mteb/CovidQA huggingface dataset:
we were unable to establish discriminating values for PCT. Recent data suggested that CRP could be of more help in assisting in the diagnosis of lower respiratory tract infections (LRTI) [15, 27, 28] . In our study, although CRP seems more discriminating than PCT, neither the experimental exclusion of extra-pulmonary bacterial infections from the excluded CAP group, nor the exclusion of viral CAP from the definite CAP patients group, made possible the determination of a discriminant cutoff. The combination of CRP and PCT was not more discriminating than each biomarker separately. An operational algorithm has been released to assist physicians in prescribing antimicrobial therapy [14, 26, 29] . According to this strategy, a PCT concentration higher than 0.25 μg/L should prompt administration of antibiotics to patients with suspected LRTI. In our study, this value was associated with poor performance. Additionally, mean PCT levels remained above this threshold both in excluded CAP
patients without infectious disorders and in definite CAP presumably related to virus. Therefore, the gold standard for the diagnosis of CAP may influence the performance and utility of PCT in this setting.
This study has some limitations. First, the adjudication committee was not blinded to the value of biomarkers measured at bedside in some patients (70 for CRP and 131 for PCT) and its CAP classification could thus have been influenced by these results. However, the lack of statistically significant differences in the mean CRP and PCT values in the definite CAP cases, whether or not these biomarkers were available for the adjudication committee, argues against a major impact of these results on adjudication committee classification. Second, another critical point is the prescription of antibiotic therapy (34 %) previous to inclusion. We cannot exclude that these previously-treated CAP patients may have altered biomarker performance and reduced the yield of bacterial cultures, although such a population reflects the usual emergency department practice. Third, multiplex PCR was performed on naso-pharyngeal sampling and not on lower respiratory tract samples, which does not allow definite
confirmation of the viral origin of CAP. However, a recent large study on CAP patients which reported a viral etiology of CAP at a comparable rate, did not find upper respiratory tract shedding in a control population without CAP explored during the same year and season [30] . Finally, even if multidetector thoracic CT scan is a better imaging examination than X-ray to explore the chest, only invasive local microbiological samples would have provided a diagnosis with certainty.
Given the diversity of the clinical and radiological CAP presentations, CAP diagnosis is often uncertain. In our population of patients treated in the emergency room with clinical symptoms evoking CAP, neither CRP nor PCT cut-off values carried sufficient weight to confirm or refute CAP diagnosis at bedside; this underlines that these biomarkers are telltales of the host inflammatory response to the intrusion of microorganisms independent of the site of infection. These results, based on a systematic thoracic CT scan evaluation of CAP-suspected patients, do not argue for the use of CRP and PCT in routine care to diagnose CAP with certainty in patients visiting the ED for suspected CAP.
Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183080/

SHA: ee6d70a53e3262cea6f85bd8b226f6b4c8b5f64b

Authors: Dellagi, Koussay; Rollot, Olivier; Temmam, Sarah; Salez, Nicolas; Guernier, Vanina; Pascalis, Hervé; Gérardin, Patrick; Fianu, Adrian; Lapidus, Nathanael; Naty, Nadège; Tortosa, Pablo; Boussaïd, Karim; Jaffar-Banjee, Marie-Christine; Filleul, Laurent; Flahault, Antoine; Carrat, Fabrice; Favier, Francois; de Lamballerie, Xavier
Date: 2011-09-29
DOI: 10.1371/journal.pone.0025738
License: cc-by
Abstract: BACKGROUND: To date, there is little information that reflects the true extent of spread of the pH1N1/2009v influenza pandemic at the community level as infection often results in mild or no clinical symptoms. This study aimed at assessing through a prospective study, the attack rate of pH1N1/2009 virus in Reunion Island and risk factors of infection, during the 2009 season. METHODOLOGY/PRINCIPAL FINDINGS: A serosurvey was conducted during the 2009 austral winter, in the frame of a prospective population study. Pairs of sera were collected from 1687 individuals belonging to 772 households, during and after passage of the pandemic wave. Antibodies to pH1N1/2009v were titered using the hemagglutination inhibition assay (HIA) with titers ≥1/40 being considered positive. Seroprevalence during the first two weeks of detection of pH1N1/2009v in Reunion Island was 29.8% in people under 20 years of age, 35.6% in adults (20–59 years) and 73.3% in the elderly (≥60 years) (P<0.0001).
