key: cord-0296821-mi7k5mkm authors: Nyaguthii, D. M.; Otieno, G. P.; Kombe, I. K.; Koech, D.; Mutunga, M.; Medley, G. F.; Nokes, D. J.; Munywoki, P. K. title: Infection patterns of endemic human coronaviruses in rural households in coastal Kenya. date: 2020-11-04 journal: nan DOI: 10.1101/2020.11.03.20225441 sha: ec3b5eb30e0a68934e5b44d8ed21c5dfe1a61830 doc_id: 296821 cord_uid: mi7k5mkm Introduction: The natural history and transmission patterns of endemic human coronaviruses are of increased interest following the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Methods: In rural Kenya 483 individuals from 47 households were followed for six months (2009-10) with nasopharyngeal swabs collected twice weekly regardless of symptoms. A total of 16,918 swabs were tested for human coronavirus (hCoV) OC43, NL63 and 229E and other respiratory viruses using polymerase chain reaction. Results: From 346 (71.6%) household members 629 hCoV infection episodes were defined with 36.3% being symptomatic: varying by hCoV type and decreasing with age. Symptomatic episodes (aHR=0.6 (95% CI:0.5-0.8) or those with elevated peak viral load (medium aHR=0.4 (0.3-0.6); high aHR=0.31 (0.2-0.4)) had longer viral shedding compared to their respective counterparts. Homologous reinfections were observed in 99 (19.9%) of 497 first infections. School-age children (55%) were the most common index cases with those having medium (aOR=5.3 (2.3-12.0)) or high (8.1 (2.9-22.5)) peak viral load most often generating secondary cases. Conclusion: Household coronavirus infection was common, frequently asymptomatic and mostly introduced by school-age children. Secondary transmission was influenced by viral load of index cases. Homologous-type reinfection was common. These data may be insightful for SARS-CoV-2. Four endemic species of human coronavirus (hCoV); HKU1, OC43, NL63 and 229E are widespread and associated primarily with mild acute respiratory illness [1] . Infections with endemic hCoVs are reportedly more severe in young children and the elderly [2, 3] . In the last two decades, three new members of this virus family have emerged as human pathogens; severe acute respiratory syndrome coronavirus (SARS-CoV) [4] , Middle East respiratory syndrome coronavirus (MERS-CoV) [5] and most recently SARS-CoV-2 [6] . The pandemic spread and continued circulation beyond the initial wave of infection suggests a potential for SARS-CoV-2 to become resident within the human population. A focus on the natural history and transmission characteristics of current little-studied endemic species of hCoV may give insight to the future behaviour of this emergent relative [7] . Using data from a study of 47 households in rural Kenya, we have previously reported baseline data on the occurrence of hCoV [8] and a detailed analysis of reinfection with hCoV-NL63 [9] . In the present study, we investigate the natural history of infection and transmission patterns of three endemic hCoV within these households. This study utilizes data from a prospective household-based cohort study conducted in one administrative location within the Kilifi health and demographic surveillance system (KHDSS) [8, 10] on the Kenyan coast. The study design and methods have been described elsewhere [8, 11] . Briefly, with a primary objective of characterising 'who infects whom' with respiratory 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint season (referred to as the study infant) and at least one elder sibling (aged <13 years) were enrolled. The study period spanned a complete RSV season from 8 th December 2009 to 5 th June 2010. Nasopharyngeal specimens (NPS) were collected from all household members irrespective of symptoms, once a week in the first four weeks and twice-a-week thereafter until the study end. A household was defined as members (who need not be related) of one or more building units who share the same cooking facility. The study had a good retention rate (>80%) of households and of individuals over the study period [11] . A previously described real time multiplex RT-PCR (mPCR) assay with targets for 15 respiratory viruses was used [12] . The target pathogens were human coronavirus (hCoV species (also called types) OC43, NL63 and 229E), RSV A and B, rhinovirus (RV), adenovirus (AdV), parainfluenza virus (types 1-4), influenza virus (types A, B and C) and human metapneumovirus (hMPV). A preliminary screen of the NPS showed the last three virus groups were uncommon during the surveillance period and hence not screened for the remainder of the NPS collections [8] . A specimen with a cycle threshold (Ct) value of ≤35.0 for a specific virus target was considered positive. Data analyses were undertaken in STATA Version 13.0 (StataCorp, College Station, Texas, USA). Descriptive statistics for continuous variables are presented as mean (± standard deviation) and median (interquartile range (IQR)). Categorical variables were summarised using counts and proportions and the chi-square test of association was used to examine the independence. The Mood's median test was used to investigate equality of median times across . 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint levels of categorical variables. Two or more groups were compared using test for equality of proportions. Type-specific individual hCoV infection episodes were defined as a period with positive mPCR result(s) of the same type with no more than 14 days apart [13] . Episodes where no samples were collected and tested for >7 days before or after the infection episode were considered leftor right-censored, respectively. An episode was considered symptomatic if the individual was identified with any of the following symptoms during the infection episode; cough, runny nose, sore throat, nasal flaring, indrawing, crackles, wheeze, fever, unable to feed, head nodding, lethargy, unable to talk, cyanosis or difficulty breathing. Co-infection was assigned when within the hCoV infection episode an NPS collection was mPCR positive for a different hCoV species or another of the viruses tested, namely; RSV, RV, or AdV. Detection of two or more individual infection episodes by the same hCoV type