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Background: Patients with COVID-19 are follow-up in primary care and long COVID is scarcely defined. The study aim was to describe SARS-CoV-2 pneumonia and cut-offs for defining long COVID in primary care follow-up patients., Methods: A retrospective observational study in primary care in Madrid, Spain, was conducted. Data was collected during 6 months (April to September) in 2020, during COVID-19 first wave, from patients ≥ 18 years with SARS-CoV-2 pneumonia diagnosed. Variables: sociodemographic, comorbidities, COVID-19 symptoms and complications, laboratory test and chest X-ray. Descriptive statistics were used, mean (standard deviation (SD)) and medians (interquartile range (IQR)) respectively. Differences were detected applying X2 test, Student's T-test, ANOVA, Wilcoxon-Mann-Whitney or Kruskal-Wallis depending on variable characteristics., Results: 155 patients presented pneumonia in day 7.8 from the onset (79.4% were hospitalized, median length of 7.0 days (IQR: 3.0, 13.0)). After discharge, the follow-up lasted 54.0 median days (IQR 42.0, 88.0) and 12.2 mean (SD 6.4) phone calls were registered per patient. The main symptoms and their duration were: cough (41.9%, 12 days), dyspnoea (31.0%, 15 days), asthenia (26.5%, 21 days). Different cut-off points were applied for long COVID and week 4 was considered the best milestone (28.3% of the sample still had symptoms after week 4) versus week 12 (8.3%). Patients who still had symptoms >4 weeks follow-up took place over 81.0 days (IQR: 50.5, 103.0), their symptoms were more prevalent and lasted longer than those ≤ 4 weeks: cough (63.6% 30 days), dyspnoea (54.6%, 46 days), and asthenia (56.8%, 29 days). Embolism was more frequent in patients who still had symptoms >4 weeks than those with symptoms ≤4 weeks (9.1% vs 1.8%, p value 0.034)., Conclusion: Most patients with SARS-CoV-2 pneumonia recovered during the first 4 weeks from the beginning of the infection. The cut-off point to define long COVID, as persisting symptoms, should be between 4 to 12 weeks from the onset of the symptoms., Competing Interests: The authors declare that they have no competing interests.

The Infectious Diseases Society of America has identified the use of SARS-CoV-2 genomic load for prognostication purposes as a key research question. We designed a retrospective cohort study that included adult patients with COVID-19 pneumonia who had at least 2 positive nasopharyngeal tests at least 24 hours apart to study the correlation between the change in the genomic load of SARS-CoV-2, as reflected by the Cycle threshold (Ct) value of the RT-PCR, with change in clinical status. The Sequential Organ Failure Assessment (SOFA) score was used as a surrogate for patients' clinical status. Among 457 patients with COVID-19 pneumonia between 3/31/2020-4/10/2020, we identified 42 patients who met the inclusion criteria. The median initial SOFA score was 2 (IQR 2-3). 20 out of 42 patients had a lower SOFA score on their subsequent tests. We identified a statistically significant inverse correlation between the change in SOFA score and change in the Ct value with a decrease in SOFA score by 0.05 (SE 0.02; p<0.05) for an increase in Ct values by 1. This correlation was independent of the duration of symptoms. Our findings suggest that an increasing Ct value in sequential tests may be of prognostic value for patients diagnosed with COVID-19 pneumonia., Competing Interests: The authors have declared that no competing interests exist.

A second cluster of COVID-19 cases imported from Europe occured in Vietnam from early March 2020. We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value <30) admitted to the National Hospital for Tropical Diseases in Hanoi between March 6 and April 15 2020. Whole SARS-CoV-2 genomes from these patients were sequenced using Illumina Miseq and analysed for common genetic variants and relationships to local and globally circulating strains. Results showed that 32 cases were Vietnamese with a median age of 37 years (range 15-74 years), and 23 were male. Most cases were acquired outside Vietnam, mainly from the UK (n = 15), other European countries (n = 14), Russia (n = 6) and countries in Asia (n = 3). No cases had travelled from China. Forty-one cases had symptoms at admission, typically dry cough (n = 36), fever (n = 20), sore throat (n = 14) and diarrhoea (n = 12). Hospitalisation was long with a median of 25 days, most commonly from 20-29 days. All SARS-CoV-2 genomes were similar (92-100% sequence homology) to the reference sequence Wuhan&#95;1 (NC&#95;045512), and 32 strains belonged to the B.1.1 lineage. The three most common variants were linked, and included C3037T, C14408T (nsp12: P323L) and A23403G (S: D614G) mutations. This group of mutations often accompanied variant C241T (39/44 genomes) or GGG 28881..28883 AAC (33/44 genomes). The prevalence of the former reflected probable European origin of viruses, and the transition D614G was dominant in Vietnam. New variants were identified; however, none could be associated with disease severity., Competing Interests: The authors have declared that no competing interests exist.