Baseline corrected cumulative incidence rates, were 42.9%, 13.9% and 0% in these age groups respectively (P<0.0001). A significant decline in antibody titers occurred soon after the passage of the epidemic wave. Seroconversion rates to pH1N1/2009 correlated negatively with age: 63.2%, 39.4% and 16.7%, in each age group respectively (P<0.0001). Seroconversion occurred in 65.2% of individuals who were seronegative at inclusion compared to 6.8% in those who were initially seropositive. CONCLUSIONS: Seroincidence of pH1N1/2009v infection was three times that estimated from clinical surveillance, indicating that almost two thirds of infections occurring at the community level have escaped medical detection. People under 20 years of age were the most affected group. Pre-epidemic titers ≥1/40 prevented seroconversion and are likely protective against infection. A concern was raised about the long term stability of the antibody responses.
Text: In April 2009, the first cases of acute respiratory infections caused by a novel triple-reassortant influenza virus, pH1N1/ 2009v, occurred in Mexico and the United States [1] . The rapid spread of infection to other continents led the World Health Organization (WHO) to declare on 11 June 2009 that a pandemic of pH1N1/2009v influenza was under way, which raised major international concern about the risk of high morbidity and lethality and the potential for severe socio-economic impact. Actually, the potential impact of this first third-millenium influenza pandemic has been revisited downwards as morbidity and case-fatality rates were less severe than initially anticipated [2] . Illness surveillance data do not allow to an accurate estimate of the true influenza infection rate, as a substantial proportion of infections are asymptomatic or mild [3] . Serological surveys can overcome this limitation, but must take into account that a significant proportion of the population that
exhibited crossprotective antibody titers before circulation of the pH1N1/2009v [4] . This so-called ''baseline immunity'' has to be subtracted from the seroprevalence observed after the pandemic wave, to determine seroincidence in serosurveys [5] [6] [7] [8] . However, except for few studies [9] [10] [11] , most of these serosurveys did not use serial measurements in the same person, which allows for a better understanding of antibody kinetics and the dynamics of infection within individuals and communities.
Reunion Island (805,500 inhabitants) is a French overseas department located in the southwestern Indian Ocean, 700 km east of Madagascar and 200 km southwest of Mauritius. The first imported case of pH1N1/2009v was identified on 5 th July 2009 (week 29) in a traveller returning from Australia. The first case indicating community transmission was detected on 21 st July (week 30). pH1N1/2009v became the predominant circulating influenza virus within four weeks of its first detection, its activity peaked during week 35 (24) (25) (26) (27) (28) (29) (30) and ended at week 38 [12] . Contrary to initial fears, the health care system was not overwhelmed, as morbidity and mortality rates were lower than predicted [12] [13] [14] .
In order to assess at the community level, the actual magnitude of the pH1N1/2009v pandemic and the extent of the herd immunity acquired after passage of the epidemic wave, a prospective population serosurvey was conducted in Reunion Island during the passage of the epidemic wave in the 2009 austral winter season (July-December 2009): prevalence of infection was assessed on a weekly basis and seroconversion rates were measured using paired sera.
The CoPanFLu-RUN was part of the CoPanFLu international project, a consortium between the French National Institute of Health and Medical Research (INSERM), the Institute of Research for Development (IRD) and the Mérieux Fondation under the promotion of the School of Advanced Studies in Public Health (EHESP). To enable the rapid implementation of the study in anticipation of the imminent spread of the pandemic wave, we used a pre-existing sample of 2442 households established in October 2006 for the investigation of the Chikungunya outbreak (SEROCHIK) and updated in May 2008 throughout a follow-up telephone survey (TELECHIK) on a basis of 1148 households [15, 16] . We took special attention to select households representing a wide range of geographic locations in order to minimize the repartition bias.
The inclusion phase started on July 21 st (week 30) and was continued up to week 44, throughout the epidemic wave and beyond. A first serum sample (sample 1) was obtained from each household member. An active telephonic inquiry was then conducted twice a week to record symptoms compatible with influenza-like illness (ILI) occurring in households. Report of ILI (fever $37.8uC associated with any respiratory or systemic symptom) led to three consecutive visits of a nurse to the incident case-dwelling (on day 0, +3 and +8 post-report) to record symptoms and collect nasal swabs from all family members (for qRT-PCR detection of pH1N1/2009v. At week 45, the active inquiry was discontinued and a second (post-epidemic) serum sample (sample 2) was obtained (weeks 45-52) to determine seroconversion rates. Sera were aliquoted and stored at 280uC.
