key: cord-0819425-yo29hay0 authors: Galanti, M.; Shaman, J. title: Direct observation of repeated infections with endemic coronaviruses date: 2020-05-03 journal: nan DOI: 10.1101/2020.04.27.20082032 sha: 8722288d173ed69c57ac05bef79ceeeb84f21f88 doc_id: 819425 cord_uid: yo29hay0 Background: While the mechanisms of adaptive immunity to pandemic coronavirus SARS-CoV-2 are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63 and OC43 provide a useful reference for understanding repeat infection risk. Methods: Here we used data from proactive sampling carried out in New York City from fall 2016 to spring 2018. We combined weekly nasal swab collection with self-reports of respiratory symptoms from 191 participants to investigate the profile of recurring infections with endemic coronaviruses. Results: During the study, 12 individuals tested positive multiple times for the same coronavirus. We found no significant difference between the probability of testing positive at least once and the probability of a recurrence for the beta-coronaviruses HKU1 and OC43 at 34 weeks after enrollment/first infection. We also found no significant association between repeat infections and symptom severity but strong association between symptom severity and belonging to the same family. Conclusion: This study provides evidence that re-infections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection. During the study, 12 individuals tested positive multiple times for the same coronavirus. We 39 found no significant difference between the probability of testing positive at least once and the 40 probability of a recurrence for the beta-coronaviruses HKU1 and OC43 at 34 weeks after 41 enrollment/first infection. We also found no significant association between repeat infections and 42 symptom severity but strong association between symptom severity and belonging to the same 43 family. 44 . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. The new coronavirus SARS-CoV-2 appears to have emerged in humans in the Hubei province of 55 China during November 2019 [1] . Human to human transmission was confirmed in early 56 January, and since then the virus has rapidly spread to all continents. The outbreak was declared 57 a pandemic by the WHO on March 11th. As of April 10th, it had spread to over 180 countries 58 with 1,521,252 confirmed cases and 92,798 deaths reported [2] . 59 60 Symptoms associated with SARS-CoV-2 vary from none to extremely severe, with elder adults 61 and people with underlying medical conditions more at risk for developing severe and potentially 62 fatal disease [3] . At present, there is no vaccine or approved antiviral treatment for SARS-CoV-63 2, and therapies rely principally on symptom management. Many institutions across the world 64 are working to develop a SARS-CoV-2 vaccine, and clinical trials with some vaccine candidates 65 have already begun [4] . 66 67 . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted May 3, 2020. . https://doi.org/10.1101/2020.04.27.20082032 doi: medRxiv preprint 4 As the pandemic progresses, infecting millions of people across the world, a key question is 68 whether individuals upon recovery are prone to repeat infection. A recent animal challenge study 69 showed evidence of (at least) short-term protection against re-infections in rhesus macaques 70 experimentally re-infected 4 weeks after first infection [5] . Typically, infections by different 71 viruses trigger different adaptive immune responses: viruses like measles elicit life-long 72 immunity; whereas others, like influenza, do not. Two main processes appear to be responsible 73 for the short-lived immunity engendered against some pathogens: 1) waning of antibodies and 74 memory cells in the host system; and 2) antigenic drift of the pathogen that enables escape from 75 the immunity built against previous strains. 76 To contextualize the issue of protective immunity to SARS-CoV-2, we here present findings 78 from a recent proactive sampling project carried out in New York City (NYC) that documented 79 rates of infection and re-infection among individuals shedding seasonal CoV (types: HKU1, 80 229E, NL63 and OC43). The results are discussed and analyzed in the broader context of 81 coronavirus infections. 82 83 84 . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted May 3, 2020. collection and extraction followed the same protocol as in [7] . 103 In addition, participants completed daily self-reports rating nine respiratory illness-related 105 symptoms (fever, chills, muscle pain, watery eyes, runny nose, sneezing, sore throat, cough, 106 . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted May 3, 2020. . https://doi.org/10.1101/2020.04.27.20082032 doi: medRxiv preprint 6 chest pain), each of which was recorded on a Likert scale (0=none, 1=mild, 2=moderate, 107 3=severe), see [6] for further survey details. 