daniel L. V., Kalyuzhniy, Oleksandr, Leggat, David J., Cohen, Kristen W., Hyrien, Ollivier, Menis, Sergey, Finak, Greg, Ballweber-Fleming, Lamar, Srikanth, Abhinaya, Plyler, Jason R., Rahaman, Farhad, Lombardo, Angela, Philiponis, Vincent, Whaley, Rachael E., Seese, Aaron, Brand, Joshua, Ruppel, Alexis M., Hoyland, Wesley, Mahoney, Celia R., Cagigi, Alberto, Taylor, Alison, Brown, David M., Ambrozak, David R., Sincomb, Troy, Mullen, Tina-Marie, Maenza, Janine, Kolokythas, Orpheus, Khati, Nadia, Bethony, Jeffrey, Roederer, Mario, Diemert, David, Koup, Richard A., Laufer, Dagna S., McElrath, Juliana M., McDermott, Adrian B., Karlsson Hedestam, Gunilla B., and Schief, William R.

Published
2024
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4. Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features

Author

Magaret, Craig A., Li, Li, deCamp, Allan C., Rolland, Morgane, Juraska, Michal, Williamson, Brian D., Ludwig, James, Molitor, Cindy, Benkeser, David, Luedtke, Alex, Simpkins, Brian, Heng, Fei, Sun, Yanqing, Carpp, Lindsay N., Bai, Hongjun, Dearlove, Bethany L., Giorgi, Elena E., Jongeneelen, Mandy, Brandenburg, Boerries, McCallum, Matthew, Bowen, John E., Veesler, David, Sadoff, Jerald, Gray, Glenda E., Roels, Sanne, Vandebosch, An, Stieh, Daniel J., Le Gars, Mathieu, Vingerhoets, Johan, Grinsztejn, Beatriz, Goepfert, Paul A., de Sousa, Leonardo Paiva, Silva, Mayara Secco Torres, Casapia, Martin, Losso, Marcelo H., Little, Susan J., Gaur, Aditya, Bekker, Linda-Gail, Garrett, Nigel, Truyers, Carla, Van Dromme, Ilse, Swann, Edith, Marovich, Mary A., Follmann, Dean, Neuzil, Kathleen M., Corey, Lawrence, Greninger, Alexander L., Roychoudhury, Pavitra, Hyrien, Ollivier, and Gilbert, Peter B.

Published
2024
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6. Mosaic HIV-1 vaccine regimen in southern African women (Imbokodo/HVTN 705/HPX2008): a randomised, double-blind, placebo-controlled, phase 2b trial

Author

Allagappen, Jon, Andriesen, Jessica, Ayres, Alison, Bekker, Linda-Gail, Borremans, Caroline, Brumskine, William, Chilengi, Roma, Dubula, Thozama, Garrett, Nigel, Gelderblom, Huub, Gill, Katherine, Hoosain, Zaheer, Hosseinipour, Mina, Hutter, Julia, Inambao, Mubiana, Innes, Craig, Kilembe, William, Kotze, Philippus, Kotze, Sheena, Laher, Fatima, Laszlo, Imre, Lazarus, Erica, Malahleha, Mookho, Mathebula, Matsontso, Matoga, Mitch, McClennen, Rachael, Mda, Pamela, Meerts, Peter, Naicker, Vimla, Naidoo, Logashvari, Philip, Tricia, Pitsi, Annah, Scheppler, Lorenz, Sopher, Carrie, Takuva, Simbarashe G., Viegas, Edna, Weijtens, Mo, Yuan, Olive, Gray, Glenda E, Mngadi, Kathryn, Lavreys, Ludo, Nijs, Steven, Gilbert, Peter B, Hural, John, Hyrien, Ollivier, Juraska, Michal, Luedtke, Alex, Mann, Philipp, McElrath, M Juliana, Odhiambo, Jackline A, Stieh, Daniel J, van Duijn, Janine, Takalani, Azwidihwi N, Willems, Wouter, Tapley, Asa, Tomaras, Georgia D, Van Hoof, Johan, Schuitemaker, Hanneke, Swann, Edith, Barouch, Dan H, Kublin, James G, Corey, Lawrence, Pau, Maria G, Buchbinder, Susan, and Tomaka, Frank

