Immunological and Genetic Investigation of SARS-CoV-2 Reinfection in an Otherwise Healthy, Young Marine Recruit

We used epidemiologic and viral genetic information to identify a case of likely reinfection in an otherwise healthy, young Marine recruit enrolled in the prospective, longitudinal COVID-19 Health Action Response for Marines (CHARM) study, and we paired these findings with serological studies. This participant had a positive RT-PCR to SARS-CoV-2 upon routine sampling on study day 7, although he was asymptomatic at that time. He cleared the infection within seven days. On study day 46, he had developed symptoms consistent with COVID-19 and tested positive by RT-PCR for SARS-CoV-2 again. Viral whole genome sequencing was conducted from nares swabs at multiple time points. The day 7 sample was determined to be lineage B.1.340, whereas both the day 46 and day 49 samples were B.1.1. The first positive result for anti-SARS-CoV-2 IgM serology was collected on day 49 and for IgG on day 91. This case appears most consistent with a reinfection event. Our investigation into this case is unique in that we compared sequence data from more than just paired specimens, and we also assayed for immune response after both the initial infection and the later reinfection. These data demonstrate that individuals who have experienced an infection with SARS-CoV-2 may fail to generate effective or long-lasting immunity, similar to endemic human beta coronaviruses.

Diagnostic accuracy of three prevailing rapid antigen tests for detection of SARS-CoV-2 infection in the general population: cross sectional study

Objective To assess the diagnostic accuracy of three rapid antigen tests (Ag-RDTs) for detecting SARS-CoV-2 infection in the general population. Design Cross-sectional study with follow-up using pseudonymised record linkage. Setting Three Dutch public health service COVID-19 test sites. Participants Consecutively included individuals aged 16 years and older presenting for SARS-CoV-2 testing. Main outcome measures Sensitivity, specificity, positive and negative predictive values of BD-Veritortm System (Becton Dickinson), PanBio (Abbott), and SD-Biosensor (Roche Diagnostics), applying routinely used sampling methods (combined oropharyngeal and nasal [OP-N] or nasopharyngeal [NP] swab), with molecular testing as reference standard. For SDBiosensor, the diagnostic accuracy with OP-N sampling was also assessed. A viral load cutoff (≥5.2 log10 SARS-CoV-2 E-gene copies/mL) served as a proxy of infectiousness. Results SARS-CoV-2 prevalence and overall sensitivities with 95% confidence intervals were 188/1441 (13.0%) and 129/188 (68.6% [61.5%-75.2%]) for BD-Veritor, 173/2056 (8.4%) and 119/173 (68.8% [61.3%-75.6%]) for PanBio, and 215/1769 (12.2%) and 160/215 (74.4% [68.0%-80.1%]) for SD-Biosensor with routine sampling, and 164/1689 (9.7%) and 123/164 (75.0% [67.7%-81.4%]) for SD-Biosensor with OP-N sampling. In those symptomatic or asymptomatic at sampling, sensitivities were 72.2%-83.4% and 54.0%-55.9%, respectively. With a viral load cut-off, sensitivities were 125/146 (85.6% [78.9%-90.9%]) for BD-Veritor, 108/121 (89.3% [82.3%-94.2%]) for PanBio, 160/182 (87.9% [82.3%-92.3%]) for SD-Biosensor with routine sampling, and 118/141 (83.7% [76.5%-89.4%]) with OP-N sampling. Specificities were >99%, and positive and negative predictive values >95%, for all tests in most analyses. 61.3% of false negative Ag-RDT participants returned for testing within 14 days (median of 3 days, interquartile range 3) of whom 90.3% tested positive. Conclusions The overall sensitivities of the three Ag-RDTs were 68.6%-75.0%, increasing to at least 85.6% after the viral load cut-off was applied. For SD-Biosensor, the diagnostic accuracy with OP-N and NP sampling was comparable. Over 55% of false negative Ag-RDT participants tested positive during follow-up.

Awareness and Occupational Exposure to Brucellosis and Other Zoonotic Diseases Among Abattoir Workers in Rwanda

