Modelling upper respiratory viral load dynamics of SARS-CoV-2

Relationships between viral load, severity of illness, and transmissibility of virus are fundamental to understanding pathogenesis and devising better therapeutic and prevention strategies for COVID-19. Here we present within-host modelling of viral load dynamics observed in the upper respiratory tract (URT), drawing upon 2172 serial measurements from 605 subjects, collected from 17 different studies. We developed a mechanistic model to describe viral load dynamics and host response and contrast this with simpler mixed-effects regression analysis of peak viral load and its subsequent decline. We observed wide variation in URT viral load between individuals, over 5 orders of magnitude, at any given point in time since symptom onset. This variation was not explained by age, sex, or severity of illness, and these variables were not associated with the modelled early or late phases of immune-mediated control of viral load. We explored the application of the mechanistic model to identify measured immune responses associated with the control of the viral load. Neutralising antibodies correlated strongly with modelled immune-mediated control of viral load amongst subjects who produced neutralising antibodies. Our models can be used to identify host and viral factors which control URT viral load dynamics, informing future treatment and transmission blocking interventions.

Higher Vaccination Rate Predicts Reduction in SARS-CoV-2 Transmission across the United States

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began proliferating widely throughout the world in late 2019/early 2020, creating a global pandemic and health crisis. Although vaccines became available to the public approximately one year after the onset of the pandemic, there still remains much hesitancy surrounding vaccination even two years into the pandemic. One key concern comes from reports of breakthrough infections among the vaccinated that show comparable levels of peak viral load as the unvaccinated, calling into question the ability of vaccines to slow or prevent transmission. Therefore young, healthy individuals who are at low risk of serious complications themselves have little incentive to receive a vaccine that they are not convinced will protect others around them. To address this important concern, this article analyzes COVID-19 incidence in the United States as a function of each state's vaccination rate. Results show that states with higher percentages of fully vaccinated individuals report fewer new cases among the remaining unvaccinated population. These data add to accumulating evidence that COVID-19 vaccinations can indeed slow the spread of SARS-CoV-2, and are an important tool in society's arsenal to put this pandemic behind us.

Sex Differences in EBV Viremia after Haplo-HSCT Imply Sex Bias during Immune Reconstitution

Objective: Posttransplant infection is common and tough to deal, patients after HSCT rely on immune reconstitution for protection. We desperately need a deeper understanding of how the system works to help the patients overcome the infection. Method: This study analyzed the disease course of EBV viremia after haplo-HSCT, as well as the laboratory testing data. The sex bias during immune reconstitution was manifested by comparing the outcomes between male and female patients, Results: 236 patients received haplo-HSCT in 2013 in our center, at a median follow up of 5 years, among whom 78 patients underwent EBV infection. The incidence of EBV viremia after transplantation is 33.1% in total, with a significant difference between men and women (40.0% and 26.7% respectively, p=0.034). Men tended to have earlier onset time (14-434d after HSCT) and longer duration (7-70d) than women (17-592d after HSCT, 7-30d). Both the initial and peak viral load were higher in men than in women (initial viral load＞10 4/ml: men 6.52% vs. women 3.13%, peak viral load＞10 5/ml: men 8.70% vs. women 3.13%). To explain this phenomenon, we analyzed the laboratory testing data on 30d and 60d after HSCT. And we found that male patients had higher plasma levels of immunoglobulin M on 60d after HSCT if infected by EBV, referring to more robust induction of innate immune (p=0.033). By contrast, female patients had significantly increased CD4+ T cell during EBV infection, representing more robust activation of adaptive immune (p=0.019). Conclusion: These findings provide a possible explanation for the observed sex biases in EBV viremia after haplo-HSCT, and provide an important basis for the recognition of immune reconstitution, furthermore, raise concern of the development of a sex-based approach to the treatment and care of male and female patients with infection after HSCT. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

