PCR-positive Individuals Research Articles

Association of C4 and CH50 levels with cough and rhinorrhea in COVID-19 patients: A retrospective analysis in the Iranian population

Association of C4 and CH50 levels with cough and rhinorrhea in COVID-19 patients: A retrospective analysis in the Iranian population

Anti-RBD IgG antibodies from endemic coronaviruses do not protect against the acquisition of SARS-CoV-2 infection among exposed uninfected individuals.

The Coronaviridae family comprises seven viruses known to infect humans, classified into alphacoronaviruses (HCoV-229E and HCoV-NL63) and betacoronaviruses (HCoV-OC43 and HCoV-HKU1), which are considered endemic. Additionally, it includes SARS-CoV (severe acute respiratory syndrome), MERS-CoV (Middle East respiratory syndrome), and the novel coronavirus SARS-CoV-2, responsible for COVID-19. SARS-CoV-2 induces severe respiratory complications, particularly in the elderly, immunocompromised individuals and those with underlying diseases. An essential question since the onset of the COVID-19 pandemic has been to determine whether prior exposure to seasonal coronaviruses influences immunity or protection against SARS-CoV-2. In this study, we investigated a cohort of 47 couples (N=94), where one partner tested positive for SARS-CoV-2 infection via real-time PCR while the other remained negative. Plasma samples, collected at least 30 days post-PCR reaction, were assessed using indirect ELISA and competition assays to measure specific antibodies against the receptor-binding domain (RBD) portion of the Spike (S) protein from SARS-CoV-2, HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1. IgG antibody levels against the four endemic coronavirus RBD proteins were similar between the PCR-positive and PCR-negative individuals, suggesting that IgG against endemic coronavirus RBD regions was not associated with protection from infection. Moreover, we found no significant IgG antibody cross-reactivity between endemic coronaviruses and SARS-CoV-2 RBDs. Taken together, results suggest that anti-RBD antibodies induced by a previous infection with endemic HCoVs do not protect against acquisition of COVID-19 among exposed uninfected individuals.

Microheterogeneity of Transmission Shapes Submicroscopic Malaria Carriage in Coastal Tanzania.

Asymptomatic carriage of malaria parasites persists even as malaria transmission declines. Low-density infections are often submicroscopic, not detected with rapid diagnostic tests (RDTs) or microscopy but detectable by polymerase chain reaction (PCR). To characterize submicroscopic Plasmodium falciparum carriage in an area of declining malaria transmission, asymptomatic persons >5 years of age in rural Bagamoyo District, Tanzania, were screened using RDT, microscopy, and PCR. We investigated the size of the submicroscopic reservoir of infection across villages, determined factors associated with submicroscopic carriage, and assessed the natural history of submicroscopic malaria over 4 weeks. Among 6076 participants, P. falciparum prevalences by RDT, microscopy, and PCR were 9%, 9%, and 28%, respectively, with roughly two-thirds of PCR-positive individuals harboring submicroscopic infection. Adult status, female sex, dry season months, screened windows, and bed net use were associated with submicroscopic carriage. Among 15 villages encompassing 80% of participants, the proportion of submicroscopic carriers increased with decreasing village-level malaria prevalence. Over 4 weeks, 23% of submicroscopic carriers (61 of 266) became RDT positive, with half exhibiting symptoms, while half (133 of 266) were no longer parasitemic at the end of 4 weeks. Progression to RDT-positive patent malaria occurred more frequently in villages with higher malaria prevalence. Microheterogeneity in transmission observed at the village level appears to affect both the size of the submicroscopic reservoir and the likelihood of submicroscopic carriers developing patent malaria in coastal Tanzania.

Understanding the role of Francisella halioticida in mussel mortalities in France: an integrative approach.