Background: Brucellosis and bovine tuberculosis are endemic in Rwandan cattle, but little is known about the awareness of zoonotic transmission and occupational exposure among abattoir workers. Methods: A cross-sectional study was conducted to investigate the awareness, practices, and history of the diseases among 100 abattoir workers from four high throughput and 18 workers from two low throughput abattoirs. Data were collected by face-to-face interviews using a questionnaire, and exposure and outcome variables were assessed by univariate and correspondence analyses.Results: It was found that 82.2%, 27.1%, 8.5%, 10.2%, and 12.7% of abattoir workers were familiar with tuberculosis, brucellosis, Q-fever, leptospirosis, and cysticercosis, respectively. Three years before the survey, the majority (67.8%) of abattoir workers reported sickness of malaria (48.3%), and symptoms of flu (5.1%), headache (5.1%), fever (5.1%), headache (5.1%), and nephritis (3.4%). Malaria-negative patients had the symptoms of fatigue (11.0%), and flu (9.3%). Respondents (7.6%) had contracted ‘abattoir-related diseases including typhoid (1.7%) and have had symptoms of diarrhea (5.9%). Few workers also reported abortion (0.9%), and orchitis (0.9%). Most abattoir workers (70.3%) usually cut their hands, a few (9.3%) wore gloves while 39.8% worked with bare and injured hands. Most (74.6%) of workers experienced splashes of animal fluids into their faces while none (0.0%) wore facemasks or safety goggles. Eating at work was observed in 28.0% of abattoir workers. Univariate and correspondence analyses showed that transporters of carcasses, butchers, and workers with 3 years’ experience and above were more likely to get sick than other groups. Conclusions: The awareness that was low for zoonotic brucellosis, Q-fever, leptospirosis, and cysticercosis was supported by not wearing protective equipment’s alerting the competent veterinary authorities to improve biosafety protection in the abattoirs. The awareness for zoonotic brucellosis and tuberculosis was highest in educated workers indicating the need for educating abattoir. Abattoir workers reported the symptoms of fever, fatigue, flu, headache, nephritis, abortion, and orchitis which are common symptoms of brucellosis, leptospirosis, and Q-fever. Abattoirs are key points for the detection of zoonotic infectious diseases; thus, routine sampling and testing of slaughtered animals and abattoir workers are needed for surveillance and control of zoonotic diseases.

Evaluations of Surface PM10 Concentration and Chemical Compositions in MERRA-2 Aerosol Reanalysis over Central and Eastern China

The chemical composition dataset of Aerosol Reanalysis of NASA’s Modern-Era Retrospective Analysis for Research and Application, version 2 (MERRAero) has not been thoroughly evaluated with observation data in mainland China due to the lack of long-term chemical components data. Using the 5-year data of PM10 mass concentrations and chemical compositions obtained from the routine sampling measurements at the World Meteorological Organization the Global Atmosphere Watch Programme regional background stations, Jing Sha (JS) and Lin’An (LA), in central and eastern China, we comprehensively evaluate the surface PM10 concentrations and chemical compositions such as sulfate (SO42−), organic carbon (OC) and black carbon (BC) derived from MERRAero. Overall, the concentrations of PM10, SO42−, OC and BC from the MERRAero agreed well with the measurements, despite a slight and consistent overestimation of BC concentrations and a moderate and persistent underestimation of PM10 concentrations throughout the study period. The MERRAero reanalysis of aerosol compositions performs better during the summertime than wintertime. By considering the nitrate particles in PM10 reconstruction, MERRAero performance can be significantly improved. The unreasonable seasonal variations of PM10 chemical compositions at station LA by MERRAero could be causative factors for the larger MERRAero discrepancies during 2016–2017 than the period of 2011–2013.

Metals alter membership but not diversity of a headwater stream microbiome

Metal contamination from mining or natural weathering is a common feature of surface waters in the American west. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination and identify candidate microbial taxa to be used to indicate metal stress in stream ecosystems. We evaluated microbiome membership from sediments at multiple sites within the principal drainage of an EPA superfund site near the headwaters of the Upper Arkansas River, Leadville, CO. From each sample, we extracted DNA and sequenced the 16S rRNA gene amplicon on the Illumina MiSeq platform. We used the remaining sediments to simultaneously evaluate environmental metal concentrations. We also conducted an artificial stream mesocosm experiment using sediments collected from two of the observational study sites. The mesocosm experiment had a 2x2 factorial design: 1) location (upstream or downstream of contaminating tributary), and 2) treatment (metal exposure or control). We found no difference in diversity between upstream and downstream sites in the field. Similarly, diversity changed very little following experimental metal exposure. However, microbiome membership differed between upstream and downstream locations and experimental metal exposure changed microbiome membership in a manner that depended on origin of the sediments used in each mesocosm. Importance Our results suggest that microbiomes can be reliable indicators of ecosystem metal stress even when surface water chemistry and other metrics used to assess ecosystem health do not indicate ecosystem stress. Results presented in this study in combination with previously published work on this same ecosystem are consistent with the idea that a microbial response to metals at the base of the food web may be affecting primary consumers. If effects of metals are mediated through shifts in the microbiome, then microbial metrics, as presented here, may aid in the assessment of stream ecosystem health which currently does not include assessments of the microbiome.