The protocol was conducted in accordance with the Declaration of Helsinki and French law for biomedical research (Nu ID RCB AFSSAPS: 2009-A00689-48) and was approved by the local Ethics Committee (Comité de Protection des Personnes of Bordeaux 2 University). Every eligible person for participation was asked for giving their written informed consent.

Viral genome detection by RT-PCR. Viral RNA was extracted from 140 mL of nasal swab eluate using the QIAamp Viral RNA kit (Qiagen) and processed for detection by TaqMan qRT-PCR targeting the heamagglutinin HA gene (SuperScript III Platinum one-step qRT-PCR system, Invitrogen) according to the recommendations of the Pasteur Institute (Van der Werf S. & Enouf V., SOP/FluA/130509). Confirmed pH1N1/2009v infection was defined as a positive qRT-PCR detection of the HA gene in at least one nasal swab.
Hemagglutination inhibition assay (HIA). A standard hemagglutination inhibition technique was adapted to detect and quantify pH1N1/2009v antibodies [17] . The antigen was prepared by diluting a non-inactivated cell culture supernatant producing a pdm H1N1v strain (strain OPYFLU-1 isolated from a young patient returning from Mexico in early May 2009) [18] . Briefly, the virus was propagated onto MDCK cells under standard conditions. The last passage (used for antigen preparation) was performed in the absence of trypsin and ht-FBS. The supernatant was collected at day seven p.i. clarified by centrifugation at 8006 g for 10 min at room temperature, aliquoted and conserved at 280uC. The hemagglutinating titer of the non inactivated viral antigen was immediately determined under the HIA format described below. The dilution providing 5.33 hemagglutinating units in a volume of 25 mL was used for subsequent HIA. Sera were heat-inactivated at 56uC for 30 min prior to use. Sequential twofold
dilutions in PBS (1/10 to 1/1280) in volumes of 25 mL were performed and distributed in V-bottom 96 well microplates. Human red blood cells (RBC) were used for hemagglutination experiments. Detection and quantification of antibody to pH1N1/2009v was performed as follows: 25 mL of virus suspension was added to the serum dilution (25 mL) and incubated for 1 hour at room temperature. Each well was then filled with 25 mL of a 1% RBC suspension in PBS (v/v: 0.33%), followed by another 30 min incubation at room temperature. The HIA titer was determined as the last dilution providing clear inhibition of hemagglutination. All experiments were performed in the presence of the same negative and positive controls, the latter including sera with 1/40, 1/80, 1/160 and 1/320 antibody titers.
The results reported in this study were based only on serological analysis of paired sera. For the sake of analysis, four successive phases were identified throughout the pandemic wave: phase A (weeks 30-31) corresponded to early epidemic time, phase B (W32-39) to the epidemic unfolding, phase C (W40-44) to the immediate post-epidemic stage and phase D (W45-52) to the late post-epidemic stage. Seropositivity was defined as a HIA titer of 1/ 40 or more. The baseline-proxy seroprevalence rate was estimated on serum samples collected in phase A. The cumulative incidence rate of infection measured the raise between the raw seroprevalence rate at any given time during the epidemic phases (S2pi) and the age-specific baseline-proxy seroprevalence rate (S1pA) (s2 pi -s1 pA ). Seroconversion was defined as a shift from seronegative at inclusion (sample 1: HIA ,1/40) to seropositive on follow-up (sample 2: HIA $1/40), or for sera tested seropositive on inclusion as a four-fold increase of HIA
titers between sample 1 and sample 2 paired sera. We also calculated the proportion of sera that tested seropositive in sample 1 for which the HIA titer decreased fourfold and passed under the cut-off value of 1/40 in sample 2. We considered this proportion as a ''seronegation'' rate.