Published
2024
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7. Immune correlates analysis of the Imbokodo (HVTN 705/HPX2008) efficacy trial of a mosaic HIV-1 vaccine regimen evaluated in Southern African people assigned female sex at birth: a two-phase case-control study

Author

Allagappen, Jon, Andriesen, Jessica, Ayres, Alison, Baral, Saman, Bekker, Linda-Gail, Besethi, Asiphe, Borremans, Caroline, Braams, Esmee, Brackett, Caroline, Brumskine, William, Chilengi, Roma, Choi, Rachel, Dubula, Thozama, Dumas, Jaiden Seongmi, Dunn, Brooke, Etikala, Radhika, Euler, Zelda, Everett, Sarah, Garrett, Nigel, Gelderblom, Huub, Gill, Katherine, Gillespie, Kevin, Goedhart, Dimitri, Goosmann, Erik, Grant, Shannon, Hands, Ellie, Haynes, Barton, Herringer, Bronwill, Hoosain, Zaheer, Hosseinipour, Mina, Hunidzarira, Portia, Hutter, Julia, Inambao, Mubiana, Innes, Craig, Keyes, Taylor, Kilembe, William, Kotze, Philippus, Kotze, Sheena, Laher, Fatima, Laszlo, Imre, Lazarus, Erica, Liao, Hua-Xin, Lin, Yong, Lu, Helen, Lucas, Judith, Malahleha, Mookho, McNair, Tara, Meerts, Peter, Mgaga, Zinhle, Montlha, Mahlodi, Mosito, Boitumelo, Moultrie, Andrew, Mudrak, Sarah, Oriol-Mathieu, Valérie, Sarzotti-Kelsoe, Marcella, Mathebula, Matson Tso, Matoga, Mitch, McClennen, Rachael, Mda, Pamela, Naicker, Vimla, Naidoo, Logashvari, Okkers, Cindy-Ann, Omarjee, Saleha, Pasmans, Hella, Philip, Tricia, Pinter, Abraham, Pitsi, Annah, Ramos, Ornelia, Randhawa, April, Roels, Sanne, Rohith, Shamiska, Rutten, Lucy, Sadoff, Jerald, Salinas, Gabriela, Salzgeber, Yvonne, Scheppler, Lorenz, Schwedhelm, Katharine, Schuller, Nicolette, Sharak, Angelina, Stanfield-Oakley, Sherry, Sopher, Carrie, Tafatatha, Terence, Takuva, Simbarashe G., Tang, Chan, Vandebosch, An, Viegas, Edna, Voillet, Valentin, Wegmann, Frank, Weijtens, Mo, Wilcox, Stephany, Williams, Anthony, Yu, Chenchen, Yu, Pei-Chun, Yuan, Olive, Zhang, Xuehan, Kenny, Avi, van Duijn, Janine, Dintwe, One, Heptinstall, Jack, Burnham, Randy, Sawant, Sheetal, Zhang, Lu, Mielke, Dieter, Khuzwayo, Sharon, Omar, Faatima Laher, Goodman, Derrick, Fong, Youyi, Benkeser, David, Zou, Rodger, Hural, John, Hyrien, Ollivier, Juraska, Michal, Luedtke, Alex, van der Laan, Lars, Giorgi, Elena E., Magaret, Craig, Carpp, Lindsay N., Pattacini, Laura, van de Kerkhof, Tom, Korber, Bette, Willems, Wouter, Fisher, Leigh H., Schuitemaker, Hanneke, Swann, Edith, Kublin, James G., Pau, Maria G., Buchbinder, Susan, Tomaka, Frank, Nijs, Steven, Lavreys, Ludo, Gelderblom, Huub C., Corey, Lawrence, Mngadi, Kathryn, Gray, Glenda E., Borducchi, Erica, Hendriks, Jenny, Seaton, Kelly E., Zolla-Pazner, Susan, Barouch, Dan H., Ferrari, Guido, De Rosa, Stephen C., McElrath, M Juliana, Andersen-Nissen, Erica, Stieh, Daniel J., Tomaras, Georgia D., and Gilbert, Peter B.

