key: cord-0780750-tdspvq2l authors: Naveca, F. G.; Nascimento, V. A.; Nascimento, F.; Ogrzewalska, M.; Pauvolid-Correa, A.; Araujo, M. F.; Arantes, I.; Batista, E. L. R.; Magalhaes, A. L. l.; Vinhal, F.; Mattos, T. P.; Riediger, I.; Debur, M. d. C.; Grinsztejn, B.; Veloso, V. G.; Brasil, P.; Rodrigues, R. R.; Rovaris, D. B.; Fernandes, S. B.; Fernandes, C.; Santos, J. H. A.; Abdalla, L. F.; Costa-Filho, R.; Silva, M.; Souza, V.; Costa, g. A.; Mejia, M.; Brandao, M. J.; Goncalves, L. F.; Silva, G. A.; Jesus, M. S. d.; Pessoa, K.; Corado, A. d. L. G.; Duarte, D. C. G.; Machado, A. B.; Zukeram, K. d. A.; Valente, N.; Lopes, R. S. title: A case series of SARS-CoV-2 reinfections caused by the variant of concern Gamma in Brazil date: 2021-11-29 journal: nan DOI: 10.1101/2021.11.29.21266109 sha: 13848bce96f6d5e3090c3014ee2900ccaba9894a doc_id: 780750 cord_uid: tdspvq2l The rapid spread of the SARS-CoV-2 Variant of Concern (VOC) Gamma during late 2020 and early 2021 in Brazilian settings with high seroprevalence raised some concern about the potential role of reinfections in driving the epidemic. Very few cases of reinfection associated with the VOC Gamma, however, have been reported. Here we describe 25 cases of SARS-CoV-2 reinfection confirmed by real-time RT-PCR twice within months apart in Brazil. SARS-CoV-2 genomic analysis confirmed that individuals were primo-infected between March and December 2020 with distinct viral lineages, including B.1.1, B.1.1.28, B.1.1.33, B.1.195 and P.2, and then reinfected with the VOC Gamma between 3 to 12 months after primo-infection. The overall mean cycle threshold (Ct) value of the first (25.7) and second (24.5) episodes were roughly similar for the whole group and 14 individuals displayed mean Ct values < 25.0 at reinfection. Sera of 14 patients tested by plaque reduction neutralization test after reinfection displayed detectable neutralizing antibodies against Gamma and other SARS-CoV-2 variants (B.1.33, B.1.1.28 and Delta). All individuals have milder or no symptoms after reinfection and none required hospitalization. The present study demonstrates that the VOC Gamma was associated with reinfections during the second Brazilian epidemic wave in 2021 and raised concern about the potential infectiousness of reinfected subjects. Although individuals here analyzed failed to mount a long-term sterilizing immunity, they developed a high anti-Gamma neutralizing antibody response after reinfection that may provide some protection against severe disease. Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection are a concerning topic for the coronavirus disease 2019 (COVID-19) response worldwide as they have implications for the long-term protective immunity induced by natural infections or by vaccines. Several cases of reinfection with distinct variants of SARS-CoV-2 have been reported 1 , but it is unclear if these reinfection cases were the consequence of a limited immunity induced by the primo-infection or reflect the reinfecting virus's ability to evade the previous immune responses. The state of Amazonas, located in the north region of Brazil, was severely hit by a second wave of COVID-19 epidemic between December 2020 and March 2021 despite the high (>70%) 2 or relatively high (30-35%) 3 estimated seroprevalence at late 2020. This was associated with the emergence and spread of the Variant of Concern (VOC) Gamma which raised some concern about the potential role of reinfections in driving the second COVID-19 wave in the Amazonas 4 . Gamma is one of the four SARS-CoV-2 VOCs currently recognized in the world 5 VOCs carry several mutations in the receptor-binding domain (RBD) of the spike (S) protein that reduce antibody neutralization and/or increase affinity for ACE2 receptor [6] [7] [8] [9] [10] , and may thus enhance the probability of reinfection. Some cases of reinfection with VOCs have been described worldwide [11] [12] [13] [14] [15] [16] [17] [18] , but the precise frequency of those events remains unclear. A study conducted in the United Kingdom (UK) identified possible reinfections in 0.7% (95% CI 0.6-0·8%) of individuals infected during September-December 2020 and found no evidence that the frequency of reinfections was higher for the VOC Alpha than for pre-existing non-VOCs 19 [20] [21] [22] , with lineage P.2 that harbors the mutation S: E484K 23, 24 and with the VOC Gamma 17, 18 . However, there is no evidence that reinfections with Gamma were more frequent than with non-VOCs. In this study, we report a series of 25 cases of reinfections with the VOC Gamma in subjects from six different Brazilian states who had been primo-infected with different non-VOC SARS-CoV-2 lineages between 3 to 12 months earlier. The large number of SARS-CoV-2 reinfections with the VOC Gamma here described demonstrate that this viral variant is able to infect recovered individuals and suggests that this event was not a rare phenomenon in Brazil. Case series and ethical aspects. In this study we include 25 cases of adults living at four different regions