Since 2014, mass mortalities of mussels Mytilus spp. have occurred in production areas on the Atlantic coast of France. The aetiology of these outbreaks remained unknown until the bacterium Francisella halioticida was detected in some mussel mortality cases. This retrospective study was conducted to assess the association between F. halioticida and these mussel mortalities. Mussel batches (n = 45) from the Atlantic coast and English Channel were selected from archived individual samples (n = 863) collected either during or outside of mortality events between 2014 and 2017. All mussels were analysed by real-time PCR assays targeting F. halioticida; in addition, 185 were analysed using histological analysis and 178 by 16S rRNA metabarcoding. F. halioticida DNA was detected by real-time PCR and 16S rRNA metabarcoding in 282 and 34 mussels, respectively. Among these individuals, 82% (real-time PCR analysis) and 76% (16S rRNA metabarcoding analysis) were sampled during a mortality event. Histological analyses showed that moribund individuals had lesions mainly characterized by necrosis, haemocyte infiltration and granulomas. Risk factor analysis showed that mussel batches with more than 20% of PCR-positive individuals were more likely to have been sampled during a mortality event, and positive 16S rRNA metabarcoding batches increased the strength of the association with mortality by 11.6 times. The role of F. halioticida in mussel mortalities was determined by reviewing the available evidence. To this end, a causation criteria grid, tailored to marine diseases and molecular pathogen detection tools, allowed more evidence to be gathered on the causal role of this bacterium in mussel mortalities.

Potential of a Bead-Based Multiplex Assay for SARS-CoV-2 Antibody Detection.

Serological assays for SARS-CoV-2 play a pivotal role in the definition of whether patients are infected, the understanding of viral epidemiology, the screening of convalescent sera for therapeutic and prophylactic purposes, and in obtaining a better understanding of the immune response towards the virus. The aim of this study was to investigate the performance of a bead-based multiplex assay. This assay allowed for the simultaneous testing of IgG antibodies against SARS-CoV-2 spike, S1, S2, RBD, and nucleocapsid moieties and S1 of seasonal coronaviruses hCoV-22E, hCoV-HKU1, hCoV-NL63, and hCoV-OC43, as well as MERS and SARS-CoV. We compared the bead-based multiplex assay with commercial ELISA tests. We tested the sera of 27 SARS-CoV-2 PCR-positive individuals who were previously tested with different ELISA assays. Additionally, we investigated the reproducibility of the results by means of multiple testing of the same sera. Finally, the results were correlated with neutralising assays. In summary, the concordance of the qualitative results ranged between 78% and 96% depending on the ELISA assay and the specific antigen. Repeated freezing-thawing cycles resulted in reduced mean fluorescence intensity, while the storage period had no influence in this respect. In our test cohort, we detected up to 36% of sera positive for the development of neutralising antibodies, which is in concordance with the bead-based multiplex and IgG ELISA.

Study of the Immune Response of COVID-19 Patients in Kirkuk Province

Abstract Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a novel coronavirus causing coronavirus disease 2019 (COVID-19); it is diagnosed based on clinical signs and laboratory detection methods such as polymerase chain reaction (PCR) and serological techniques. Objective: The objective of the study is to use other diagnostic methods that support the PCR method of diagnosis for COVID-19. Materials and Methods: The study included 90 COVID-19 patients and 26 control group. Nasopharyngeal swabs were collected from the suspected patients with COVID-19 infection for the detection of the RNA virus by PCR technique. If the PCR was positive, the serum samples were collected and used for the quantitative detection of SARS-CoV-2 S1 (IgM, IgG) by using enzyme linked immunosorbent assay. Results: The result of this study showed that in a total of 116 participants, there was a significant difference between IgM and IgG reactivity (±) and the number of PCR-positive and negative individuals with P value <0.0001 and P value = 0.003, respectively. In addition, a significant increase in the levels of IgM and IgG (P ≤ 0.0001 for IgM and P ≤ 0.0001 for IgG) was recorded in patients compared with healthy control. Moreover, a significant correlation between IgM level with P = 0.0018 and the onset of symptoms as well as positive correlation was noticed between IgG concentration and the onset of symptoms (P = 0.0272). Conclusion: The study concluded that antibodies developed against COVID-19 infection could appear at early stages of the infection without the confirmation of real time polymerase chain reaction, and this could be a beneficial tool for early screening of suspected as well as asymptomatic individuals.