Published
2024
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8. Safety and pharmacokinetics of VRC07-523LS administered via different routes and doses (HVTN 127/HPTN 087): A Phase I randomized clinical trial

Author

Walsh, Stephen R., Gay, Cynthia L., Karuna, Shelly T., Hyrien, Ollivier, Skalland, Timothy, Mayer, Kenneth H., Sobieszczyk, Magdalena E., Baden, Lindsey R., Goepfert, Paul A., del Rio, Carlos, Pantaleo, Guiseppe, Andrew, Philip, Karg, Carissa, He, Zonglin, Lu, Huiyin, Paez, Carmen A., Baumblatt, Jane A. G., Polakowski, Laura L., Chege, Wairimu, Anderson, Maija A., Janto, Sophie, Han, Xue, Huang, Yunda, Dumond, Julie, Ackerman, Margaret E., McDermott, Adrian B., Flach, Britta, Piwowar-Manning, Estelle, Seaton, Kelly, Tomaras, Georgia D., Montefiori, David C., Gama, Lucio, and Mascola, John R.

Subjects
AIDS vaccines -- Physiological aspects -- Dosage and administration, HIV infection -- Prevention, Biological sciences
Abstract

Background Broadly neutralizing antibodies (bnAbs) are a promising approach for HIV-1 prevention. In the Antibody Mediated Prevention (AMP) trials, a CD4-binding site targeting bnAb, VRC01, administered intravenously (IV), demonstrated 75% prevention efficacy against highly neutralization-sensitive viruses but was ineffective against less sensitive viruses. VRC07-523LS is a next-generation bnAb targeting the CD4-binding site and was engineered for increased neutralization breadth and half-life. We conducted a multicenter, randomized, partially blinded Phase I clinical trial to evaluate the safety and serum concentrations of VRC07-523LS, administered in multiple doses and routes to healthy adults without HIV. Methods and findings Participants were recruited between 2 February 2018 and 9 October 2018. A total of 124 participants were randomized to receive 5 VRC07-523LS administrations via IV (T1: 2.5 mg/kg, T2: 5 mg/kg, T3: 20 mg/kg), subcutaneous (SC) (T4: 2.5 mg/kg, T5: 5 mg/kg), or intramuscular (IM) (T6: 2.5 mg/kg or P6: placebo) routes at 4-month intervals. Participants and site staff were blinded to VRC07-523LS versus placebo for the IM group, while all other doses and routes were open-label. Safety data were collected for 144 weeks following the first administration. VRC07-523LS serum concentrations were measured by ELISA through Day 112 in all participants and by binding antibody multiplex assay (BAMA) thereafter in 60 participants (10 per treatment group) through Day 784. Compartmental population pharmacokinetic (PK) analyses were conducted to evaluate the VRC07-523LS serum PK. Neutralization activity was measured in a TZM-bl assay and antidrug antibodies (ADAs) were assayed using a tiered bridging assay testing strategy. Injections and infusions were well tolerated, with mild pain or tenderness reported commonly in the SC and IM groups, and mild to moderate erythema or induration reported commonly in the SC groups. Infusion reactions reported in 3 of 20 participants in the 20 mg/kg IV group. Peak geometric mean (GM) concentrations (95% confidence intervals [95% CIs]) following the first administration were 29.0 [mu]g/mL (25.2, 33.4), 58.5 [mu]g/mL (49.4, 69.3), and 257.2 [mu]g/mL (127.5, 518.9) in T1-T3 with IV dosing; 10.8 [mu]g/mL (8.8, 13.3) and 22.8 [mu]g/mL (20.1, 25.9) in T4-T5 with SC dosing; and 16.4 [mu]g/mL (14.7, 18.2) in T6 with IM dosing. Trough GM (95% CIs) concentrations immediately prior to the second administration were 3.4 [mu]g/mL (2.5, 4.6), 6.5 [mu]g/mL (5.6, 7.5), and 27.2 [mu]g/mL (23.9, 31.0) with IV dosing; 0.97 [mu]g/mL (0.65, 1.4) and 3.1 [mu]g/mL (2.2, 4.3) with SC dosing, and 2.6 [mu]g/mL (2.05, 3.31) with IM dosing. Peak VRC07-523LS serum concentrations increased linearly with the administered dose. At a given dose, peak and trough concentrations, as well as serum neutralization titers, were highest in the IV groups, reflecting the lower bioavailability following SC and IM administration. A single participant was found to have low titer ADA at a lone time point. VRC07-523LS has an estimated mean half-life of 42 days across all doses and routes (95% CI: 40.5, 43.5), over twice as long as VRC01 (15 days). Conclusions VRC07-523LS was safe and well tolerated across a range of doses and routes and is a promising long-acting bnAb for inclusion in HIV-1 prevention regimens. Trial registration ClinicalTrials.gov/ NCT03387150 (posted on 21 December 2017)., Author(s): Stephen R. Walsh 1,2,*, Cynthia L. Gay 3, Shelly T. Karuna 4, Ollivier Hyrien 4, Timothy Skalland 4, Kenneth H. Mayer 2,5, Magdalena E. Sobieszczyk 6, Lindsey R. Baden [...]