108 109 For this analysis, only the 191 participants who contributed at least six separate pairs of 110 nasopharyngeal samples in the same season were included. We defined an infection (or viral) 111 episode as a group of consecutive weekly specimens from a given individual that were positive 112 for the same virus (allowing for a one-week gap to account for false negatives and temporary low 113 shedding). We classified all infection episodes as symptomatic or asymptomatic according to 114 individual symptom scores in the days surrounding the date of the first positive swab of an 115 episode. We used multiple definitions as a standard for symptomatic infection does not exist 116 (Table 1) . These symptom definitions are described in reference to a -3 to +7-day window 117 around the date of the initial positive swab for each infection episode. The daily symptom score 118 is defined as the sum of the 9 individual symptoms (range: 0-27) on a given day. Total symptom 119 score is the daily symptom score summed over the -3 to +7-day window. . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. Figures S1 toS 4) . The probability of reinfection with beta-coronaviruses at > 38 171 weeks after prior infection was robust across different thresholds, whereas short terms 172 reinfection signals could be an artifact due to PCR amplification. This shifted threshold also 173 . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. Table 178 1. In particular, all the individuals who were completely asymptomatic during the first recorded 179 occurrence, did not report any symptoms during subsequent infection(s) with the same 180 coronavirus type. However, there was a significant association between severity of symptoms 181 associated with any coronavirus infection and belonging to the same family cluster (p<.0001, 182 one-way analysis of variance). Figure Infection with these viruses generally produces mild and even asymptomatic infection [10] . 194 Serological studies have shown that more than 90% of the population presents a baseline level of 195 antibodies against these endemic coronaviruses, with first seroconversion occurring at a young 196 . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. . https://doi.org/10.1101/2020.04.27.20082032 doi: medRxiv preprint age [11] [8] . Shortly after infection, baseline antibody titers increase sharply; this response has 197 been demonstrated for both natural and experimentally-induced infections [12] [13] [9] . 198 Antibody titers start increasing roughly one week following infection, reach a peak after about 2 199 weeks [13] , and by 4 months to 1 year have returned to baseline levels [13] [9] . A challenge 200 study [13] showed that the likelihood of developing an infection after inoculation correlated with 201 participants' concentration of antibodies at enrollment. Moreover, a positive correlation has been 202 shown between antibody rise after infection, severity of clinical manifestation and viral shedding 203 [12] , with milder cases linked to less substantial post-infection antibody rises. 204 Instances of natural re-infections with the same virus type have been documented previously [9] 205 in which repeated infections with OC43 and 229E were recorded by serological testing. 206 Subsequent infections were separated by at least 8 months, though study participants were tested 207 every 4 months. Participants in a separate challenge study were inoculated with coronavirus 208 229E and then re-challenged with the same virus after one year [13] . In most cases, re-infection 209 occurred, though it presented with decreased symptoms severity and shortened duration of 210 shedding. 211 The adaptive immune response to coronavirus is mainly directed towards the most variable part 213 of the virus, a region that is not conserved across types; consequently, cross-reactive protection 214 between different types does not appear to be an important factor [14, 15] . In addition, the effects 215 of antigenic drift on re-infection have not been elucidated [16] and more studies are warranted to 216 understand whether repeat infections are ascribable to rapid virus evolution rather than a decline 217 in antibody titers. 218 . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. T cells, that upon survival in the host lead to life-long protection against reinfection [18] . 227 Similarly, a longer immunity profile has been hypothesized for SARS and MERS due to their 228 increased severity and to the systemic response that infection induces [14] . Specific antibodies 229 were detectable for at least 2 years in SARS and MERS survivors [19] [20] . Although 230 longitudinal studies on SARS survivors have not detected specific SARS IGG antibody 231 persistence 5 years after infection, they have found that specific memory T cells persist in the 232 peripheral blood of recovered SARS patients, and at higher levels in patients who experienced 233 severe disease [21] . Whether the presence of these memory T cells would be enough to induce a 234 fast, protective response upon reinfection with SARS has not been assessed. 