Characteristics and long-term prognosis of Danish residents with a positive intrathecal antibody index test for herpes simplex virus or varicella-zoster virus compared with individuals with a positive cerebrospinal fluid PCR: a nationwide cohort study

We compared characteristics and outcomes of individuals who in the cerebrospinal fluid (CSF) were positive for herpes simplex virus (HSV) or varicella-zoster virus (VZV)-intrathecal antibody index test ([AI]-positive) vs. individuals who were PCR-positive for HSV type 1 (HSV1), type 2 (HSV2), and for VZV. Nationwide cohort study of all Danish residents with positive CSF-AI or -PCR for HSV or VZV (1995-2021). We calculated short- and long-term risks as age-, sex-, and comorbidity-adjusted odds ratios (aOR), adjusted hazard ratios (aHR), and absolute risk differences with 95% CIs. Compared with individuals with positive PCR for HSV1 (n=321), HSV2 (n=497), and VZV (n=1054), individuals with a positive AI for HSV (n=177) and VZV (n=219) had CSF pleocytosis less frequently (leucocyte count >10/μL: HSV-AI: 39%, VZV-AI: 52%, HSV1-PCR: 81%, HSV2-PCR: 92%, VZV-PCR: 83%), and were less frequently diagnosed with central nervous system infection ([aOR {95%CI}]: HSV-AI vs. HSV1-PCR: [0.1 {0.1, 0.2}], HSV-AI vs. HSV2-PCR: [0.1 {0.0, 0.1}], VZV-AI vs. VZV-PCR: [0.2 {0.2, 0.3}]). Individuals with a positive HSV-AI or VZV-AI had increased risk of demyelinating disease ([aOR {95%CI}; aHR {95%CI}]: HSV-AI vs. HSV1-PCR: [4.6 {0.9, 24.5}; aHR not applicable], HSV-AI vs. HSV2-PCR: [10.4 {2.3, 45.9}; 12.4 {2.3, 66.0}], VZV-AI vs. VZV-PCR: [aOR not applicable; 10.3 {1.8, 58.8}]). Disability pension was less frequent among HSV-AI than HSV1-PCR cohort members (5-year risk difference:-23.6%, 95%CI:-35.2,-11.8), and more frequent among VZV-AI than VZV-PCR cohort members (5-year risk difference: 16.8%, 95%CI: 5.0, 28.7). AI-positive individuals differ from PCR-positive individuals in several aspects. AI appears unspecific for current central nervous system infections.

The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs.

Early in the coronavirus disease 2019 (COVID-19) pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. We assessed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A viral loads relative to symptom duration in symptomatic adults (≥16 years) presenting for testing in Georgia (4/2022-4/2023; Omicron variant predominant). Participants provided symptom duration and recent testing history. Nasal swabs were tested by Xpert Xpress SARS-CoV-2/Flu/RSV assay and cycle threshold (Ct) values recorded. Nucleoprotein concentrations in SARS-CoV-2 polymerase chain reaction (PCR)-positive samples were measured by single molecule array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. Of 348 newly-diagnosed SARS-CoV-2 PCR-positive individuals (65.5% women, median 39.2 years), 317/348 (91.1%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth/fifth day. Ag RDT sensitivity estimates were 30.0%-60.0% on the first day, 59.2%-74.8% on the third day, and 80.0%-93.3% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0 years), median influenza viral loads peaked on the second day of symptoms. In a highly immune adult population, median SARS-CoV-2 viral loads peaked around the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza.

B-089 Development of a Secondary Standard for Quantitation of IgG Antibodies to SARS-CoV-2 Proteins in a Multiplex Assay

Abstract Background Serological surveillance is essential for monitoring disease burden and vaccine uptake at an individual and population level. During the pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), several serological assays were developed and obtained emergency use authorization to detect antibodies after infection. At that time, the need was to differentiate the infected from the naïve population, and these qualitative assays played a critical role in disease management. In the wake of vaccinations, there is a need for the development of quantitative assays. The world health organization (WHO) developed an international standard for quantitation. We performed this study to develop and validate an in-house secondary standard for our multiplex assay based on this WHO standard. Methods We developed a novel multiplex assay for quantifying human IgG antibodies to four different SARS-CoV-2 antigens in human serum or plasma. We have used Luminex® xMAP® technology for this assay and immobilized four recombinant proteins, namely, the receptor-binding domain of S1(RBD), nucleocapsid protein (NP), S1 protein (S1), and trimeric Spike protein (trimer) on internally coded magnetic microspheres. We procured lyophilized WHO quantification standard 20/136 from the National Institute for Biological Standards and Control (NIBSC), which has the arbitrary assignment of 1000 BAU/mL after reconstitution in 0.25 mL. We tested this standard in the range of 10 to 0.01 BAU/mL for the standard curve. We tested NIBSC 20/162 control reagent using this assay for the linearity of dilution. Thirty-seven samples from the NIBSC verification panel were also tested for this evaluation. We also quantified IgG antibodies in 25 samples from vaccinated individuals, ten samples from vaccine breakthrough individuals, 25 samples from PCR-positive individuals, and 75 samples collected before 2019. Results The secondary standard was calibrated using the 20/136 standard. The NIBSC 20/136 and the secondary standard displayed a wide dynamic range of quantitation. The difference in the expected and actual concentrations was less than 20%. Multiple dilutions of the serum or plasma samples were used to get readings within the standard curve range. Excellent linearity was noted at various sample dilutions to get the correct quantification. We observed that vaccinated individuals had a higher concentration of binding antibodies to S1, Trimer, and RBD and were negative for NP antibodies. Conversely, the acute samples from infected individuals collected less than ten days post-positive PCR showed higher antibodies to NP than different spike proteins. The vaccine break-through infection samples showed lower NP antibodies than unvaccinated but infected individuals. Conclusion Our development of a secondary standard calibrated against WHO international standard is vital for quantitatively measuring different SARS-CoV-2 antibodies. A secondary standard can help manufacturers and users to normalize results from various assays and lots over a prolonged period.