Background: Minimally invasive autopsy (MIA) is a validated and safe method to establish the cause of death (COD), mainly in low-resource settings. However, the additional clinical value of MIA in Coronavirus disease (COVID-19) patients in a high-resource setting is unknown. The objective was to assess if and how MIA changed clinical COD and contributing diagnoses in deceased COVID-19 patients., Methods and Findings: A prospective observational cohort from April to May 2020 in a 981-bed teaching hospital in the epicenter of the COVID-19 pandemic in Belgium was established. Patients who died with either PCR-confirmed or radiologically confirmed COVID-19 infection were consecutively included. MIA consisted of whole-body CT and CT-guided Tru-Cut® biopsies. Diagnostic modalities were clinical chart review, radiology, microbiology, and histopathology which were assessed by two independent experts per modality. MIA COD and contributing diagnoses were established during a multi-disciplinary meeting. Clinical COD (CCOD) and contributing diagnosis were abstracted from the discharge letter. The main outcomes were alterations in CCOD and contributing diagnoses after MIA, and the contribution of each diagnostic modality. We included 18 patients, of which 7 after intensive care unit hospitalization. MIA led to an alteration in 15/18 (83%) patients. The CCOD was altered in 5/18 (28%) patients. MIA found a new COD (1/5), a more specific COD (1/5), a less certain COD (1/5), or a contributing diagnosis to be the COD (2/5). Contributing diagnoses were altered in 14/18 (78%) patients: 9 new diagnoses, 5 diagnoses dismissed, 3 made more specific, and 2 made less certain. Overall, histopathology contributed in 14/15 (93%) patients with alterations, radiology and microbiology each in 6/15 (40%), and clinical review in 3/15 (20%). Histopathology was deemed the most important modality in 10 patients, radiology in two patients, and microbiology in one patient., Conclusion: MIA, especially histological examination, can add valuable new clinical information regarding the cause of death in COVID-19 patients, even in a high-resource setting with wide access to premortem diagnostic modalities. MIA may provide important clinical insights and should be applied in the current ongoing pandemic., Trial Registration: Clinicaltrials.gov identifier: NCT04366882., Competing Interests: The authors have declared that no competing interests exist.

Background: As a pandemic, a most-common pattern resembled organizing pneumonia (OP) has been identified by CT findings in novel coronavirus disease (COVID-19). We aimed to delineate the evolution of CT findings and outcome in OP of COVID-19., Materials and Methods: 106 COVID-19 patients with OP based on CT findings were retrospectively included and categorized into non-severe (mild/common) and severe (severe/critical) groups. CT features including lobar distribution, presence of ground glass opacities (GGO), consolidation, linear opacities and total severity CT score were evaluated at three time intervals from symptom-onset to CT scan (day 0-7, day 8-14, day > 14). Discharge or adverse outcome (admission to ICU or death), and pulmonary sequelae (complete absorption or lesion residuals) on CT after discharge were analyzed based on the CT features at different time interval., Results: 79 (74.5%) patients were non-severe and 103 (97.2%) were discharged at median day 25 (range, day 8-50) after symptom-onset. Of 67 patients with revisit CT at 2-4 weeks after discharge, 20 (29.9%) had complete absorption of lesions at median day 38 (range, day 30-53) after symptom-onset. Significant differences between complete absorption and residuals groups were found in percentages of consolidation (1.5% vs. 13.8%, P = 0.010), number of involved lobe > 3 (40.0% vs. 72.5%, P = 0.030), CT score > 4 (20.0% vs. 65.0%, P = 0.010) at day 8-14., Conclusion: Most OP cases had good prognosis. Approximately one-third of cases had complete absorption of lesions during 1-2 months after symptom-onset while those with increased frequency of consolidation, number of involved lobe > 3, and CT score > 4 at week 2 after symptom-onset may indicate lesion residuals on CT., Competing Interests: The authors have declared that no competing interests exist.

