key: cord-0905162-rlbqgb55 authors: Díaz, Yamilka; Ortiz, Anyuri; Weeden, Adriana; Castillo, Daniel; González, Claudia; Moreno, Brechla; Martínez-Montero, Mabel; Castillo, Marlene; Vasquez, Grettel; Sáenz, Lisseth; Franco, Danilo; Pitti, Yaneth; Chavarria, Oris; Gondola, Jessica; Moreno, Ambar M.; Ábrego, Leyda; Beltrán, Davis; Guerra, Ilka; Chang, Jim; Chaverra, Zumara; Guerrero, Isela; Valoy, Alejandra; Gaitán, Melissa; Araúz, Dimelza; Morán, Ernesto; Chen-Germán, Maria; Valdespino, Elimelec; Rodríguez, Rita; Corrales, Rita; Chen-Camaño, Roderick; Pascale, Juan Miguel; Martínez, Alexander A.; López-Vergès, Sandra title: SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama date: 2021-06-06 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2021.06.004 sha: a182b0b1d962290459f404f6c90552011ac17ce4 doc_id: 905162 cord_uid: rlbqgb55 We report a case of reinfection by SARS-CoV-2 with the second virus harboring amino acid changes in the Spike protein (141-143del, D215A, ins215AGY, L452R, D614 G), orf1a, helicase, orf3a, and Nucleocapside. The virus associated with the reinfection, from an endemic lineage containing the S:L452R immune escape mutation, was circulating in Panama at the time. In March 2020, WHO declared the COVID-19 pandemic. As it is evolving, more cases of reinfection by SARS-CoV-2 are being reported (Gupta et al., 2020; To et al., 2020) , even if it is considered a rare event. New variants with the potential to spread more efficiently have been described (Naveca et al., 2019; Tegally et al., 2021) . Some mutations in the Spike (S) protein could increase viral infectivity (Korber et al., 2020; Tegally et al., 2021; Volz et al., 2021) or decrease sensitivity to neutralizing antibodies (Hoffmann et al., 2020; J. Li et al., 2020; Q. Li et al., 2020; Naveca et al., 2019; Resende et al., 2021; Tchesnokova et al., 2021) and have been associated with secondary SARS-CoV-2 infections. Here, we report a case of reinfection with SARS-CoV-2 in Panama, confirmed by complete genome sequencing, in which the second virus contained new and previously described mutations implicated in immune escape and higher transmission. SARS-CoV-2 diagnosis: Viral RNA (vRNA) was extracted from the first nasopharyngeal swab sample using Qiagen viral RNA extraction kit, and from the second using Chemagic™360 kit. SARS-CoV-2 was detected using the RT-qPCR Powercheck kits version 1.0 and version 2.0, respectively. The cutoff value for both was CT<35. Whole genome sequencing showed that both viruses belong to two endemic lineages ( Figure The a.a. mutations identified in the S protein are located in the subunit S1 (Supplementary Table 1 (RBD) for ACE2 receptor, D614G being between in the RBD and the amino acid bridge between S1 and S2 subunits. The mutations S197L, M234I are located in the link region between the RNA-binding domain and the dimerization domain, whereas the P383L is in the C-terminal domain of the N protein (Supplementary Table 1 , Supplementary Figure 2B , (Cubuk et al., 2021) . We describe the first confirmed SARS-CoV-2 reinfection in Panama, in an immunocompetent patient who presented mild symptomatic disease during both infections. Reinfections of seasonal coronaviruses have been described in settings where a high rate of community infection and/or incomplete immunologic protection took place (Edridge et al., 2020) . Previous SARS-CoV-2 reinfection reported cases showed that an induced neutralizing antibody response generated by the first infection is not sufficient for protection (Tohidinia and Sefid, 2020) . Several variables could be implicated in a reinfection, including: not proper immune response, low amount of neutralizing antibodies or viruses with mechanisms to evade the immune response. A caveat of this clinical case is that there is no serological sample between both infections to determine if the patient developed neutralizing antibodies after the first exposure. However, the mild symptoms after the reinfection could indicate some partial protection, and the genetic characterization of the viruses showed that the second virus harbored some mutations already described as implicated in escape from neutralizing antibodies. The fact that the second virus was isolated could suggest from Panamanian endemic lineages, A.2.4 (Franco et al., 2020) for the first, and A.2.5., containing Spike mutations D614G and L452R, for the second. Most of the fifthteen induced a.a. changes in the second virus, like the ones in ORF1a, have not been previously described. Most mutations detected in S and N, whose coding genes have the highest degree of variability in the SARS-CoV-2 genome (Vilar and Isom, 2020) has been previously associated with features that could facilitate reinfection. D614G mutation in S, with higher affinity for ACE2 receptor, results in increased infectivity and higher virus transmission (Korber et al., 2020; Q. Li et al., 2020) ; probably explaining why this mutation, detected in most dominant variants, has overtook the entire globe (Vilar and Isom, 2020). Spike mutation L452R, decreasing sensitivity to neutralizing antibodies, has been associated with immune escape and reinfection, and is present in the variant of interest (VOI) B.1.526.1, and the variants of concern (VOC) B.1.427 and B.1.429 (Hoffmann et al., 2020; J. Li et al., 2020; Q. Li et al., 2020; Naveca et al., 2019; Resende et al., 2021; Tchesnokova et al., 2021) . Currently, the lineage A.2.5 is the only A lineage with this mutation widely spread in B lineages. The observed three a.a. deletion (L141del, G142del, V143del) in S was located in an epitope involved in the generation of neutralizing antibodies (Tohidinia and Sefid, 2020) and Y144del was detected in the VOC B.1.1.7. D215A in the NTD of Spike hasn't been described, however D215G has been detected in the VOC B.1.351. As NTD has a role in interaction with the receptor, future studies are needed to analyze the role of J o u r n a l P r e -p r o o f these Spike mutations. In the N protein, residues S194 and M234 are one of the most mutated (Vilar and Isom, 2020), suggesting a purifying selection, and mutation P365S was associated with B cell epitopes (Tohidinia and Sefid, 2020) , suggesting that it could also let to an immune escape phenotype. These changes may reflect the ability of the second virus to escape neutralizing antibodies that could have been produced during the previous infection. Future studies associated with the genomic surveillance of the virus should be done to determine the prevalence of the mutations described, as well as their role in SARS-CoV-2 transmission and immune escape, and to know if they contribute to the reinfection cases in the country and could become another VOI. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. 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