Correlates with Vaccine Protective Capacity and COVID-19 Disease Symptoms Identified by Serum Proteomics in Vaccinated Individuals.

In the last two years, the coronavirus disease 19 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a scientific and social challenge worldwide. Vaccines have been the most effective intervention for reducing virus transmission and disease severity. However, genetic virus variants are still circulating among vaccinated individuals with different disease symptomatology. Understanding the protective- or disease-associated mechanisms in vaccinated individuals is relevant to advances in vaccine development and implementation. To address this objective, serum-protein profiles were characterized by quantitative proteomics and data-analysis algorithms in four cohorts of uninfected and SARS-CoV-2-infected vaccinated individuals with asymptomatic, non-severe, and severe disease symptomatology. The results show that immunoglobulins were the most overrepresented proteins in infected cohorts when compared to PCR-negative individuals. The immunoglobulin profile varied between different infected cohorts and correlated with protective- or disease-associated capacity. Overrepresented immunoglobulins in PCR-positive individuals correlated with protective response against SARS-CoV-2, other viruses, and thrombosis in asymptomatic cases. In non-severe cases, correlates of protection against SARS-CoV-2 and HBV together with risk of myasthenia gravis and allergy and autoantibodies were observed. Patients with severe symptoms presented risk for allergy, chronic idiopathic thrombocytopenic purpura, and autoantibodies. The analysis of underrepresented immunoglobulins in PCR-positive compared to PCR-negative individuals identified vaccine-induced protective epitopes in various coronavirus proteins, including the spike receptor-binding domain RBD. Non-immunoglobulin proteins were associated with COVID-19 symptoms and biological processes. These results evidence host-associated differences in response to vaccination and the possibility of improving vaccine efficacy against SARS-CoV-2.

Comparing Rapid Ag Test and PCR in SARS-CoV-2 Management in Rural Egypt

Like elsewhere around the globe, SARS-CoV-2 infection is spreading in rural Egypt. Due to high sensitivity and specificity, the gold standard of diagnostics is reverse transcription polymerase chain reaction PCR (RT-PCR). Rural areas without access to certified laboratories cannot take advantage of RT-PCR testing, and thus are dependent upon rapid antigen testing, a point-of-care test that requires less training and can produce results within 15 minutes. Rapid antigen testing can give an advantage to medical teams in rural settings by affording effective and early control of SARS-CoV-2 infection spread. We sought to assess the contribution of different COVID-19 testing procedures in rural Egypt. We conducted a prospective cohort study in a rural lab in Giza, Egypt. Approximately 223 individuals with potential SARS-CoV-2 infection were involved in the study during the pandemic peak in Giza, Egypt, from March 4 – May 30, 2021. Subjects were subjected to RT-PCR and rapid antigen testing, and the performance of each testing procedure was compared. Between March 4 – May 30, 2021, approximately 223 symptomatic individuals were included in this study. 190 patients (85.2%) were indicated as PCR positive for SARS-CoV-2, while 33 (14.8%) were PCR negative. In comparison, a rapid antigen test showed 178 out of 223 patients (79.8%) were indicated as positive, or 94% of the PCR-positive individuals. In Giza, a rural area of Egypt, RT-PCR had an optimal balance of sensitivity and specificity, however, the turnaround time was a limiting factor. Antigen testing, performed as a rapid point-of-care test, can play an effective role in rural outbreak control due to its ease of use and rapid results.

