Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected 78 million individuals and is responsible for over 1.7 million deaths to date. Infection is associated with the development of variable levels of antibodies with neutralizing activity, which can protect against infection in animal models 1,2. Antibody levels decrease with time, but, to our knowledge, the nature and quality of the memory B cells that would be required to produce antibodies upon reinfection has not been examined. Here we report on the humoral memory response in a cohort of 87 individuals assessed at 1.3 and 6.2 months after infection with SARS-CoV-2. We find that titres of IgM and IgG antibodies against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 decrease significantly over this time period, with IgA being less affected. Concurrently, neutralizing activity in plasma decreases by fivefold in pseudotype virus assays. By contrast, the number of RBD-specific memory B cells remains unchanged at 6.2 months after infection. Memory B cells display clonal turnover after 6.2 months, and the antibodies that they express have greater somatic hypermutation, resistance to RBD mutations and increased potency, indicative of continued evolution of the humoral response. Immunofluorescence and PCR analyses of intestinal biopsies obtained from asymptomatic individuals at 4 months after the onset of coronavirus disease 2019 (COVID-19) revealed the persistence of SARS-CoV-2 nucleic acids and immunoreactivity in the small bowel of 7 out of 14 individuals. We conclude that the memory B cell response to SARS-CoV-2 evolves between 1.3 and 6.2 months after infection in a manner that is consistent with antigen persistence. Antibody responses to SARS-CoV-2 were initially characterized in a cohort of individuals convalescing from COVID-19 at approximately 40 days (1.3 months) after infection 1. Between 31 August and 16 October 2020, 100 participants returned for a 6-month follow-up study visit. Although the initial criteria allowed enrolment of the close contacts of individuals with SARS-CoV-2 infection confirmed by reverse-transcription PCR (RT-PCR) 1 , 13 of the contacts did not seroconvert and were excluded from further analyses. The remaining 87 participants with RT-PCR-confirmed SARS-CoV-2 infection and/ or seroconversion returned for analysis at approximately 191 days (6.2 months; range of 165 to 223 days) after the onset of symptoms. In this cohort, symptoms lasted for a median of 12 days (range of 0 to 44 days) during the acute phase, and 10 (11%) of the participants were hospitalized. Consistent with other reports 3,4 , 38 (44%) of the participants reported persistent long-term symptoms attributable to COVID-19 (Methods, Supplementary Tables 1, 2). The duration and severity of symptoms during acute disease was significantly greater among participants with persistent post-acute symptoms at the second study visit (Extended Data Fig. 1m-q). Importantly, all 87 participants tested negative for SARS-CoV-2 at the 6-month follow...

Highlights d A hPSC-derived cell and organoid platform is used to study SARS-CoV-2 tissue tropism d Human pancreatic alpha and beta cells are permissive to SARS-CoV-2 infection d Human hepatocyte and cholangiocyte organoids are permissive to SARS-CoV-2 infection d hPSC-derived cells/organoids show similar chemokine responses as COVID-19 tissues

This is a PDF file of a peer-reviewed paper that has been accepted for publication. Although unedited, the content has been subjected to preliminary formatting. Nature is providing this early version of the typeset paper as a service to our authors and readers. The text and figures will undergo copyediting and a proof review before the paper is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

There is an urgent need to create novel models using human disease-relevant cells to study SARS-CoV-2 biology and to facilitate drug screening. As SARS-CoV-2 primarily infects the respiratory tract, we developed a lung organoid model using human pluripotent stem cells (hPSC-LOs). The hPSC-LOs, particularly alveolar type II-like cells, are permissive to SARS-CoV-2 infection, and showed robust induction of chemokines upon SARS-CoV-2 infection, similar to what is seen in COVID-19 patients. Nearly 25% of these patients also have gastrointestinal manifestations, which are associated with worse COVID-19 outcomes 1. We therefore also generated complementary hPSC-derived colonic organoids (hPSC-COs) to explore the response of colonic cells to SARS-CoV-2 infection. We found that multiple colonic cell types, especially enterocytes, express ACE2 and are permissive to SARS-CoV-2 infection. Using hPSC-LOs, we performed a high throughput screen of FDA-approved drugs and identified entry inhibitors of SARS-CoV-2, including imatinib, mycophenolic acid (MPA), and quinacrine dihydrochloride (QNHC). Treatment at physiologically relevant levels of these drugs significantly inhibited SARS-CoV-2 infection of both hPSC-LOs and hPSC-COs. Together, these data demonstrate that hPSC-LOs and hPSC-COs infected by SARS-CoV-2 can serve as disease models to study SARS-CoV-2 infection and provide a valuable resource for drug screening to identify candidate COVID-19 therapeutics. The development of anti-SARS-CoV-2 drugs could change the scope of the ongoing COVID-19 pandemic. While this strategy is being pursued, high throughput screens are typically performed in transformed cell lines which fail to capture the physiologically relevant dynamics of human SARS-CoV-2 infection. To overcome limitations of these cell lines, several adult organoid models have been developed to study SARS-CoV-2 2-4. Here, we developed human pluripotent stem cell-derived lung and colonic organoids (hPSC-LOs and hPSC-COs) optimized as in vitro platforms for high throughput drug screening. hPSC-LOs are permissive to SARS-CoV-2 We differentiated hPSCs to lung organoids (hPSC-LOs) based on previously reported stepwise strategies 5-13 (Extended Data Fig. 1a-1c). qRT-PCR and RNA-seq profiling validates the expression of alveolar type II (AT2) cell markers in the hPSC-LOs (Extended Data Fig. 1d, 1e). Intra-cellular flow cytometry further confirmed the presence of Pro-SP-C + cells in hPSC-LOs (Extended Data Fig. 1f). Single cell transcriptomic profiles of hPSC-LOs identified AT2-like cells, which were enriched for adult human lung AT2 cell markers (Fig. 1a-1c and Extended Data Fig. 2a-2c).

No abstract