Published
2024
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9. Immune correlates analysis of the ENSEMBLE single Ad26.COV2.S dose vaccine efficacy clinical trial

Author

Fong, Youyi, McDermott, Adrian B., Benkeser, David, Roels, Sanne, Stieh, Daniel J., Vandebosch, An, Le Gars, Mathieu, Van Roey, Griet A., Houchens, Christopher R., Martins, Karen, Jayashankar, Lakshmi, Castellino, Flora, Amoa-Awua, Obrimpong, Basappa, Manjula, Flach, Britta, Lin, Bob C., Moore, Christopher, Naisan, Mursal, Naqvi, Muhammed, Narpala, Sandeep, O’Connell, Sarah, Mueller, Allen, Serebryannyy, Leo, Castro, Mike, Wang, Jennifer, Petropoulos, Christos J., Luedtke, Alex, Hyrien, Ollivier, Lu, Yiwen, Yu, Chenchen, Borate, Bhavesh, van der Laan, Lars W. P., Hejazi, Nima S., Kenny, Avi, Carone, Marco, Wolfe, Daniel N., Sadoff, Jerald, Gray, Glenda E., Grinsztejn, Beatriz, Goepfert, Paul A., Little, Susan J., Paiva de Sousa, Leonardo, Maboa, Rebone, Randhawa, April K., Andrasik, Michele P., Hendriks, Jenny, Truyers, Carla, Struyf, Frank, Schuitemaker, Hanneke, Douoguih, Macaya, Kublin, James G., Corey, Lawrence, Neuzil, Kathleen M., Carpp, Lindsay N., Follmann, Dean, Gilbert, Peter B., Koup, Richard A., and Donis, Ruben O.