Vaccine effectiveness against Delta, Omicron BA.1, and BA.2 in a highly vaccinated Asian setting: a test-negative design study

ObjectivesWe compared the vaccine effectiveness over time of the primary series and booster against infection and severe disease with the Delta, Omicron BA.1, and BA.2 variants in Singapore, an Asian setting with high vaccination coverage.MethodsWe conducted a test-negative case-control study on all adult residents in Singapore who underwent PCR testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in acute hospitals. Individuals with a negative PCR from 1 September, 2021, to 30 November, 2021, and 1 December, 2021, to 25 April, 2022, served as controls for the Delta and Omicron variants respectively, and PCR-positive individuals within these two time periods served as cases. Associations between vaccination status and SARS-CoV-2 infection and severe disease with the Delta or Omicron variants were measured using Poisson regressions. Vaccine effectiveness was calculated by taking 1 minus risk ratio.ResultsThere were 68 114 individuals comprising 58 495 controls and 9619 cases for the Delta period, of whom 53 093 completed the primary series and 9161 were boosted. For the Omicron period, 104 601 individuals comprising 80 428 controls, 8643 BA.1 cases, and 15 530 BA.2 cases were included, of whom 29 183 and 71 513 were vaccinated with the primary series and boosted, respectively. The primary series provided greater protection against infection with Delta (45%, 95% CI 40–50%) than against infection with Omicron (21%, 95% CI 7–34% for BA.1; 18%, 95% CI 6–29% for BA.2) at <2 months from vaccination. Vaccine effectiveness of the booster was similar against infection with BA.1 (44%, 95% CI 38–50%) and BA.2 (40%, 95% CI 35–40%). Protection against severe disease by the booster for BA.1 (83%, 95% CI 76–88%) and BA.2 (78%, 95% CI 73–82%) was comparable to that by the primary series for Delta (80%, 95% CI 73–85%).ConclusionOur findings support the use of a booster dose to reduce the risk of severe disease and mitigate the impact on the healthcare system in an Omicron-predominant epidemic.

The BioFire® RP2.1 Panel Did Not Identify Concurrent Respiratory Virus Infection in Adults with Variable SARS-CoV-2 Disease Severity and Infection Duration.

SARS-CoV-2 emerged in 2019 and rapidly surged into a global pandemic. The rates of concurrent infection with other respiratory pathogens and the effects of possible coinfections on the severity of COVID-19 cases and the length of viral infection are not well defined. In this retrospective study, nasopharyngeal swab samples collected in Colorado between March 2020 and May 2021 from SARS-CoV-2 PCR-positive individuals were tested for a panel of 21 additional respiratory pathogens, including 17 viral and 4 bacterial pathogens. We detected significant positive correlations between levels of SARS-CoV-2 RNA and infectious virus titers for both cohorts, as well as a positive correlation between viral RNA levels and disease severity scores for one cohort. We hypothesized that severe COVID-19 cases and longer SARS-CoV-2 infections may be associated with concurrent respiratory infections. Only one individual exhibited evidence of a concurrent infection- SARS -CoV-2 and human rhinovirus/enterovirus- leading us to conclude that viral respiratory coinfections were uncommon during this time and thus not responsible for the variations in disease severity and infection duration observed in the two cohorts examined. Mask wearing and other public health measures were imposed in Colorado during the time of collection and likely contributed to low rates of coinfection.

On the caveats of a multiplex test for SARS-CoV-2 to detect seroconversion after infection or vaccination

The Covid-19 pandemic, caused by SARS-CoV-2, has resulted in over 6 million reported deaths worldwide being one of the biggest challenges the world faces today. Here we present optimizations of all steps of an enzyme-linked immunosorbent assay (ELISA)-based test to detect IgG, IgA and IgM against the trimeric spike (S) protein, receptor binding domain (RBD), and N terminal domain of the nucleocapsid (N-NTD) protein of SARS-CoV-2. We discuss how to determine specific thresholds for antibody positivity and its limitations according to the antigen used. We applied the assay to a cohort of 126 individuals from Rio de Janeiro, Brazil, consisting of 23 PCR-positive individuals and 103 individuals without a confirmed diagnosis for SARS-CoV-2 infection. To illustrate the differences in serological responses to vaccinal immunization, we applied the test in 18 individuals from our cohort before and after receiving ChAdOx-1 nCoV-19 or CoronaVac vaccines. Taken together, our results show that the test can be customized at different stages depending on its application, enabling the user to analyze different cohorts, saving time, reagents, or samples. It is also a valuable tool for elucidating the immunological consequences of new viral strains and monitoring vaccination coverage and duration of response to different immunization regimens.

