ABSTRACT
Background. In the Guatemala AGricultural workers and Respiratory Impact (AGRI) study, we evaluated the clinical and socioeconomic burdens of respiratory disease in a cohort of Guatemalan banana farm workers. Methods. All eligible workers were offered enrollment from June 15-December 30, 2020, and annually, then followed for influenza-like illnesses (ILI) through: 1) selfreporting to study nurses, 2) sentinel surveillance at health posts, and 3) absenteeism. Workers with ILI submitted nasopharyngeal swabs for influenza, RSV, and SARS-CoV-2 testing, then completed surveys at days 0, 7, and 28. Enrollment and acute-illness serum samples were tested for anti-SARS-CoV-2 nucleocapsid IgG (anti-N, Roche Elecsys ), and neutralizing antibodies (NAb) were tested in a subset using a lentivirus-based pseudovirion assay. Results. Through October 10, 2021, 1,833 workers were enrolled. The majority were male (84%), young (mean 31 years), and healthy (< 13% had comorbidity). Through October 10, 2021, 1,833 workers developed 169 ILIs (12.0/100 person-years) and 43 (25.4%) of these ILIs were laboratory-confirmed SARS-CoV-2 (3.1/100 person-years). Workers with SARS-CoV-2-positive ILI reported more anosmia (p< 0.01), dysgeusia (p< 0.01), difficulty concentrating (p=0.01), and irritability (p=0.01), and greater clinical and well-being severity scores (Flu-iiQ) than testnegative ILIs (Fig 1);they also had greater absenteeism (p< 0.01) and lost income (median US$127.1, p< 0.01). Among 1334 workers enrolled in 2020, 616 (46.2%) had anti-N IgG suggestive of prior SARS-CoV-2 infection. COVID-19 incidence density for IgG-seropositive workers was 0.4/100 Person Years (PY), lower than those who were seronegative (2.3/100 PY) (Fig 2). At enrollment, anti-N IgG titers in serum correlated with neutralizing antibody titers (R2 =0.26, p< 0.0001). Notably, in < 6 months from enrollment, most workers with follow-up NAb testing (65/77, 84%) exhibited a 95% decrease in neutralizing antibody titers. Conclusion. Guatemalan farm workers suffered a significant burden of COVID-19, including more severe clinical and economic outcomes than other respiratory illnesses. Ongoing vaccination programs and longitudinal serology will provide additional insight into long-term immunity.
ABSTRACT
Background. Saliva samples are less invasive but not considered the gold standard for detecting SARS-CoV-2, and they are not validated for the Roche Cobas Liat platform. We aimed to evaluate the performance of a saliva sample compared to nasopharyngeal (NP) swab in the detection of SARS-CoV-2 on the Roche Cobas Liat platform at a research site in rural Guatemala. Methods. Adults in an existing cohort study with influenza-like illness (ILI) provided clinical data and underwent NP swab (Copan) collection by trained nurses. Swabs were immediately placed into universal transport media (UTM), stored at 2-8 degreeC for less than 30 minutes and then tested on the Cobas Liat platform for SARS-CoV-2. Consenting subjects who had not eaten or drank in the last 2 hours were asked to provide a 5-mL saliva sample directly into an RNAse free container. The saliva sample remained at 2-8 degreeC for 24 hours, then diluted 1:2 with 0.85% saline (to reduce viscosity) and run on the same assay. We used descriptive statistics to compare the performance of saliva to NP swabs. Results. Of the 28 subjects screened (1/10/22 - 4/26/22), 23 (82%) were consented and enrolled. The majority of subjects were male (78.3%) with a mean age of 31 years (range: 18-59 years). Of the 23 subjects enrolled, 14 (30.4%) reported fever and cough, 16 (34.8%) reported cough only, 14 (30.4%) reported fever only, and 2 (4.3%) reported cough and nasal congestion. The median symptom duration was 3.0 days (IQR: 1.5-5 days). Of the 23 subjects, 5 (23.7%) tested positive for SARS-CoV-2 in both sample types (NP swab and saliva);3 (13%) were discordant, including 1 (4.3%) saliva-positive only and 2 (8.7%) NP-positive only. Compared to NP swab, preliminary performance of saliva in detection of SARS-CoV-2 included a sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of 71.4%, 93.7%, 87%, 83.3%, and 88.2%, respectively. The Fisher's exact test p-value (0.003) shows concordance between both tests. Conclusion. Our preliminary results show good precision between NP and saliva samples in detection of SARS-CoV-2 on the Roche Cobas Liat platform. Ongoing data collection will provide greater insight on the discordant results, but our findings support the continued use of saliva in the detection of SARS-CoV-2 in this population.
ABSTRACT
Background: Universal pre-operative screening with SARS-CoV-2 PCR has been adopted by institutions to mitigate risk to healthcare workers (HCW) during aerosol- generating procedures such as intubation. However, there remains uncertainty regarding rates of false negative results and optimal sampling type. The objective was to determine the reliability of single, pre-operative SARS-CoV-2 testing from the nasopharynx in children undergoing general anesthesia. Methods: Children < 18 years of age who underwent intubation for a procedure received pre-operative testing 24-48 hours prior with a nasopharyngeal (NP) swab or wash, in conjunction with intra-operative nasal wash (NW) and tracheal aspirate (TA) sampling. All paired samples underwent testing using the Simplexa DiaSorin platform or a modified Centers for Disease Control assay. Cohen's Kappa was used for interrater reliability of each sample result. McNemar's Test was used to compare result proportions by sample type. Positive and negative predictive values (PPV, NPV) were calculated based on the intraoperative NW as the reference standard. Analyses were conducted using SAS (v 9.4). Results: We collected full sample sets from 364 children from April 14 to May 15;66% of pre-operative samples were NP swabs. The median age was 6 years (IQR 2,13), 55% were male, 68% were white and 41% of children had a high-risk comorbidity. Most surgeries were conducted by general surgery (23%), followed by orthopedics (19%). Only 2.5% of children had respiratory symptoms, and 4.8% had a documented fever within a week of the procedure. SARS-CoV-2 positive samples occurred in 4/364 (1%) of pre-operative samples, 8/363 (2.2%) of intra-operative samples, and 8/348 (2.3%) of TA samples. The pre-operative test had 100% PPV and 99% NPV, and the TA had 100% PPV and 98.6% NPV (Table 1). There was very good agreement (Figure) between pre- and intraoperative upper respiratory sampling, with a Kappa of 0.66, (95% CI 0.35-0.97). There was no statistical difference in results by sample type. (Table Presented). Conclusion: There is a high PPV and NPV of pre-operative SARS-CoV-2 PCR testing among children undergoing anesthesia. These data can help inform guidelines regarding appropriate precautions for HCW performing high risk procedures in asymptomatic pediatric patients. (Table Presented).