Understanding humoral responses to SARS-CoV-2 is critical for improving diagnostics, therapeutics, and vaccines. Deep serological profiling of 232 COVID-19 patients and 190 pre-COVID-19 era controls using VirScan revealed over 800 epitopes in the SARS-CoV-2 proteome, including 10 epitopes likely recognized by neutralizing antibodies. Pre-existing antibodies in controls recognized SARS-CoV-2 ORF1, while only COVID-19 patients primarily recognized spike and nucleoprotein. A machine learning model trained on VirScan data predicted SARS-CoV-2 exposure history with 99% sensitivity and 98% specificity; a rapid Luminex-based diagnostic was developed from the most discriminatory SARS-CoV-2 peptides. Individuals with more severe COVID-19 exhibited stronger and broader SARS-CoV-2 responses, weaker antibody responses to prior infections, and higher incidence of CMV and HSV-1, possibly influenced by demographic covariates. Among hospitalized patients, males make greater SARS-CoV-2 antibody responses than females.

The relationship between SARS-CoV-2 viral load and risk of disease progression remains largely undefined in coronavirus disease 2019 (COVID-19). Here, we quantify SARS-CoV-2 viral load from participants with a diverse range of COVID-19 disease severity, including those requiring hospitalization, outpatients with mild disease, and individuals with resolved infection. We detected SARS-CoV-2 plasma RNA in 27% of hospitalized participants, and 13% of outpatients diagnosed with COVID-19. Amongst the participants hospitalized with COVID-19, we report that a higher prevalence of detectable SARS-CoV-2 plasma viral load is associated with worse respiratory disease severity, lower absolute lymphocyte counts, and increased markers of inflammation, including C-reactive protein and IL-6. SARS-CoV-2 viral loads, especially plasma viremia, are associated with increased risk of mortality. Our data show that SARS-CoV-2 viral loads may aid in the risk stratification of patients with COVID-19, and therefore its role in disease pathogenesis should be further explored.

The sensitivity and specificity of PCR, serology (ELISA) and lymphoproliferative response to Leishmania antigen for the detection of Leishmania infantum infection were evaluated in a cohort of 126 dogs exposed to natural infection in Brazil. For PCR, Leishmania DNA from bone-marrow was amplified with both minicircle and ribosomal primers. The infection status and time of infection of each dog were estimated from longitudinal data. The sensitivity of PCR in parasite-positive samples was 98 %. However, the overall sensitivity of PCR in post-infection samples, from dogs with confirmed infection, was only 68 %. The sensitivity of PCR varied during the course of infection, being highest (78-88 %) 0-135 days postinfection and declining to around 50 % after 300 days. The sensitivity of PCR also varied between dogs, and was highest in sick dogs. The sensitivity of serology was similar in parasite-positive (84 %), PCR-positive (86 %) and post-infection (88 %) samples. The sensitivity of serology varied during the course of infection, being lowest at the time of infection and high (93-100 %) thereafter. Problems in determining the specificity of serology are discussed. The sensitivity and specificity of cellular responsiveness were low. These data suggest that PCR is most useful in detecting active or symptomatic infection, and that serology can be a more sensitive technique for the detection of all infected dogs.

CD4 + T cells are central to long-term immunity against viruses through the functions of T helper-1 (Th1) and T follicular helper (Tfh) cell subsets. To better understand the role of these subsets in COVID-19 immunity, we conducted a longitudinal study of SARS-CoV-2-specific CD4 + T cell and antibody responses in convalescent subjects who seroconverted during the first wave of the pandemic in Boston, Massachusetts, United States, across a range of COVID-19 disease severities. Analyses of spike (S) and nucleocapsid (N) epitope-specific CD4 + T cells using peptide and major histocompatibility complex class II (peptide:MHCII) tetramers demonstrated expanded populations of T cells recognizing the different SARS-CoV-2 epitopes in most subjects compared to pre-pandemic controls. Individuals who experienced a milder disease course not requiring hospitalization had a greater percentage of circulating Tfh (cTfh) and Th1 cells among SARS-CoV-2-specific cells. Analysis of SARS-CoV-2-specific CD4 + T cells responses in a subset of individuals with sustained anti-S antibody responses following viral clearance also revealed an increased proportion of memory cTfh cells. Our findings indicate efficient early disease control also predicts favorable long-term adaptive immunity.

SARS-CoV-2 kinetics remain understudied, including the impact of remdesivir. In hospitalized individuals, peak sputum viral load occurred in week 2 of symptoms while peak viremia occurred within a week of symptom-onset, suggesting early systemic seeding of SARS-CoV-2. Remdesivir treatment was associated with faster rates of viral decay.