// Threat Assessment Brief Reinfection with SARS-CoV-2: considerations for public health response 21 September 2020 Introduction Cases with suspected or possible reinfection with SARS-CoV-2 have been recently reported in different countries [1-4]. In many of these cases, it is uncertain if the individual’s Polymerase Chain Reaction (PCR) test remained positive for a long period of time following the first episode of infection or whether it represents a true reinfection. The aim of this Threat Assessment Brief is to elucidate the characteristics and frequency of confirmed SARS-CoV-2 reinfection in the literature, to summarise the findings about SARS-CoV-2 infection and antibody development, and to consider the following questions: • How can a SARS-CoV-2 reinfection be identified? • How common are SARS-CoV-2 reinfections? • What is known about the role of reinfection in onward transmission? • What do these observations mean for acquired immunity? Finally, options for public health response are proposed. Issues to be considered • Some patients with laboratory-confirmed SARS-CoV-2 infection have been identified to be PCR-positive over prolonged periods of time after infection and clinical recovery [5,6]. • The duration of viral RNA detection (identification of viral RNA through PCR testing in a patient) has been shown to be variable, with the detection of RNA in upper respiratory specimens shown up to 104 days after the onset of symptoms [7-9]. • Of note, patients have also been reported to have intermittent negative PCR tests, especially when the virus concentration in the sampled material becomes low or is around the detection limit of a test [4]. • It is important to note that the identification of SARS-CoV-2 RNA through PCR (i.e. viral RNA shedding) does not equate to the presence of viable, infectious virus within a patient. • Additional challenges to classifying suspected cases as ‘confirmed’ reinfections have been the absence of testing results and the lack of genetic sequencing. Confirmation is further complicated because common criteria for the identification of reinfections have not yet been established. • As described below, additional tests must be run to check for viable virus, and when considering an individual patients’ situation, test results must be interpreted in combination with additional epidemiological and clinical characteristics. Suggested citation: European Centre for Disease Prevention and Control. Reinfection with SARS-CoV: considerations for public health response: ECDC; 2020 © European Centre for Disease Prevention and Control. Stockholm, 2020. THREAT ASSESSMENT BRIEF Reinfection with SARS-CoV-2: considerations for public health response Event background Elucidating the characteristics and frequency of reinfection is crucial, as it could impact on our understanding of acquired immunity after natural infection. This section focuses on recent published or pre-print case reports from Hong Kong, Nevada, USA, Belgium, Ecuador and India that describe reinfections based on genetic sequencing as confirmation of second infections with SARS-CoV-2, following a first confirmed infection [10-14]. There are also media reports of cases in the Netherlands, Spain and several additional cases globally that are under investigation and not yet present in the literature [15-18]. Hong Kong A publication by To et al [10] reports an episode of SARS-CoV-2 infection detected in mid-August 2020, in Hong Kong, in an immunocompetent 33 year old man during routine airport screening, 142 days after the first positive PCR. The patient presented with symptoms of cough, sore throat, fever and headache for three days during the first episode and was hospitalised for isolation purposes, although his symptoms had mostly resolved upon hospitalisation. The patient was discharged two weeks later after two subsequent negative SARS-CoV-2 PCR assays on nasopharyngeal and throat swabs. During the second infection, the patient was asymptomatic and was reported to have a slightly elevated C-reactive protein, a relatively high viral load which decreased over time, and a seroconversion of SARS-CoV-2-IgG, all suggesting that the second episode was a new acute SARS-CoV-2 infection. The patient’s reinfection was differentiated from prolonged PCR positivity after the first infection through whole genome analysis. The two SARS-CoV-2 strains belonged to different clades/lineages with 24 nucleotide differences, which is a high amount given the relatively slow rate of mutation observed for SARS-CoV-2 to date. These clades match the epidemiology of the main clades circulating where the patient was likely infected (i.e. the first strain clustered with viruses from Hong Kong while the second strain clustered with viruses from Spain). Viral culture for the second episode was pending at the time of publication. Nevada, USA Tillet et al [11], report a case of a 25 year old immunocompetent male with COVID-19-like symptoms of sore throat, cough, headache and nausea who tested positive for SARS-CoV-2 