Published
2022
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10. High-frequency home self-collection of capillary blood correlates IFI27 expression kinetics with SARS-CoV-2 viral clearance

Author

Lim, Fang Yun, Kim, Soo-Young, Kulkarni, Karisma N., Blazevic, Rachel L., Kimball, Louise E., Lea, Hannah G., Haack, Amanda J., Gower, Maia S., Stevens-Ayers, Terry, Starita, Lea M., Boeckh, Michael, Hyrien, Ollivier, Schiffer, Joshua T., Theberge, Ashleigh B., and Waghmare, Alpana

Subjects
Blood banks -- Health aspects, Health care industry
Abstract

To the Editor: Blood transcriptional profiling is a powerful tool to evaluate immune responses to infection; however, blood collection via traditional phlebotomy remains a barrier to precise characterization of the [...]

Published
2023

12. Subcritical multitype Markov branching processes with immigration generated by Poisson random measures.

Author

Slavtchova-Bojkova, Maroussia, Hyrien, Ollivier, and Yanev, Nikolay M.

Subjects
*RANDOM measures, *BRANCHING processes, *MARKOV processes, *EMIGRATION & immigration, *GAUSSIAN distribution
Abstract

We investigate multitype subcritical Markov branching processes with immigration driven by Poisson random measures. Limiting distributions are established for various rates of the Poisson measures when they are asymptotically equivalent to exponential or regularly varying functions. Results analogous to a strong LLN are proved, and limiting normal distributions are obtained when the local intensity of the Poisson measure increases with time. When it decreases, conditional limiting distributions are established. When the intensity converges to a constant, a stationary limiting distribution is obtained. The asymptotic behavior of the first and second moments of the processes is also investigated. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Neutralizing antibody responses over time in demographically and clinically diverse individuals recovered from SARS-CoV-2 infection in the United States and Peru: A cohort study

Author

Karuna, Shelly, Li, Shuying Sue, Grant, Shannon, Walsh, Stephen R., Frank, Ian, Casapia, Martin, Trahey, Meg, Hyrien, Ollivier, Fisher, Leigh, Miner, Maurine D., Randhawa, April K., Polakowski, Laura, Kublin, James G., Corey, Lawrence, and Montefiori, David

Subjects
Antigen-antibody reactions -- Health aspects, Immune response -- Health aspects, Biological sciences
Abstract

Background People infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) experience a wide range of clinical manifestations, from asymptomatic and mild illness to severe illness and death, influenced by age and a variety of comorbidities. Neutralizing antibodies (nAbs) are thought to be a primary immune defense against the virus. Large, diverse, well-characterized cohorts of convalescent individuals provide standardized values to benchmark nAb responses to past SARS-CoV-2 infection and define potentially protective levels of immunity. Methods and findings This analysis comprises an observational cohort of 329 HIV-seronegative adults in the United States (n = 167) and Peru (n = 162) convalescing from SARS-CoV-2 infection from May through October 2020. The mean age was 48 years (range 18 to 86), 54% of the cohort overall was Hispanic, and 34% identified as White. nAb titers were measured in serum by SARS-CoV-2.D614G Spike-pseudotyped virus infection of 293T/ACE2 cells. Multiple linear regression was applied to define associations between nAb titers and demographic variables, disease severity and time from infection or disease onset, and comorbidities within and across US and Peruvian cohorts over time. nAb titers peaked 28 to 42 days post-diagnosis and were higher in participants with a history of severe Coronavirus Disease 2019 (COVID-19) (p 55 years, male sex assigned at birth, and, in some cases, body mass index were also independently associated with higher nAb titers, whereas hypertension was independently associated with lower nAb titers. nAb titers did not differ by race, underlying pulmonary disease or smoking. Two months post-enrollment, nAb ID50 (ID80) titers declined 3.5 (2.8)-fold overall. Study limitations in this observational, convalescent cohort include survivorship bias and missing early viral loads and acute immune responses to correlate with the convalescent responses we observed. Conclusions In summary, in our cohort, nAb titers after SARS-CoV-2 infection peaked approximately 1 month post-diagnosis and varied by age, sex assigned at birth, disease severity, and underlying comorbidities. Our data show great heterogeneity in nAb responses among people with recent COVID-19, highlighting the challenges of interpreting natural history studies and gauging responses to vaccines and therapeutics among people with recent infection. Our observations illuminate potential correlations of demographic and clinical characteristics with nAb responses, a key element for protection from COVID-19, thus informing development and implementation of preventative and therapeutic strategies globally. Trial registration ClinicalTrials.gov NCT04403880., Author(s): Shelly Karuna 1,*, Shuying Sue Li 1, Shannon Grant 1, Stephen R. Walsh 2, Ian Frank 3, Martin Casapia 4, Meg Trahey 1, Ollivier Hyrien 1, Leigh Fisher 1, [...]