1010. Cross-Species Translation of Correlates of Protection for COVID-19 Vaccine Candidates Using Quantitative Tools

Background Several COVID-19 vaccines have been authorized, and the need for rapid, further modification is anticipated. This work uses a Model-Based Meta-Analysis (MBMA) to relate, across species, immunogenicity to peak viral load (VL) after challenge and to clinical efficacy. Together with non-clinical and/or early clinical immunogenicity data (ECID), this enables prediction of a candidate vaccine’s clinical efficacy. The goal of this work was to enable the accelerated development of vaccine candidates by supporting Go/No-Go and study design decisions, and the resulting MBMA can be instrumental in decisions not to progress candidates to late stage development. Methods A literature review with pre-specified inclusion/exclusion criteria enabled creation of a database including nonclinical serum neutralizing titers (SN), peak VL after challenge with SARS-CoV-2 (VL), along with data from several clinical vaccine candidates. Rhesus Macaque (RM) and golden hamster (GH) were selected (due to availability and consistency of data) for MBMA modeling. For both RM and GH, peak post-challenge VL in lung and nasal tissues were used as surrogates for clinical disease and were related to pre-challenge SN via the MBMA. The VL predictions from the RM MBMA were scaled to incidence rates in humans, with a scaling factor between RM and human SN estimated using early Phase 3 efficacy data. This enabled clinical efficacy predictions based on ECID. To qualify the model’s predictive power, efficacies of COVID-19 vaccine candidates were compared to those predicted from the MBMA and their respective Ph1/2 SN data. More recently available clinical data enable building a clinical MBMA; comparing this to the RM MBMA further supports SN as predictive. Results The MBMA analyses identified a sigmoidal decrease in VL (increasing protection) with increase in SN in all three species, with more SN needed (in both RM and GH) for protection in nasal swabs than in BAL (see figure). The comparison between predicted and reported clinical efficacies demonstrated the model’s predictive power across vaccine platforms. RM and GH MBMA Protection Models and Translational Prediction with Observed Efficacies Sizes of circles indicate relative weight of the data in the respective quantitative model. Model and data visualizations have been harmonized (across tissue-types) separately for each of RM and GH using VACHER (Lommerse, et al., CPT:PSP, in press). Conclusion By quantifying adjustments needed between species and assays, translational MBMA can inform development decisions by using nonclinical SN and VL, and ECID to predict protection from COVID-19. Disclosures Anna Largajolli, PhD, Certara (Employee) Nele Plock, PhD, Certara (Employee, Shareholder)Merck & Co., Inc. (Independent Contractor) Bhargava Kandala, PhD, Merck & Co., Inc. (Employee, Shareholder) Akshita Chawla, PhD, Merck & Co., Inc. (Employee, Shareholder) Seth H. Robey, PhD, Merck & Co., Inc. (Employee, Shareholder) Kenny Watson, PhD, Certara (Employee, Shareholder) Raj Thatavarti, MS, Certara (Employee, Shareholder) Sheri Dubey, PhD, Merck & Co., Inc. (Employee, Shareholder) S. Y. Amy Cheung, PhD, Certara (Employee, Shareholder) Rik de Greef, MSc, Certara (Employee, Shareholder) Jeffrey R. Sachs, PhD, Merck & Co., Inc. (Employee, Shareholder)

944. CMV Peak Viral Load, Recurrence, Duration, and Outcomes in Kidney Transplant Recipients

Background Cytomegalovirus (CMV) infection continues to cause morbidity in kidney transplant recipients, despite prophylaxis and pre-emptive therapy. Predictors of poor outcomes remain incompletely characterized. We questioned whether markers of CMV replication (CMV peak viral load, recurrent episodes, or duration of CMV DNAemia) are associated with adverse outcomes in the current era. Methods We studied 605 people who underwent kidney transplant at Johns Hopkins University (2010 – 2018). Mean follow-up was 45.5 months. The average age was 51.85 years and 39.7% were female. Donor-seropositive, recipient seronegative (D+/R-) patients received valganciclovir 900 mg/day for 6 months, while R+ patients received valganciclovir 450 mg/day for 3 months. CMV recurrence was defined as CMV DNAemia after two undetectable CMV PCR’s. Outcomes of acute rejection, graft failure, and death were evaluated in univariate analysis; p values were calculated by Fisher’s exact test. Results Peak CMV viral load was not associated with any outcomes (Table 1). There was a trend of increased graft failure in people who had long duration ( >6 month) DNAemia (Table 2). More than two episodes of CMV reactivation was associated with graft failure and rejection (Table 3). Conclusion CMV reactivation is associated with kidney rejection and failure in univariate models. Multivariate analyses and longitudinal modeling will provide increased data upon which to better instruct preventative strategies. Acknowledgments Funding for the research study was provided by Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA Disclosures Robin K. Avery, MD, Aicuris (Grant/Research Support)Astellas (Grant/Research Support)Chimerix (Research Grant or Support)Merck (Grant/Research Support)Oxford Immunotec (Grant/Research Support)Qiagen (Grant/Research Support)Takeda/Shire (Grant/Research Support) Yuexin Tang, PhD, JnJ (Other Financial or Material Support, Spouse’s employment)Merck & Co., Inc. (Employee, Shareholder) Kieren Marr, MD, Merck (Grant/Research Support, Advisor or Review Panel member)

