Highlights d 1.6 million tests identified 1,388 SARS-CoV-2 infections in Guangdong by 19 March d Virus genomes can be recovered using a variety of sequencing approaches d Analyses reveal multiple viral importations with limited local transmission d Effective control measures helped reduce and eliminate chains of viral transmission

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Background Some COVID-19 cases test positive again for SARS-CoV-2 RNA following negative test results and discharge, raising questions about the meaning of virus detection. Better characterization of re-positive cases is urgently needed. Methods Clinical data were obtained through Guangdong's COVID-19 surveillance network. Neutralization antibody titre was determined using microneutralization assays. Potential infectivity of clinical samples was evaluated by cell inoculation. SARS-CoV-2 RNA was detected using three different RT-PCR kits and multiplex PCR with nanopore sequencing. Findings Among 619 discharged COVID-19 cases, 87 re-tested as SARS-CoV-2 positive in circumstances of social isolation. All re-positive cases had mild or moderate symptoms at initial diagnosis and were younger on average (median, 28). Re -positive cases ( n = 59) exhibited similar neutralization antibodies (NAbs) titre distributions to other COVID-19 cases ( n = 218) tested here. No infectious strain could be obtained by culture and no full-length viral genomes could be sequenced from re-positive cases. Interpretation Re -positive SARS-CoV-2 cases do not appear to be caused by active reinfection and were identified in ~14% of discharged cases. A robust NAb response and potential virus genome degradation were detected in almost all re-positive cases, suggesting a substantially lower transmission risk, especially through respiratory routes.

Background COVID-19 pandemic is underway. Some COVID-19 cases re-tested positive for SARS-CoV-2 RNA after discharge raising the public concern on their infectivity. Characterization of re-positive cases are urgently needed for designing intervention strategies. Methods Clinical data were obtained through Guangdong COVID-19 surveillance network. Neutralization antibody titre was determined using a microneutralization assay. Potential infectivity of clinical samples was evaluated after the cell inoculation. SARS-CoV-2 RNA was detected using three different RT-PCR kits and multiplex PCR with nanopore sequencing. Results Among 619 discharged COVID-19 cases, 87 were re-tested as SARS-CoV-2 positive in circumstance of social isolation. All re-positive cases had mild or moderate symptoms in initial diagnosis and a younger age distribution (mean, 30.4). Re-positive cases (n=59) exhibited similar neutralization antibodies (NAbs) titre distributions to other COVID-19 cases (n=150) parallel-tested in this study. No infective viral strain could be obtained by culture and none full-length viral genomes could be sequenced for all re-positive cases. Conclusions Re-positive SARS-CoV-2 was not caused by the secondary infection and was identified in around 14% of discharged cases. A robust Nabs response and a potential virus genome degradation were detected from nearly all re-positive cases suggesting a lower transmission risk, especially through a respiratory route.

Objectives To understand persistence of the virus in body fluids and immune response of infected host to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), an agent of coronavirus disease 2019 (COVID-19). Methods We determined the kinetics of viral load in several body fluids through real time reverse transcription polymerase chain reaction (rRT-PCR), serum antibodies of IgA, IgG and IgM by enzyme linked immunosorbent assay (ELISA), and neutralizing antibodies by microneutralization assay in 35 COVID-19 cases from two hospitals in Guangdong, China. Results We found higher viral loads and prolonged shedding of virus RNA in severe cases of COVID-19 in nasopharyngeal (1.3×10 6 vs 6.4×10 4 , p<0.05; 7∼8w) and throat (6.9×10 6 vs 2.9×10 5 , p<0.05; 4∼5w), while comparable in sputum samples (5.5×10 6 vs 0.9×10 6 , p<0.05; 4∼5w). Viraemia was rarely detected (2.8%, n=1/35). We detected early seroconversion of IgA and IgG at 1 st week after illness onset (day 5, 5.7%, n=2/35). Neutralizing antibodies were produced in the second week, and observed in all 35 included cases after 3 rd week illness onset. The levels of neutralizing antibodies correlated with IgG (r s =0.85, p<0.05; kappa=0.85) and IgA (r s =0.64, p<0.05; kappa=0.61) in severe, but not mild cases (IgG, r s =0.42, kappa=0.33; IgA, r s =0.32, kappa=0.22). No correlation with IgM in either severe (r s =0.17, kappa=0.06) or mild cases (r s =0.27, kappa=0.15) was found. Conclusions We revealed a prolonged shedding of virus RNA in upper respiratory tract, and evaluated the consistency production of IgG, IgA, IgM and neutralizing antibodies in COVID-19 cases.