of Brazil, including West-Central (n=13), South (n=7), North (n=3) and Southeast (n=2) that presented two episodes of COVID-19 with at least 90 days apart. The first and second episodes occurred between March and December 2020 and between December 2020 and June 2021, respectively. All patients had nasopharyngeal and oropharyngeal swabs (NPS) collected in viral transport media (VTM) and tested by SARS- is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint We analyzed 25 individuals that presented two episodes of COVID-19 within an interval of 3 to 12 months period (Table 1, Figure S1 ). They were predominantly female (64%), unvaccinated (92%) and with an age that ranged from 17 to 73 years old. Most cases had no reported comorbidities (80%) and presented mild clinical symptoms (92%) including fever, myalgia, cough, sore throat, nausea, anosmia, ageusia, and back pain in the first episode of COVID-19. Two individuals required hospitalization at primo-infection. Patients is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 29, 2021. ; https://doi.org/10.1101/2021.11.29.21266109 doi: medRxiv preprint (Ctfirst -Ctsecond > 3.0). The overall mean between onset symptoms and collection date were 4 days in the first infection and 3.5 in the reinfection ( Table 1) . Whole SARS-CoV-2 genomes were recovered from all 50 samples analyzed. Most of them were high quality sequences (<1% of N) with a few exceptions (<15% of N) that were recovered from samples with low viral load (Ct > 33), limit Ct value for sequencing procedure. All SARS-CoV-2 genomes recovered contained enough SNP markers to confidently assign the corresponding SARS-CoV-2 lineage with high support (1.0). The Table 1 ). The ML phylogenetic analysis confirmed the initial lineage assignment on the majority of cases (Fig S2 A (Fig 1B and Table 1 ). The levels of Nab in reinfected subjects were next compared with a group of 30 hospitalized individuals that were primo-infected with variant Gamma and 10 individuals with hybrid immunity that were either primo-infected with a non-VOC variant and then fully vaccinated (n = 5) or infected with the variant Gamma after vaccination (n = 5, breakthrough cases). The three groups displayed similar levels of NAb against Gamma (P > 0.05), but levels against Delta in reinfected and in individuals with hybrid immunity were significantly higher (P < 0.0003) than in hospitalized individuals primo-infected with Gamma (Fig 1C) . is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 29, 2021. ; This study describes 25 We may also speculate that mild severity of the first COVID-19 episode in patients is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 29, 2021. ; https://doi.org/10.1101/2021.11.29.21266109 doi: medRxiv preprint study were reinfected between 3 and 12 months after the primo-infections, a time-frame thus consistent with the hypothesis of waning humoral immunity. According to this model, reinfection will become increasingly common as the epidemic progresses, and this may also partially explain the much larger number of reinfections with variant Gamma here reported when compared with previous locally prevalent variants in Brazil. There is limited evidence on the risk of SARS-CoV-2 transmission from reinfected individuals to susceptible contacts. Several studies demonstrated that Ct values that inversely correlate with the log viral load also negatively correlate with cultivable virus 53,54 and the transmission risk 55, 56 . It was reported that up to 70% of patients remained positive in culture at a Ct ≤ 25 53, 54 and that 85% of case-contact pairs with plausible onward transmission had a case Ct < 25 55, 56 , suggesting that a Ct ≤ 25 could be used as a good surrogate of infectivity. Notably, our analyses revealed that samples taken at first and second infections displayed is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 29, 2021. ; https://doi.org/10.1101/2021.11.29.21266109 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 29, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 29, 2021. ; specimens and the submitting laboratories where genetic sequence data were generated and shared via the GISAID, on which this research is based (Supplementary Table 1 ). . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 29, 2021. ; https://doi.org/10.1101/2021.11.29.21266109 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted November 29, 2021. ; https://doi.org/10.1101/2021.11.29.21266109 doi: medRxiv preprint . 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The graph illustrates the epidemiological history of Gamma reinfection cases (n = 25), detailing its key events. When available, the onset of symptoms and sample collection for primo-infection and reinfection cases are represented in a timeline drawn for each individual. Sample collection events are accompanied by their observed real time PCR cycle threshold (Ct). Additionally, vaccination events are indicated. All time intervals are calculated from the onset of symptoms of the individual's primo-infection.