Published
2021
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27. Poisson random measures and supercritical multitype Markov branching processes.

Author

Slavtchova-Bojkova, Maroussia, Hyrien, Ollivier, and Yanev, Nikolay M.

Subjects
*RANDOM measures, *BRANCHING processes, *MARKOV processes, *CELL populations, *GAUSSIAN distribution, *CELLULAR evolution
Abstract

We consider multitype Markov branching processes with immigration occurring at time points generated by Poisson random measures. These models find applications to study evolution of multitype cell populations in which new cells join the population according to a time-varying immigration mechanism. The focus of this paper is the supercritical case. We investigate the limiting behavior of the process for different rates of the Poisson random measures. In particular, we prove a result analogous to a strong LLN and establish limiting normal distributions. [ABSTRACT FROM AUTHOR]

Published
2023
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28. Poisson Random Measures and Noncritical Multitype Markov Branching Processes

Author

Slavtchova-Bojkova, Maroussia N., Hyrien, Ollivier, and Yanev, Nikolay M.

Subjects
Poisson Measures, Immigration, Multitype Markov Branching Processes, Limiting Distributions
Abstract

We investigate noncritical multi-type Markov branching processes with immigration generated by Poisson measures. Limiting distributions are obtained when the rates of the Poisson measures are asymptotically equivalent to exponential or regularly varying functions. In particular, results analogous to a strong LLN are presented, and limiting normal distributions are obtained when the rates increase. When the rates decrease, then conditional limiting distributions are established. A stationary limiting distribution is obtained when the mean Poisson measure grows linearly. The asymptotic behaviour of the first and second moments of the processes is also investigated. NFSR of the Ministry of Education and Science of Bulgaria, grant No. KP–06-H22/3.

Published
2021

40. An international, interlaboratory ring trial confirms the feasibility of an extraction-less "direct" RT-qPCR method for reliable detection of SARS-CoV-2 RNA in clinical samples.

Author

Mills, Margaret G., Bruce, Emily, Huang, Meei-Li, Crothers, Jessica W., Hyrien, Ollivier, Oura, Christopher A. L., Blake, Lemar, Brown Jordan, Arianne, Hester, Susan, Wehmas, Leah, Mari, Bernard, Barby, Pascal, Lacoux, Caroline, Fassy, Julien, Vial, Pablo, Vial, Cecilia, Martinez, Jose R. W., Oladipo, Olusola Olalekan, Inuwa, Bitrus, and Shittu, Ismaila

Subjects
COVID-19, SARS-CoV-2, PATHOLOGICAL laboratories, POLYMERASE chain reaction, TESTING laboratories, RNA
Abstract

Reverse transcription–quantitative polymerase chain reaction (RT-qPCR) is used worldwide to test and trace the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). "Extraction-less" or "direct" real time–reverse transcription polymerase chain reaction (RT-PCR) is a transparent and accessible qualitative method for SARS-CoV-2 detection from nasopharyngeal or oral pharyngeal samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged 10 global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international interlaboratory ring trial. Participating laboratories were provided a common protocol, common reagents, aliquots of identical pooled clinical samples, and purified nucleic acids and used their existing in-house equipment. We observed 100% concordance across laboratories in the correct identification of all positive and negative samples, with highly similar cycle threshold values. The test also performed well when applied to locally collected patient nasopharyngeal samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that direct RT-PCR assay methods can be clearly translated across sites utilizing readily available equipment and expertise and are thus a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic. [ABSTRACT FROM AUTHOR]

Published
2022
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41. A Deferred-Vaccination Design to Assess Durability of COVID-19 Vaccine Effect After the Placebo Group Is Vaccinated.