on 18 April 2020, 24 days post-symptom onset. The patient was isolated and his symptoms resolved nine days after testing. The patient tested negative twice in the weeks following symptom resolution and felt well until 31 May 2020, when the patient sought care for fever, headache, dizziness, cough, nausea and diarrhoea. The patient’s symptoms worsened five days later, with hypoxia and shortness of breath leading the patient to be hospitalised and to receive oxygen support. A chest x-ray performed at that time indicated viral or atypical pneumonia and RT-PCR was positive for SARS-CoV-2. Seven days post-symptom onset during the second episode the patient was reactive for IgG/IgM for SARS-CoV-2. Specimens from the first and second episodes were available and whole genome sequencing was performed. SARS-CoV-2 sequences determined from both episodes were found to cluster in the same clade, but with seven nucleotide differences between them. The authors used the substitution rate which calculates the number of mutations over a respective time period and compared the result of the difference between the two viruses, with the expected substitution rate of naturally occurring mutations in SARS-CoV-2 viruses in general over the same time period. The calculations for the difference between episode one and two resulted in a value of 83.6, which by far exceeded the currently observed naturally occurring substitution rate of 23.1, and suggested two independent infections with different viruses. Viral culture and sub-genomic RNA were not performed. Belgium Van Elslande et al [12] reported a case of reinfection in a 51 year old woman who presented with headache, fever, myalgia, cough, chest pain, dyspnoea and anosmia to her general practitioner on 9 March 2020. The patient was immunocompetent, but took a daily dose of oral corticosteroids for asthma. A nasopharyngeal swab was positive for SARS-CoV-2 with a Ct value of 25.6. The patient self-isolated at home and reported persistent symptoms for nearly five weeks. Three months (10 June 2020) after her initial symptoms, the patient presented with headache, cough, fatigue and rhinitis. Her nasopharyngeal swab was again positive for SARS-CoV-2 (Ct value 32.6). The symptoms lasted for one week and again resolved without hospitalisation. Neutralising antibodies were assessed six weeks after the second episode’s symptom onset and were present at that time (1/320). Full length genome sequencing showed 11 differences between the two episodes’ isolates, confirming infection with different strains. Viral culture was not performed, and neutralising antibodies were not assessed between the two episodes. 2 THREAT ASSESSMENT BRIEF Reinfection with SARS-CoV-2: considerations for public health response Ecuador Prado-Vivar et al [13] report a case of reinfection in a 46 year old immunocompetent male who presented on 12 May 2020 after three days of headache and drowsiness. At 11 days post-symptom onset, an oropharyngeal swab was positive for SARS-CoV-2 with a Ct value of 36.85 (ORF3a gene). The patient’s symptoms improved and a repeat PCR on 3 June 2020 was negative. In July 2020, the patient reported close contact with a relative that was later diagnosed with COVID-19. Two days following this contact, on 20 July 2020, the patient presented with symptoms including headache, fever, cough and shortness of breath. On 22 July 2020, another oropharyngeal sample tested positive for SARS-CoV-2 (no Ct values reported). Although the patient’s symptoms during the second episode were more severe than the first episode, hospitalisation was not required. Qualitative IgG/IgM was negative for IgG and positive for IgM on 16 May 2020; a test for antibodies on 18 August during the second episode was positive for IgG and IgM. Genome sequencing and phylogenetic analysis showed that the infection episodes belonged to different clades with nine variant differences. Viral culture was not performed, and neutralising antibodies were not assessed between the two episodes. India Gupta et al [14] report two cases of reinfection, both in immunocompetent health workers posted in the COVID-19 unit at a tertiary hospital in India. Patient I1, a 25 year old man, was found PCR positive on 5 May 2020 (Ct: 36) during routine surveillance of health workers. He was asymptomatic but isolated as per institutional policy until he became PCR negative. He continued working thereafter and was found PCR-positive again on 17 August (Ct 16.6). The patient was again isolated and remained asymptomatic throughout the second episode. Antibody testing, neutralising antibodies and viral culture results were not reported. Sequencing of samples from both episodes was performed along with genomic analysis; the first and second episodes revealed nine variant differences. Patient I2, a 28 year old woman, was found PCR positive on 17 May 2020 (Ct: 28.16), also during routine surveillance of health workers. She was asymptomatic but isolated as per institutional policy until she became PCR negative.