in a household within a span of 14 days constituted a household outbreak. For each household hCoV introduction, a primary (index) case was defined as the first person(s) to test positive for hCoV by mPCR while secondary case(s) were the rest of the members who are part of the same household outbreak. For individuals with multiple hCoV infection episodes, reinfections were classified as either homologous (same hCoV species) or heterologous (different hCoV species) with respect to previously detected species during the study period. As an example, if an individual has 3 infections in the temporal order OC43, NL63 and OC43, then the second infection episode would be heterologous to the first, and the third homologous to the first infection episode and heterologous to the second episode. Durations of virus shedding were estimated using a midpoint method which was defined as the period starting midway between the first positive sample and the previous negative sample and ending midway between the last positive sample and the subsequent negative sample. Further details on this approach are provided elsewhere [13] . Kaplan Meir (KM) curves were used to 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint describe the survival functions (time to end of virus shedding) by different categorical variables across the three endemic hCoV types. Adjusted hazard ratios (aHR) obtained from multivariable Cox proportional hazards (PH) models were used to estimate the influence of several factors on the duration of shedding and symptoms. Logistic regression models were used to identify risk factors for spread of infection from the primary cases to other household members. The risk factors considered were age, sex, household size, presence of respiratory symptoms, presence of other respiratory pathogens and peak viral load in an infection episode. The peak/highest viral load was defined as the lowest Ct value in an individual infection episode and was categorised into three levels; low (>=30), medium (20-29) and high (<20). To account for clustering either at individual or household level, robust cluster variance estimator was used in the Cox PH and logistic regression models discussed above. A total of 483 individuals from 47 households had NPS collected over the six-month period. 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint positive for both OC43 and 229E and 13 (0.08%) were positive for both NL63 and 229E. Only one sample was positive for all three hCoV tested. Higher individual crude attack rates (Table 1) The pattern of shedding of each of the three hCoV types and of all hCoVs, is displayed in 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint value <0.001 and 229E; ! (&) $ = 25.5, p-value <0.001). Of the total episodes, 29 (11.2%), 51 (23.6%), 28 (20%) and 105 (16.7%) of OC43, NL63, 229E or any hCoV infection episodes, respectively were either right or left-censored and were excluded in survival analysis. On average, the peak viral load of the individual infection episodes was higher in symptomatic compared to asymptomatic episodes ( Figure 2 ). This was supported by linear regression model, The duration of virus shedding varied by hCoV type with the longest median duration observed for OC43 (7.5 days, IQR: 3.5 -13.5) and the shortest median duration for 229E (3.5 days, IQR: 3.5 -7.0) ( Figure 3 ). The results of the survival analysis of shedding durations are shown in 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint CI: 0.14-0.36, p-value <0.001) compared to individuals with low peak viral load. Recovery The median duration of symptoms (Supplementary Table S1) was 7.0, 4.0, 3.5 and 4.0 days, for OC43, NL63, 229E and any hCoV, respectively. For any hCoV median durations tended to decline with increasing age, increase in the presence of other respiratory viruses and increase for high peak viral load. There was some variation between hCoV type. The rate of recovery from symptoms (Supplementary Table S2 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint high peak viral load (aHR=0.14 95% CI: 0.07 -0.29, p-value<0.001). Similarly, a lower recovery rate was observed for any hCoV infection episodes with medium peak viral load (aHR 0.45, 95% CI: 0.29 -0.68, p-value < 0.001) and high peak viral load (aHR=0.35, 0.23 -0.54, p-value<0.001). Details of reinfections in the study cohort are given in Table 3 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint The risk of generating a secondary case after introduction of any of the three endemic hCoV in the household was higher for index cases whose peak viral load was medium (aOR=5.29, 95% 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint compared those with a low peak viral load. However, being a symptomatic index case was not associated with increased risk of infecting other members of the household (aOR=0.97, 95% CI: 0.42 -2.21, p-value=0.933) compared to asymptomatic index cases (Supplementary Table S3 ). Longitudinal studies of households have played an important role in developing understanding of the epidemiology of respiratory viruses [7, 14] . Here we continue this approach, reporting an intensive surveillance of 483 household members in rural coastal Kenya [11] , to delineate the natural history of infection and transmission patterns of three endemic coronaviruses (OC43, NL63 and 229E). This involved the application of sensitive molecular diagnostic methods [7, 14] , and additionally applied sampling that was frequent and irrespective of observed symptoms [8] . The hCoV types were common in this setting with each of the 47 households, and about 72% of the enrolled household members, experiencing infection with at least one of three targets over the six months of the study. A note of caution in interpreting the results of this study is that infection status determined by PCR assay is not necessarily indicative of active infection or an individual's infectiousness. Crude attack rates were highest for hCoV-OC43 and lowest for 229E, higher in general for younger age classes (<15 years of age), school-age children and for males. These results are broadly consistent with the findings by Monto et al. who also found highest incidence for OC43, lowest for 229E, and higher incidence among those aged below 5 years for NL63 and OC43 [7] . 