Author

Follmann, Dean, Fintzi, Jonathan, Fay, Michael P., Janes, Holly E., Baden, Lindsey R., El Sahly, Hana M., Fleming, Thomas R., Mehrotra, Devan V., Carpp, Lindsay N., Juraska, Michal, Benkeser, David, Donnell, Deborah, Fong, Youyi, Han, Shu, Hirsch, Ian, Huang, Ying, Huang, Yunda, Hyrien, Ollivier, Luedtke, Alex, and Carone, Marco

Subjects
COVID-19 vaccines, VACCINATION, VACCINE effectiveness, PLACEBOS, VACCINE trials
Abstract

Multiple candidate vaccines to prevent COVID-19 have entered large-scale phase 3 placebo-controlled randomized clinical trials, and several have demonstrated substantial short-term efficacy. At some point after demonstration of substantial efficacy, placebo recipients should be offered the efficacious vaccine from their trial, which will occur before longer-term efficacy and safety are known. The absence of a placebo group could compromise assessment of longer-term vaccine effects. However, by continuing follow-up after vaccination of the placebo group, this study shows that placebo-controlled vaccine efficacy can be mathematically derived by assuming that the benefit of vaccination over time has the same profile for the original vaccine recipients and the original placebo recipients after their vaccination. Although this derivation provides less precise estimates than would be obtained by a standard trial where the placebo group remains unvaccinated, this proposed approach allows estimation of longer-term effect, including durability of vaccine efficacy and whether the vaccine eventually becomes harmful for some. Deferred vaccination, if done open-label, may lead to riskier behavior in the unblinded original vaccine group, confounding estimates of long-term vaccine efficacy. Hence, deferred vaccination via blinded crossover, where the vaccine group receives placebo and vice versa, would be the preferred way to assess vaccine durability and potential delayed harm. Deferred vaccination allows placebo recipients timely access to the vaccine when it would no longer be proper to maintain them on placebo, yet still allows important insights about immunologic and clinical effectiveness over time. [ABSTRACT FROM AUTHOR]

Published
2021
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42. SARS-CoV-2 Viral Load in the Nasopharynx at Time of First Infection Among Unvaccinated Individuals: A Secondary Cross-Protocol Analysis of 4 Randomized Trials.

Author

Fisher, Leigh H., Kee, Jia Jin, Liu, Albert, Espinosa, Claudia M., Randhawa, April K., Ludwig, James, Magaret, Craig A., Robinson, Samuel T., Gilbert, Peter B., Hyrien, Ollivier, Kublin, James G., Rouphael, Nadine, Falsey, Ann R., Sobieszczyk, Magdalena E., El Sahly, Hana M., Grinsztejn, Beatriz, Gray, Glenda E., Kotloff, Karen L., Gay, Cynthia L., and Leav, Brett

Published
2024
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43. An age-dependent branching process model for the analysis of CFSE-labeling experiments