The sample size was calculated for identifying risk factors in the prospective cohort study. Considering on average three individuals per household, an intra-household correlation of 0.3, a power greater than 80% could be obtained with a sample size of 840 comprising 2500 individuals, assuming exposure levels ranging from 10% to 90% and a relative risk greater than 1.3. With 2,500 subjects, the study allowed 1-2% absolute precision around the estimated values for seroconversion rates. Data entry used EpiData version 3.1 (The Epidata Association, Odense, Denmark). SAS version 9.1 (SAS Inc., Cary, NC, USA) was used for statistical analysis. The characteristics of the study cohort were compared to those of the population of Reunion Island and a Chi2 test (or Fisher's exact test when non applicable) was used to analyse differences in age, sex and geographic location. Cumulative incidence rates of infection (i.e. seroincidence) and seroconversion rates were standardized according to the
age structure of the community (French National Institute for Statistics and Economical Studies (INSEE) source).
Baseline-proxy seroprevalence, cumulative incidence rates of infection, as well as seroconversion and seronegation rates, were expressed as percentages. Cumulative reverse distribution curves were used to show the distribution of antibody titers. In all tests, a P value,0.05 was considered significant.

We estimated 95% confidence intervals (CIs) of proportions by using a cluster bootstrap technique with 1000 re-samples [19] . After bootstraping, we used an ANOVA model to compare mean cumulative incidence proportions between pandemic phases, within each age group. We used an alternating logistic regression model (ALR) with an exchangeable log Odds Ratio (OR) to test the intra-household correlation-adjusted association between factors and the seroconversion outcome.
Data were analysed with respect to subject age. Initially, four age groups were considered: the children and adolescents (,20 yrs), young adults (20-39 yrs), middle-age adults (40-59 yrs), and elderly adults ($60 yrs). As the cumulative incidence of infection of the second and third groups were very close, both groups were merged into one adults group (20-59 yrs). Therefore we refer further in our study to three age groups: children and adolescents (,20 yrs), adults (20-59 yrs), elderly ($60 yrs).
A total of 2,164 individuals from 772 households were enrolled between weeks 30 and 44 in the CoPanFlu-RUN cohort, allowing the collection of 1,932 sera at inclusion (sample 1). During this period, 136 households (17.7% of households) containing 464 individuals (21.4% of individuals) reported at least one case of ILI. Sixty subjects among the 464 individuals (12.9%, belonging to 33 households [24.3%]) were qRT-PCR positive, which documented the pH1N1/2009v infection. No positive qRT-PCR could be detected after week 37 and no ILI was reported after week 40, the end of the epidemic wave. The second follow up serum sample (sample 2) was obtained for 1,759 subjects at least five weeks after the end of the epidemic wave (weeks 45-52) which allowed the constitution of a serobank of 1,687 paired-sera. The profile of the cohort and the major outcomes are displayed in Figure 1 . Details on inclusions and serum sample timing with respect to the circulation of pH1N1/2009v over the island are
provided in figure 2 . The socio-demographic and space-time characteristics of the cohort are detailed in Table 1 . Compared to the community of Reunion Island, the sample of 1,687 individuals for whom pairedsera were available, was older (,20 yrs: 27% vs 35%, and $60 yrs: 17,9% vs 11,3%) and composed of a slight excess of females (54.1% vs 51.5%). The imbalance was due to a deficit in subjects aged under 40 years, reflecting men at work and the fact that parents declined the second serum for children younger than five.
Baseline-proxy (,pre-epidemic) HIA titers to the pH1N1/ 2009v were measured on sample 1 ( Table 2) , obtained from 249 subjects (103 households) recruited at the very beginning of the investigation during weeks 30 and 31 (phase A, Figure 2 ), when the epidemic activity in the cohort was still very low. Age distribution in this group was similar to that of the whole cohort (data not shown). The overall, the baseline-proxy seroprevalence rate (HIA $1/40), over all ages, was 43.4% (95%CI: 37.4%-49.6%). However the majority of positive sera had low antibody titers, at the cut off value for confirmation (i.e. = 1/40). The proportions of sera with HIA titer .1/40 were 0%, 3.0% and 24.6% in the young, middle-aged and older age groups respectively. These results indicate that pre-epidemic baseline antibody cross reactivity was stronger in the elderly ($60 yrs) and weaker in children and adolescents (,20 yrs) and adults (20-59 yrs), with highly significant differences between age groups
(P,0.0001).