Physiological responses of gopher tortoises (Gopherus polyphemus) to trapping

With a growing number of species of conservation concern, understanding the physiological effects of routine sampling of vertebrate species remains a priority to maintain the welfare status of wildlife and ensure such activities are not counter to conservation goals. The gopher tortoise (Gopherus polyphemus) is a species of conservation concern throughout its range and is among the most frequently trapped turtles globally (for both research and conservation activities). Several studies have found equivocal results on the effects of trapping and handling on the glucocorticoid stress response. In this study, we tested how multiple physiological biomarkers (i.e. plasma lactate, corticosterone (cort), heterophil:lymphocyte ratio (HLR) and bactericidal ability (BA)) respond to four different combinations of trapping conditions in comparison to baseline reference sampling. We found that trapping and handling of gopher tortoises yielded a rapid rise in plasma lactate concentration followed by elevations of cort and stress-associated immune changes. In visibly distressed animals that were in traps for fewer than 2 hours, lactate, cort, HLR and BA were all elevated, and generally more so than animals that remained calm in traps for a similar amount of time. Animals that had been trapped and then held for a 3-hour restraint showed similar degrees of physiological alteration as those that showed outward signs of distress. This study demonstrates that trapping may yield physiological disturbances in gopher tortoises, although the intensity of this response is highly variable between individuals and the duration of such alterations remains unknown. This research emphasizes the need for continued work to refine trapping and handling processes in an effort to minimize impacts on individuals and populations.

Routine SARS-CoV-2 wastewater surveillance results in Turkey to follow Covid-19 outbreak

1.AbstractA global pandemic of Coronavirus Disease 2019 (Covid-19) caused by severe acute respiratory syndrome coronavirus 2 (SAR-CoV-2) declared by WHO in March 2019 is still ongoing. As of 13th of December 2020, 70 million people were infected by SARS-CoV-2 and 1.5 million people lost their lives globally (WHO, 2020). Since March 2019, diagnosis of Covid-19 cases has been done through PCR test of samples from nasopharyngeal and throat swabs. However, in March 2019, it was reported that the faeces [1] and urine [2] of all infected people contain SARS-CoV-2. Later, numerous researchers [3-7] detected SARS-CoV-2 in faeces of both symptomatic and asymptomatic patients. Moreover, some studies [1,4,8-12] suggested the possibility of extended duration of viral shedding in faeces after the patients’ respiratory samples tested negative. In this respect, SARS-CoV-2 wastewater-based epidemiology (WBE), i.e., wastewater surveillance, aiming to estimate the distribution of asymptomatic and symptomatic individuals in a specific region has received worldwide attention. Various research groups worldwide [1, 13-54] have started SARS-CoV-2 detection in wastewater since WBE provides tracking whole population by testing a small number of wastewater samples in a specific region and can predict SARS-CoV-2 RNA in human faeces a few days to a week before onset of symptoms. This makes WBE quite economic tool for continual tracking of decreasing or increasing trend of the Covid-19 in a particular region. However, up to date, almost all of the WBE studies have been performed with samples from a few treatment plants. There was no reported nationwide wastewater surveillance study that has been integrated into a national Covid-19 management strategy by decision makers. Nationwide, SARS-CoV-2 surveillance studies have great potential to reflect the actual distribution of Covid-19 cases in a community by accounting not only symptomatic patients tested but also asymptomatic patients having no or mild symptoms and not been tested. As opposed to clinical surveillance studies, wastewater-based surveillance studies will reflect the number of cases in a community by testing one sample from a treatment plant serving this community instead of performing individual swab tests.Turkey, which is among the few countries that started wastewater based surveillance studies at the early stages of pandemic is a leading country, performing a nationwide surveillance study. The distribution of Covid-19 cases throughout the country via SARS-CoV-2 measurements in influent, effluent and sludge samples of wastewater treatment plants (WWTPs) located in 81 cities through May 2020-June 2020 was conducted [36, 51, 52]. In June 2020, nationwide routine sampling through 22 regional identified cities has been started. However, from June to September 2020 all samples were detected negative due to problems with RT-pCR primer targeting RdRp gene of SARS-CoV-2 genome. Since September 2020, routine sampling from 22 cities of Turkey with 2 weeks sampling period (weekly for mega city Istanbul) has been continued and regional Covid-19 distributions have been reported as viral loads on color-scale maps. To the best our knowledge, this is the first routine nationwide surveillance study indicating Covid-19 distribution regularly using color-scale presentation on a map.