933. Incidence and Risk Factors for Cytomegalovirus Infection in Intestinal Transplant Recipients

Background Cytomegalovirus (CMV) infection is the most common infection after solid organ transplantation. Data on CMV infection in intestinal transplant recipients is limited. Methods This is a single-center retrospective cohort study which includes all consecutive intestinal transplant recipients who were transplanted between 2009 and 2019. We excluded recipients that showed CMV seronegativity of both donor and recipient. We also excluded those patients who did not have more than 3 months of follow-up. Univariate and multivariate analyses were performed to identify the risk factors for CMV infection. Of note, at our center CMV prophylaxis in intestinal transplant recipients is one year of valganciclovir. Results A total of 173 recipients were transplanted; 46 recipients were because of CMV serostatus and 32 due to short follow-up. Ninety-five recipients were included finally. The characteristics of our cohort are summarized in Table 1. Of note, the median age was 32 years [range 0-67] and 44 (46.3%) were male. Eighteen (18.9%) recipients needed to stop valganciclovir prophylaxis due to the side effect, especially cytopenia. Twenty-one recipients developed CMV infection including asymptomatic viremia (12/21, 57.1%), CMV syndrome (5/21, 23.8%) and end-organ disease (2 (9.5%) pneumonitis and 2 (9.5%) colitis) at median time of 155 [Interquartile range, IQR 28-254] days from transplant. The median peak viral load and time to negativity were 16000 [IQR 1500-43892] IU/ml and 56 [IQR 49-109] days, respectively. Younger age (p=0.007, Odds ratio 1.03, 95% confidence interval 1.003-1.055) was the independent factor associated with CMV infection. Conclusion Despite prolonged prophylaxis, 21 (22.1%) of intestinal transplant recipients developed CMV infection around 5 months post-transplant. This may be because they cannot tolerate valganciclovir prophylaxis and early termination was required. Further strategy should be developed to prevent CMV infection in this vulnerable population. Disclosures All Authors: No reported disclosures

Mathematical Modeling of Vaccines That Prevent SARS-CoV-2 Transmission

SARS-CoV-2 vaccine clinical trials assess efficacy against disease (VEDIS), the ability to block symptomatic COVID-19. They only partially discriminate whether VEDIS is mediated by preventing infection completely, which is defined as detection of virus in the airways (VESUSC), or by preventing symptoms despite infection (VESYMP). Vaccine efficacy against transmissibility given infection (VEINF), the decrease in secondary transmissions from infected vaccine recipients, is also not measured. Using mathematical modeling of data from King County Washington, we demonstrate that if the Moderna (mRNA-1273QS) and Pfizer-BioNTech (BNT162b2) vaccines, which demonstrated VEDIS > 90% in clinical trials, mediate VEDIS by VESUSC, then a limited fourth epidemic wave of infections with the highly infectious B.1.1.7 variant would have been predicted in spring 2021 assuming rapid vaccine roll out. If high VEDIS is explained by VESYMP, then high VEINF would have also been necessary to limit the extent of this fourth wave. Vaccines which completely protect against infection or secondary transmission also substantially lower the number of people who must be vaccinated before the herd immunity threshold is reached. The limited extent of the fourth wave suggests that the vaccines have either high VESUSC or both high VESYMP and high VEINF against B.1.1.7. Finally, using a separate intra-host mathematical model of viral kinetics, we demonstrate that a 0.6 log vaccine-mediated reduction in average peak viral load might be sufficient to achieve 50% VEINF, which suggests that human challenge studies with a relatively low number of infected participants could be employed to estimate all three vaccine efficacy metrics.