COVID-19 Disease in Presenting to the Pediatric Emergency Department: A Multicenter Study of 8886 Cases

BackgroundThe aim was to evaluate the epidemiological, clinical, laboratory, and radiologic data of children with SARS-CoV-2 positivity by polymerase chain reaction (PCR) together with treatment strategies and clinical outcomes and to evaluate cases of multisystem inflammatory syndrome in children (MIS-C) in this population.MethodsThis was a multicenter retrospective observational cohort study performed in the pediatric emergency departments of 19 tertiary hospitals. From March 11, 2020, to May 31, 2021, children who were diagnosed with confirmed nasopharyngeal/tracheal specimen SARS-CoV-2 PCR positivity or positivity for serum-specific antibodies against SARS-CoV-2 were included. Demographics, presence of chronic illness, symptoms, history of contact with SARS-CoV-2 PCR-positive individuals, laboratory and radiologic investigations, clinical severity, hospital admissions, and prognosis were recorded.ResultsA total of 8886 cases were included. While 8799 (99.0%) cases resulted in a diagnosis of SARS-CoV-2 with PCR positivity, 87 (1.0%) patients were diagnosed with MIS-C. Among SARS-CoV-2 PCR-positive patients, 51.0% were male and 8.5% had chronic illnesses. The median age was 11.6 years (IQR: 5.0–15.4) and 737 (8.4%) patients were aged <1 year. Of the patients, 15.5% were asymptomatic. The most common symptoms were fever (48.5%) and cough (30.7%) for all age groups. There was a decrease in the rate of fever as age increased (p < 0.001); the most common age group for this symptom was <1 year with the rate of 69.6%. There was known contact with a SARS-CoV-2 PCR-positive individual in 67.3% of the cases, with household contacts in 71.3% of those cases. In terms of clinical severity, 83 (0.9%) patients were in the severe-critical group. There was hospital admission in 1269 (14.4%) cases, with 106 (1.2%) of those patients being admitted to the pediatric intensive care unit (PICU). Among patients with MIS-C, 60.9% were male and the median age was 6.4 years (IQR: 3.9–10.4). Twelve (13.7%) patients presented with shock. There was hospital admission in 89.7% of these cases, with 29.9% of the patients with MIS-C being admitted to the PICU.ConclusionMost SARS-CoV-2 PCR-positive patients presented with a mild clinical course. Although rare, MIS-C emerges as a serious consequence with frequent PICU admission. Further understanding of the characteristics of COVID-19 disease could provide insights and guide the development of therapeutic strategies for target groups.

Behavioral factors associated with SARS‐CoV‐2 infection in Japan

BackgroundThe relative burden of COVID‐19 has been less severe in Japan. One reason for this may be the uniquely strict restrictions imposed upon bars/restaurants. To assess if this approach was appropriately targeting high‐risk individuals, we examined behavioral factors associated with SARS‐CoV‐2 infection in the community.MethodsThis multicenter case–control study involved individuals receiving SARS‐CoV‐2 testing in June–August 2021. Behavioral exposures in the past 2 weeks were collected via questionnaire. SARS‐CoV‐2 PCR‐positive individuals were cases, while PCR‐negative individuals were controls.ResultsThe analysis included 778 individuals (266 [34.2%] positives; median age [interquartile range] 33 [27–43] years). Attending three or more social gatherings was associated with SARS‐CoV‐2 infection (adjusted odds ratio [aOR] 2.00 [95% CI 1.31–3.05]). Attending gatherings with alcohol (aOR 2.29 [1.53–3.42]), at bars/restaurants (aOR 1.55 [1.04–2.30]), outdoors/at parks (aOR 2.87 [1.01–8.13]), at night (aOR 2.07 [1.40–3.04]), five or more people (aOR 1.81 [1.00–3.30]), 2 hours or longer (aOR 1.76 [1.14–2.71]), not wearing a mask during gatherings (aOR 4.18 [2.29–7.64]), and cloth mask use (aOR 1.77 [1.11–2.83]) were associated with infection. Going to karaoke (aOR 2.53 [1.25–5.09]) and to a gym (aOR 1.87 [1.11–3.16]) were also associated with infection. Factors not associated with infection included visiting a cafe with others, ordering takeout, using food delivery services, eating out by oneself, and work/school/travel‐related exposures including teleworking.ConclusionsWe identified multiple behavioral factors associated with SARS‐CoV‐2 infection, many of which were in line with the policy/risk communication implemented in Japan. Rapid assessment of risk factors can inform decision making.