Author

Zand Martin S, Chen Rui, and Hyrien Ollivier

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background Over the past decade, flow cytometric CFSE-labeling experiments have gained considerable popularity among experimentalists, especially immunologists and hematologists, for studying the processes of cell proliferation and cell death. Several mathematical models have been presented in the literature to describe cell kinetics during these experiments. Results We propose a multi-type age-dependent branching process to model the temporal development of populations of cells subject to division and death during CFSE-labeling experiments. We discuss practical implementation of the proposed model; we investigate a competing risk version of the process; and we identify the classes of cellular dependencies that may influence the expectation of the process and those that do not. An application is presented where we study the proliferation of human CD8+ T lymphocytes using our model and a competing risk branching process. Conclusions The proposed model offers a widely applicable approach to the analysis of CFSE-labeling experiments. The model fitted very well our experimental data. It provided reasonable estimates of cell kinetics parameters as well as meaningful insights into the processes of cell division and cell death. In contrast, the competing risk branching process could not describe the kinetics of CD8+ T cells. This suggested that the decision of cell division or cell death may be made early in the cell cycle if not in preceding generations. Also, we show that analyses based on the proposed model are robust with respect to cross-sectional dependencies and to dependencies between fates of linearly filiated cells. Reviewers This article was reviewed by Marek Kimmel, Wai-Yuan Tan and Peter Olofsson.

Published
2010
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45. Clinical Endpoints for Evaluating Efficacy in COVID-19 Vaccine Trials.

Author

Mehrotra, Devan V., Janes, Holly E., Fleming, Thomas R., Annunziato, Paula W., Neuzil, Kathleen M., Carpp, Lindsay N., Benkeser, David, Brown, Elizabeth R., Carone, Marco, Cho, Iksung, Donnell, Deborah, Fay, Michael P., Fong, Youyi, Han, Shu, Hirsch, Ian, Huang, Ying, Huang, Yunda, Hyrien, Ollivier, Juraska, Michal, and Luedtke, Alex

Subjects
COVID-19, COVID-19 vaccines, VACCINE trials, VACCINE effectiveness, SARS-CoV-2
Abstract

Several vaccine candidates to protect against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or coronavirus disease 2019 (COVID-19) have entered or will soon enter large-scale, phase 3, placebo-controlled randomized clinical trials. To facilitate harmonized evaluation and comparison of the efficacy of these vaccines, a general set of clinical endpoints is proposed, along with considerations to guide the selection of the primary endpoints on the basis of clinical and statistical reasoning. The plausibility that vaccine protection against symptomatic COVID-19 could be accompanied by a shift toward more SARS-CoV-2 infections that are asymptomatic is highlighted, as well as the potential implications of such a shift. [ABSTRACT FROM AUTHOR]

Published
2021
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48. Lp Microlocal Supercritical Markov Branching Processes with Non-Homogeneous Poisson Immigration

Author

Hyrien, Ollivier, Mitov, Kosto V., and Yanev, Nikolay M.

Subjects
Branching processes, Mathematics::Probability, Immigration, Poisson process, Limit theorems
Abstract

The paper proposes an extension of Sevastyanov (1957) model allowing an immigration in the moments of a homogeneous Poisson process. Markov branching processes with time-nonhomogeneous Poisson immigration are considered as models in cell proliferation kinetics and limit theorems are proved in the supercritical case. Some of the limiting results can be interpreted as generalizations of the classical result of Sevastyanov (1957) and new effects are obtained due to the non-homogeneity., 2010 Mathematics Subject Classification: 60J80.

Published
2016

50. Subcritical Markov Branching Processes with Non-Homogeneous Poisson Immigration

Author

Hyrien, Ollivier, Mitov, Kosto V., and Yanev, Nikolay M.

Subjects
Branching processes, Immigration, Poisson process, Limit theorems
Abstract

[Mitov Kosto V.; Митов Косто В.]; [Yanev Nikolay M.; Janev N. M.; Janev Nikolaj; Янев Николай М.] The paper proposes an extension of Sevastyanov (1957) model based on a Markov branching process allowing an immigration component in the moments of a homogeneous Poisson process. Now Markov branching processes are also considered but assuming a time-nonhomogeneous Poisson immigration. These processes could be interpreted as models in cell proliferation kinetics with stem cell immigration. Limit theorems are proved in the subcritical case and new effects are obtained due to the non-homogeneity. 2000 Mathematics Subject Classification: 60J80.

Published
2015

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