Detection and Prevalence of Listeria in U.S. Produce Packinghouses and Fresh-Cut Facilities

ABSTRACT Listeria monocytogenes (LM) contamination of produce can often be traced back to the environment of packinghouses and fresh-cut facilities. Because there is limited information on the detection, prevalence, and distribution of this pathogen in produce operations, environmental “routine sampling” plans for LM and other Listeria spp. were developed and implemented in three packinghouses and five fresh-cut facilities in the United States. For routine sampling, a total of 2,014 sponge samples were collected over six to eight separate samplings per operation, performed over 1 year; vector and preproduction samples (n = 156) were also collected as needed to follow up on positive findings. In addition, a single “validation sampling” visit by an outside expert was used to evaluate the routine sampling. Among the 2,014 routine sponge samples collected, 35 and 30 were positive for LM and Listeria species other than LM (LS), respectively. LM prevalence varied from 0.8 to 5.8% for packinghouses and <0.4 to 1.6% for fresh-cut facilities. Among the 394 validation sponge samples, 23 and 13 were positive for LM and LS, respectively. Validation sampling found statistically significantly higher LM prevalence compared with routine sampling for three of eight operations. For all samples collected, up to eight isolates per sample were characterized by sequencing of sigB, which allowed for classification into sigB allelic types. Among the 97 samples with more than one Listeria isolate characterized, 28 had more than one sigB allelic type present, including 18 sponges that were positive for LM and another Listeria species and 13 sponges that were positive for more than one LM subtype. This indicates that collection of multiple isolates is necessary to capture Listeria diversity present in produce operations. Additionally, 17 of 77 sponges that were positive for LM were positive at only one enrichment time (i.e., 24 or 48 h), indicating that LM testing after two different enrichment times provides enhanced sensitivity. HIGHLIGHTS

Metals alter membership but not diversity of a headwater stream microbiome

Metal contamination from mining or natural weathering is a common feature of surface waters in the American west. Traditionally, stream macroinvertebrate community metrics have been used for stream quality assessments. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination in a manner similar to what has been observed for stream macroinvertebrates, and if so, identify candidate microbial taxa to be used to indicate metal stress in stream ecosystems. We evaluated microbiome membership from sediments at multiple sites within the principal drainage of an EPA superfund site near the headwaters of the Upper Arkansas River, Leadville, CO. From each sample, we extracted DNA and sequenced the 16S rRNA gene amplicon on the Illumina MiSeq platform. We used the remaining sediments to simultaneously evaluate environmental metal concentrations. We also conducted an artificial stream mesocosm experiment using sediments collected from two of the observational study sites. The mesocosm experiment had a 2×2 factorial design: 1) location (upstream or downstream of contaminating tributary), and 2) treatment (metal exposure or control). We found no difference in diversity between upstream and downstream sites in the field. Similarly, diversity changed very little following experimental metal exposure. However, microbiome membership differed between upstream and downstream locations and experimental metal exposure changed microbiome membership in a manner that depended on origin of the sediments used in each mesocosm.ImportanceOur results suggest that microbiomes can be reliable indicators of ecosystem metal stress even when surface water chemistry and other metrics used to assess ecosystem health do not indicate ecosystem stress. Several results presented in this study are consistent with the idea that a microbial response to metals at the base of the food web may be affecting consumers one trophic level above. If effects of metals are mediated through shifts in the microbiome, then microbial metrics, as presented here, may aid in the assessment of stream ecosystems health.

Review of pathology and cost benefit analysis of hernia sacs processed over a 19-year period

AimHernia sacs with pathological evaluation over a 19-year period were analysed with regards to pathological diagnoses, full costing and the impact on patient management.Materials and methodsThe database of the Department of Pathology were searched over the study period (2001 to 2019 inclusive) for hernia sacs. The total cost of complete pathology examination was calculated on average numbers and rates of pay that existed over the study period.ResultsA total of 3619 hernia sacs from the abdominal, hiatus/diaphragmatic, inguinal and femoral hernias were retrieved. Of these 3592 cases (99.25%) had sections taken for histological evaluation. A total of 3437 cases representing 95.7% of all hernia sacs did not show any pathological abnormality. If non-neoplastic clinically insignificant lesions seen in hernia sacs is included, then 3552 of 3592 (98.9%) hernia sacs underwent full pathological evaluation for no patient benefit.On average two blocks or tissue sections per case were processed incurring a technical cost of $53 175.00. The total pathologist cost in reporting the 3592 cases was approximately $39 870.00 and rose to $40 410.00 when interpretation of ancillary tests was factored in. $95 328.90 (average $26.90 per specimen with a yearly average total cost of $5 017.31) was spent over the 19-year period in full pathological examination of 3592 hernia sacs.ConclusionGiven the low return on investment and the difficult to quantify time savings and reallocation, we do not advocate the routine sampling of hernia sacs. Gross examination will suffice in 99% of the cases. Selective cases may be sampled if clinically indicated.