The reverse cumulative distribution curves of HIA titers are displayed for each age group and for the whole cohort on Figure 3 . The proportion of seropositive sera (HI $1/40) steadily increased during the epidemic unfolding (phase B, W32-39) and in immediate post epidemic period (phase C, W40-44) when it reached its maximum level, then declined in the late post epidemic period (phase D, W45-52). This decline was significant enough to return the reverse cumulative distribution curve to baseline levels in the elderly. The cumulative incidence rates, obtained after subtraction of the age-specific baseline-proxy seroprevalence from the raw seroprevalence at each phase of the epidemic are shown in Table 2 (note that the cumulative incidence rates of infection represented for the group ''all ages'' were standardized according to age structure of the community). The cumulative incidence rates were much higher in children and adolescents (,20 yrs), indicating very active transmission of
infection within this age group. As mentioned earlier, cumulative incidence rates peaked in phase C (W40-44), and then declined indicating some lability of the humoral immune response against the pH1N1/2009v. The age-related difference observed in the incidence rates was highly statistically significant (P,0.0001).
To estimate more appropriately the decline of antibody titers occurring after the peak of the humoral response to the pH1N1/ 2009v, we considered paired-sera from the group of 264 subjects for whom the first serum sample (sample 1) was obtained just after the epidemic wave (phase C, W40-44), and the corresponding second sample was collected at the end of the survey (phase D, W45-52). Seronegation rates were 27.0% (61/226) for all age groups, 17.4% (12/69) in children and adolescents (,20 yrs), 32.3% (41/127) in adults (20-59 yrs) and 26.7% (8/30) in the elderly ($60 yrs). Differences between the seronegation rates according to age were statistically weakly significant (P = 0.0671).
We then considered the 1687 individuals for whom paired sera were available and we measured the seroconversion rates according to age and to the time of first serum sample collection (phase A, B or C). Criteria of seroconversion were defined in the method section. As shown in table 3, there was a sharp decline in seroconversion rates across all the age groups, depending on whether participants were enrolled during phase A, phase B, or phase C (P,0.0001). To interpret these data, one should remember that antibodies at seroprotective levels (HIA $1/40), in serum samples 1 collected during the per epidemic phase B or early post epidemic phase C could represent either base line cross reactive antibodies or rising pH1N1/2009 specific antibodies due to a recent or ongoing infection. This ambiguity could lead to underestimation of the seroconversion rate for subjects enrolled in phases B and C. In order to solve this ambiguity, we specifically considered the group of 249 subjects in whom
cross reactive antibodies were detected at the time of phase A (W30-31). The seroconversion rate of this group is the most indicative of the exposure of individuals to the whole epidemic wave. It was the highest (63,2%, P,0.0001) in children and adolescents (,20 yrs), and still significantly high in adults (39.4%, P,0.0001).
We then tested in this particular group, the impact of (baseline) pre-epidemic cross reactive antibodies on the rate of seroconversion to pH1N1/2009 (Table 4) . No subject with HIA titer superior to 1/40 had evidence of seroconversion to pH1N1/2009. The seroconversion rate in individuals with a HIA titer equal to 1/40 was linked with age, being more important in children and adolescents (,20 yrs). The highest seroconversion rate (.56%) was registered in subjects with HIA titers inferior to 1/40, particularly for the under 20 years where it reached 85%. Hence, the risk of seroconversion decreased when pre-epidemic HIA titer was high after controlling for age (P,0.0001) (Figure 4) . The multivariate adjusted odds ratio for seroconversion were 0.15 (95%CI: 0.06-0.37, P,0.0001) per two-fold increase in baseline titer, 1.79 (95%CI: 1.23-2.59, P,0.003) per other household members who seroconverted, 5.33 (95%CI: 1.56-19.27, P,0.008) Figure 1 . The cohort profile and major outcomes. Figure 1
details the three phases of the protocol: i) inclusion (weeks 30-44) and serum samples S1 collection; ii) follow up for detection of ILI in households, qRT-PCR on nasal swabs and estimation of cumulative seroincidence rates; iii) end of the study (weeks 45-52) and samples S2 collection. HIA on paired sera (S1+S2) allowed estimating seroconversion rates. doi:10.1371/journal.pone.0025738.g001 Bp (baseline-proxy) seroprevalence rates were estimated on weeks 30-31 in each age group. b Cumulative incidence rates measured the raise between raw seroprevalence rates and age-specific baseline-proxy seroprevalence rate. In the group ''All ages'', cumulative incidence rates were standardized according to age structure of the community. doi:10.1371/journal.pone.0025738.t002 Data are numbers, percentages (95% confidence intervals) and ALR parameter test P value for comparison of seroconversion proportions according to time of first sample (S1) collection at inclusion, in each age group, after