Trajectory of viral load in a prospective population-based cohort with incident SARS-CoV-2 G614 infection

Importance: SARS-CoV-2 viral trajectory has not been well-characterized in documented incident infections. These data will inform SARS-CoV-2 natural history, transmission dynamics, prevention practices, and therapeutic development. Objective: To prospectively characterize early SARS-CoV-2 viral shedding in persons with incident infection. Design: Prospective cohort study. Setting: Secondary data analysis from a multicenter study in the U.S. Participants: The samples derived from a randomized controlled trial of 829 community-based asymptomatic participants recently exposed (<96 hours) to persons with SARS-CoV-2. Participants collected daily mid-turbinate swabs for SARS-CoV-2 detection by polymerase-chain-reaction and symptom diaries for 14-days. Persons with negative swab for SARS-CoV-2 at baseline who developed infection during the study were included in the analysis. Exposure: Laboratory-confirmed SARS-CoV-2 infection. Main outcomes and measures: The observed SARS-CoV-2 viral shedding characteristics were summarized and shedding trajectories were examined using a piece-wise linear mixed-effects modeling. Whole viral genome sequencing was performed on samples with cycle threshold (Ct)<34. Results: Ninety-seven persons (57% women, median age 37-years) developed incident infections during 14-days of follow-up. Two-hundred fifteen sequenced samples were assigned to 15 lineages that belonged to the G614 variant. Forty-two (43%), 18(19%), and 31(32%) participants had viral shedding for 1 day, 2-6 days, and >7 days, with median peak viral load Ct of 38.5, 36.7, and 18.3, respectively. Six (6%) participants had 1-6 days of observed viral shedding with censored duration. The peak average viral load was observed on day 3 of viral shedding. The average Ct value was lower, indicating higher viral load, in persons reporting COVID-19 symptoms than asymptomatic. Using the statistical model, the median time from shedding onset to peak viral load was 1.4 days followed by a median of 9.7 days before clearance. Conclusions and Relevance: Incident SARS-CoV-2 G614 infection resulted in a rapid viral load peak followed by slower decay and positive correlation between peak viral load and shedding duration; duration of shedding was heterogeneous. This longitudinal evaluation of the SARS-CoV-2 G614 variant with frequent molecular testing may serve as a reference for comparing emergent viral lineages to inform clinical trial designs and public health strategies to contain the spread of the virus.

A novel RT-LAMP workflow for rapid salivary diagnostics of COVID-19 and effects of age, gender and time from symptom onset

Objectives: Rapid diagnostics is pivotal to curb SARS-CoV-2 transmission, and saliva has emerged as a practical alternative to naso/oropharyngeal (NOP) specimens. We aimed to develop a direct RT-LAMP workflow for viral detection in saliva, and to provide more information regarding its potential in COVID-19 diagnostics. Methods: Clinical and contrived specimens were used to screen/optimize formulations and sample processing protocols. Salivary viral load was determined in symptomatic patients to evaluate clinical performance (n = 90) and to characterize saliva based on age, gender and time from onset of symptoms (n = 49). Results: The devised workflow achieved 93.2% sensitivity, 97% specificity, and 0.895 Kappa for salivas containing >102 copies/μL. Further analyses in saliva showed peak viral load in the first days of symptoms and lower viral loads in females, particularly among young individuals (<38 years). NOP RT-PCR data did not yield relevant associations. Conclusions: This novel saliva RT-LAMP workflow can be applied to point-of-care testing. This work reinforces that saliva better correlates with transmission dynamics than NOP specimens, and reveals gender differences that may reflect higher transmission by males. To maximize detection, testing should be done immediately after symptom onset, especially in females.

Inferring SARS-CoV-2 variant within-host kinetics

SARS-CoV-2 variants are causing epidemic rebounds in many countries. By analyzing longitudinal cycle threshold (Ct) values from screening tests in the general population and hospitals, we find that infections caused by variant lineages have higher peak viral load than wild type lineages and, for the B.1.1.7 lineage, have a longer infectious period duration. Linking within-host kinetics to transmission data suggests that infections caused by variants have higher transmission potentials and that their epidemiological fitness may depend on the demography of the host population.