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint The three hCoV types had differing durations of shedding ranging from 3.5 days (229E) to 7.5 days (OC43). However, these median time estimates are influenced by our sampling frequency: predominantly every 3-4 days. The duration of shedding was longer in episodes with high peak virus load and which were symptomatic. Consistent with findings from other studies, we report occurrence of hCoV infection episodes among asymptomatic individuals [15] [16] [17] who had lower viral load [18] and shorter durations of virus shedding compared to symptomatic episodes. Despite asymptomatic infections being predominant (>70% of episodes) the above findings suggest they were less likely to transmit infection compared to symptomatic individuals. The duration of symptomatic episodes was related to peak virus load as reported elsewhere [25] and tended to decline with increasing age. suggesting previous infection does not provide solid immunity. This is supported by our observation that, within the short period of the study, reinfections were common and as frequently of homologous as heterologous type. Overall, 20% of individuals with a first infection of one or other type, were reinfected by the same type at least once, most commonly for type NL63 (24.5%). Homologous reinfections were frequently (>30%) symptomatic. We report no difference in the proportion of symptomatic cases between the first episodes and reinfection episodes and note that the time to reinfection with homologous was similar to heterologous episodes (~40 days). Our observations indicate that immunity to reinfection is commonly short lived and does not appear to be type specific. A recent serological study involving 10 adult men detected reinfections from seasonal coronaviruses but most frequently occurring after an interval of 12 months [19] . A limitation of our analysis is that reinfections might in fact have been prolonged shedding from a single infection. This is likely not a major 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint effect as in most presumed reinfections (>70%) there were at least 4 PCR test negative results between episodes. Older children (siblings and cousins) and other adults were the major introducers of hCoV transmission into the household compared to RSV transmission in the same households whereby older children (> 32%) were the leading primary cases [11] . Similarly, children have been reported to form the highest proportion of index cases in the USA and UK [7, 20] . However, presence of older adults, children, smokers and individuals with chronic ailments within the households in the UK study was associated with increased household transmission [20] . Secondary transmission of hCoV to other household members upon introduction was high (48%) for any of the three hCoVs (ranged from 39% to 62% across type). This differs from a recent study in England which concluded that the vast majority (>90%) of observed hCoV infections were acquired outside the household [20] . In our study, the risk of secondary transmission was higher among index cases with high viral loads. Interestingly, there was no significant association between the presence of symptoms among index cases and the risk of secondary transmission, as observed elsewhere [20] . In conclusion, endemic coronaviruses are common within the household setting, infecting all age groups, and often without eliciting symptoms. Secondary transmission following household introduction is associated with viral load but not, it appears, with symptomatic status, and homologous reinfection is common for all hCoV types. 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint The authors have no competing interests to declare. DMN and GPO contributed equally to the drafting of the manuscript. 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint . 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint Key: aHR, adjusted Hazard Ratio; hCoV-hCoV coinfection denotes infection episodes in which an individual tested positive for two or more hCoVs. 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 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 4, 2020. ; https://doi.org/10.1101/2020.11.03.20225441 doi: medRxiv preprint Genetic Recombination, and Pathogenesis of Coronaviruses Rhinovirus and coronavirus infection-associated hospitalizations among older adults Clinical disease in children associated with newly described coronavirus subtypes Identification of a Novel Coronavirus in Patients with Severe Acute Respiratory Syndrome Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet Coronavirus Occurrence and Transmission Over 8 Years in the HIVE Cohort of Households in Michigan Continuous Invasion by Respiratory Viruses Observed in Rural Households During a Respiratory Syncytial Virus Seasonal Outbreak in Coastal Kenya Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya Profile: The Kilifi Health and Demographic Surveillance System (KHDSS) The Source of Respiratory Syncytial Virus Infection In Infants: A Household Cohort Study In Rural Kenya Added value of an oropharyngeal swab in detection of viruses in children hospitalized with lower respiratory tract infection Influence of age, severity of infection, and co-infection on the duration of respiratory syncytial virus (RSV) shedding Frequency of Acute Respiratory Illnesses and Circulation of Respiratory Viruses in Households With Children Over 3 Surveillance Seasons Role of respiratory viruses in acute upper and lower respiratory tract illness in the first year of life: a birth cohort study Frequent detection of respiratory viruses without symptoms: toward defining clinically relevant cutoff values Serial viral infections in infants with recurrent respiratory illnesses Human rhinovirus and coronavirus detection among allogeneic hematopoietic stem cell transplantation recipients Seasonal coronavirus protective immunity is short-lasting Household transmission of seasonal coronavirus infections: Results from the Flu Watch cohort study