235 Our study confirms that seasonal coronaviruses are widespread in the general population with 236 infections directly documented for a large fraction of the participants in our study. The methods 237 for our analysis are based on the hypothesis that infection probabilities are comparable among 238 participants enrolled at different times in the study. However, the seasonality of endemic 239 coronaviruses, which are mostly absent during the summer months, and the relative magnitude 240 . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. . https://doi.org/10.1101/2020.04.27.20082032 doi: medRxiv preprint across years of seasonal coronavirus epidemics are limitations. In US the prevalence of OC43 241 during the 2016-17 season was much higher than during the 2017-18 season, whereas the 242 opposite trend was observed for HKU1 [22] . Moreover, our estimates of infection and re-243 infection probabilities must be considered as a lower bound, due to the occurrence of weekly 244 swabs missed by the participants and due to the design of the study itself, which may have 245 missed infections of short duration in between consecutive weekly tests. Nevertheless, this study 246 confirms that re-infections with the same coronavirus type occur in a time window shorter than 1 247 year, and finds no significant association between repeat infections and symptom severity. 248 Instead, it provides evidence of possible genetic determinants of innate immune response, as 249 individuals asymptomatic during first infection did not experience symptoms during subsequent 250 infections, and members of the same families reported similar symptom severity. We recognize 251 that the self-reporting of symptoms is an important limitation in this analysis and that parents 252 reported symptoms for their dependents, which possibly introduced bias. Moreover, the majority 253 of the repeated coronavirus infections were found in children, a cohort more vulnerable to 254 infection because of their immature immune system [23] , and 26% of the episodes in the 255 repeated infections were co-infections with other respiratory viruses (see Supplementary Table 256 S2). Another potential limitation of our study is the high sensitivity of PCR tests, that can 257 amplify very small amounts of genetic material, possibly not ascribable to active infections. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. . https://doi.org/10.1101/2020.04.27.20082032 doi: medRxiv preprint . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. . https://doi.org/10.1101/2020.04.27.20082032 doi: medRxiv preprint . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted May 3, 2020. . https://doi.org/10.1101/2020.04.27.20082032 doi: medRxiv preprint . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted May 3, 2020. . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted May 3, 2020. . https://doi.org/10.1101/2020.04.27.20082032 doi: medRxiv preprint The proximal origin of SARS-CoV-2 Situation Report Reinfection could not occur in SARS-CoV-2 infected rhesus macaques Longitudinal active sampling for respiratory viral infections across age groups Asymptomatic summertime shedding of respiratory viruses First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood Rises in titers of antibody to human coronaviruses OC43 and 229E in Seattle families during 1975-1979 Rates of asymptomatic respiratory virus infection across age groups Development of a nucleocapsid-based human coronavirus immunoassay and estimates of individuals exposed to coronavirus in a U.S. metropolitan population Enzyme-LinkedImmunosorbent Assay for Detection of Antibody in Volunteers Experimentally Infected with Human Coronavirus Strain 229E The course or immune response to experimental coronavirus infection of man Middle East respiratory syndrome vaccines Antibody to virus components in volunteers experimentally infected with human coronavirus 229E group viruses Viral Infections of Humans Neutralizing antibody decay and lack of contact transmission after inoculation of 3-and 4-day-old piglets with porcine respiratory coronavirus Effective clearance of mouse hepatitis virus from the central nervous system requires both CD4+ and CD8+ T cells Longitudinal profile of antibodies against SARS-coronavirus in SARS patients and their clinical significance Persistence of Antibodies against Middle East Respiratory Syndrome Coronavirus Lack of Peripheral Memory B Cell Responses in Recovered Patients with Severe Acute Respiratory Syndrome: A Six-Year Follow-Up Study Evolution of the immune system in humans from infancy to old age It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)The copyright holder for this preprint this version posted May 3, 2020. CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 3, 2020. . https://doi.org/10.1101/2020.04.27.20082032 doi: medRxiv preprint