Viral kinetics in SARS-CoV-2 infected asymptomatic patients

Introduction: As the daily number of patients diagnosed with SARS-CoV-2 infection by PCR increases, the necessity to identify truly infectious cases becomes more significant. We aimed to identify a cut-off Ct value of the COVID-19 RT-PCR assay for likely infectivity by assessing the COVID-19 IgG status and investigating the utility of the Rapid Antigen Test (RAT) in identifying infectious cases among asymptomatic individuals. Methods: Nasopharyngeal/throat swabs were simultaneously taken for COVID-19 RT-PCR and RAT from 552 asymptomatic individuals at De Soysa Maternity Hospital, Colombo, from 23rd of November to 19th of December 2020. In addition, SARS-CoV-2 IgG (against nucleoprotein) status in PCR positive individuals was evaluated when simultaneously taken sera was available. Results: COVID-19 RT-PCR positive rate among asymptomatic individuals was 14.3% (n=79). The overall sensitivity of RAT was 30.4% but increased to 73.9% when Ct values below 25 were considered. The COVID-19 IgG response was evaluated in 37 PCR positive subjects and the overall seropositivity was 40.5%. The optimal Ct thresholds for discrimination of COVID-19 IgG status were 30.5 and 30.29 for the E and S gene respectively. There was a significant positive correlation between Ct values of the E gene and IgG ratio values (r=0.345, p&lt;0.05). The Ct thresholds for RAT positivity were 26.5 and 26.06 for E and S genes respectively, with a significant negative correlation (p&lt;0.001). Conclusion: We conclude that it is possible to define a cut off Ct value in SARS-CoV-2 PCR (with some error margin for practical purposes) for likely non-infectivity. It was also deduced that positive COVID-19 rapid antigen result seems to be more predictive of infectivity in comparison to positive PCR result.

Household and individual level risk factors associated with declining malaria incidence in Meghalaya, India: implications for malaria elimination in low-endemic settings

BackgroundA detailed analysis of household and individual level Plasmodium infection patterns in two low-endemic districts of Meghalaya was undertaken to better understand the epidemiology of malaria in northeast India.MethodsSocio-demographic and behavioural information from residents (aged 1–69 years) of households were collected through pre-tested, questionnaire conducted in 2018 and 2019. Blood samples collected from participants were tested for Plasmodium falciparum and/or Plasmodium vivax infection using rapid diagnostic test, microscopy and PCR. Plasma samples from a subset of participants were analysed for antibodies against thirteen P. falciparum and four P. vivax antigens. Associations between household and individual level risk factors, and Plasmodium infections were evaluated using multilevel logistic regression models.ResultsA total of 2753 individuals from 827 households were enrolled in 2018, and 834 individuals from 222 households were enrolled in 2019. Of them, 33 (1.2%) were positive by PCR for P. falciparum in 2018 and none were positive for P. vivax. In 2019, no PCR-positive individuals were detected. All, but one, infections were asymptomatic; all 33 infections were sub-microscopic. Reported history of malaria in the past 12 months (OR = 8.84) and history of travel in the past 14 days (OR = 10.06) were significantly associated with Plasmodium infection. A significant trend of increased seropositivity with age was noted for all 17 antigens. Although adults (≥ 18 years) consistently had the highest seropositivity rates, a sizeable proportion of under-five children were also found to be seropositive. Almost all individuals (99.4%) reported sleeping under an insecticide-treated bed-net, and household indoor residual spray coverage in the 12 months preceding the survey was low (23%). Most participants correctly identified common signs and symptoms of malaria, i.e., fever (96.4%), headache (71.2%), chills (83.2%) and body-ache (61.8%). Almost all participants (94.3%) used government-provided services for treatment of malaria.ConclusionThis study explored the epidemiology of malaria in two communities in Meghalaya, India, in the context of declining transmission. The presence of widespread asymptomatic infections and seropositivity among under-five children suggest that low-level Plasmodium transmission persists in this region. Implications of the study findings for malaria elimination efforts in low-transmission settings are discussed.

Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids.

Aleutian mink disease virus (AMDV), which causes Aleutian disease, is widely spread both in farmed mink and wild mustelids. However, only limited data are available on the role of wild animals in AMDV transmission and spread. Our aim was to shed light on AMDV transmission among wild mustelids and estimate the effect of intense farming practices on the virus circulation by studying AMDV prevalence and genetic diversity among wild mustelids in Poland. We compared AMDV seroprevalence and proportion of PCR-positive individuals in American mink, polecats, otters, stone martens, and pine martens and used the phylogenetic analysis of the NS1 region to study transmission. In addition, we used a metagenomic approach to sequence complete AMDV genomes from tissue samples. In eastern Poland, AMDV seroprevalence in wild mustelids varied from 22 per cent in otters to 62 per cent and 64 per cent in stone martens and feral mink, respectively. All studied antibody-positive mink were also PCR positive, whereas only 10, 15, and 18 per cent of antibody-positive polecats, pine martens, and stone martens, respectively, were PCR positive, suggesting lower virus persistence among these animal species as compared to feral mink. In phylogenetic analysis, most sequences from feral mink formed region-specific clusters that have most likely emerged through multiple introductions of AMDV to feral mink population over decades. However, virus spread between regions was also observed. Virus sequences derived from farmed and wild animals formed separate subclusters in the phylogenetic tree, and no signs of recent virus transmission between farmed and wild animals were observed despite the frequent inflow of farmed mink escapees to wild populations. These results provide new information about the role of different mustelid species in AMDV transmission and about virus circulation among the wild mustelids. In addition, we pinpoint gaps of knowledge, where more studies are needed to achieve a comprehensive picture of AMDV transmission.

Mitigating SARS-CoV-2 in the Deployed Environment.

ABSTRACTIntroductionUnlike other communal living environments (universities, boarding schools, and camps) that have been suspended during the COVID-19 pandemic, the deployed military force must continue its mission. Early challenges in the 2020 deployed environment included limited availability of living and quarantine space and limited testing capacity. This is a brief report of stringent quarantine strategies employed to newly arriving cohorts at a NATO and U.S. military base to prevent release of SARS-CoV-2 into a larger base population.MethodsWith awareness of the worldwide pandemic, beginning in late February 2020, all personnel arriving to the Hamid Karzai International Airport NATO base were quarantined for 14 days to prevent interaction with the wider base population. Testing capacity was limited. Names, locations, and dates of those within quarantine were tracked to improve contact tracing. Between February and April 2020, the first cases of SARS-CoV-2 were diagnosed on a military base in Afghanistan within quarantine.ResultsWithin quarantine, 11 males became PCR positive for SARS-CoV-2 during April 2020. Five of the 11 were PCR tested for symptoms of fever, cough, or loss of taste. A sixth individual, who had been asymptomatic upon leaving the base after completion of quarantine, later developed symptoms and tested positive. Another five asymptomatic individuals were found with antibody testing just before planned release from 14 days of quarantine post-exposure and confirmed with PCR testing. All PCR-positive individuals were diagnosed before being released into the general population of the base because of strict screening, quarantine, and exit criteria.ConclusionQuarantine creates significant strain on resources in a deployed environment. Group quarantine facilities where social distancing is limited allow for the possibility for intra-quarantine transmission of SARS-CoV-2. Ideally, PCR testing is done upon entry into quarantine and upon exit. With the possibility of false-negative PCR or limited PCR testing, we recommend daily symptom screening, pulse oximetry, temperature checks, and small quarantine groups that must “graduate” together—all meeting exit criteria. Any introduction of new individual, even with negative testing, to a group increases risk of SARS-CoV-2 transmission.Upon exit of quarantine, testing should be performed, regardless of entry testing. If PCR is limited, serology testing should be done, followed by PCR, if positive. Serology testing can be combined with clinical judgment to conserve PCR testing for quarantine release of asymptomatic individuals.