In February 2020, the Novel Coronavirus (COVID-19) was raging in Wuhan, China and quickly spreading to the rest of the world. This period was fraught with uncertainty for those in the affected areas. The present investigation examined the role of two potential coping resources during this stressful period of uncertainty: flow and mindfulness. Participants in Wuhan and other major cities affected by COVID-19 (N = 5115) completed an online survey assessing subjective experiences of flow, mindfulness, and well-being. Longer quarantine was associated with poorer well-being; flow and mindfulness were associated with better well-being on some measures. However, flow-but not mindfulness-moderated the link between quarantine length and well-being, such that people who experienced high levels flow showed little or no association between quarantine length and poorer well-being. These findings suggest that experiencing flow (typically by engaging in flow-inducing activities) may be a particularly effective way to protect against potentially deleterious effects of a period of quarantine., Competing Interests: The authors have declared that no competing interests exist.

Background: The coronavirus (SARS-COV-2) is now a global concern because of its higher transmission capacity and associated adverse consequences including death. The reproductive number of coronavirus provides an estimate of the possible extent of the transmission. This study aims to provide a summary reproductive number of coronavirus based on available global level evidence., Methods: A total of three databases were searched on September 15, 2020: PubMed, Web of Science, and Science Direct. The searches were conducted using a pre-specified search strategy to record studies reported the reproductive number of coronavirus from its inception in December 2019. It includes keywords of coronavirus and its reproductive number, which were combined using the Boolean operators (AND, OR). Based on the included studies, we estimated a summary reproductive number by using the meta-analysis. We used narrative synthesis to explain the results of the studies where the reproductive number was reported, however, were not possible to include in the meta-analysis because of the lack of data (mostly due to confidence interval was not reported)., Results: Total of 42 studies included in this review whereas 29 of them were included in the meta-analysis. The estimated summary reproductive number was 2.87 (95% CI, 2.39-3.44). We found evidence of very high heterogeneity (99.5%) of the reproductive number reported in the included studies. Our sub-group analysis was found the significant variations of reproductive number across the country for which it was estimated, method and model that were used to estimate the reproductive number, number of case that was considered to estimate the reproductive number, and the type of reproductive number that was estimated. The highest reproductive number was reported for the Diamond Princess Cruise Ship in Japan (14.8). In the country-level, the higher reproductive number was reported for France (R, 6.32, 95% CI, 5.72-6.99) following Germany (R, 6.07, 95% CI, 5.51-6.69) and Spain (R, 3.56, 95% CI, 1.62-7.82). The higher reproductive number was reported if it was estimated by using the Markov Chain Monte Carlo method (MCMC) method and the Epidemic curve model. We also reported significant heterogeneity of the type of reproductive number- a high-value reported if it was the time-dependent reproductive number., Conclusion: The estimated summary reproductive number indicates an exponential increase of coronavirus infection in the coming days. Comprehensive policies and programs are important to reduce new infections as well as the associated adverse consequences including death., Competing Interests: The authors have declared that no competing interests exist.

Despite the profound health and economic implications of Covid-19, there is only limited knowledge to date about the role of economic concerns, health worries and social distancing for mental health outcomes during the pandemic. We analyze online survey data from the nationally representative "Understanding America Study" (UAS) covering the period of March 10-31st 2020 (sample size: 6,585). Mental health is assessed by the validated PHQ-4 instrument for measuring symptoms of depression and anxiety. About 29% (CI:27.4-.30.4%) of the US adult population reported some depression/anxiety symptoms over the study period, with symptoms deteriorating over the month of March. Worsening mental health was most strongly associated with concerns about the economic consequences of the pandemic, while concerns about the potential implications of the virus for respondents' own health and social distancing also predicted increases in symptoms of depression and anxiety during the early stages of the pandemic in the US, albeit less strongly. Our findings point towards the possibility of a major mental health crisis unfolding simultaneously with the pandemic, with economic concerns being a key driving force of this crisis. These results highlight the likely importance of economic countermeasures and social policy for mitigating the impact of Covid-19 on adult mental health in the US over and above an effective public health response., Competing Interests: The authors have declared that no competing interests exist.

Many affected counties have had experienced a shortage of personal protective equipment (PPE) during the coronavirus disease (COVID-19) pandemic. We aimed to investigate the needs of healthcare professionals and the technical difficulties faced by them during the initial outbreak. A cross-sectional web-based survey was conducted among the healthcare workforce in the most populous cities from three Latin American countries in April 2020. In total, 1,082 participants were included. Of these, 534 (49.4%), 263 (24.3%), and 114 (10.5%) were physicians, nurses, and other professionals, respectively. At least 70% of participants reported a lack of PPE. The most common shortages were shortages in gown coverall suits (643, 59.4%), N95 masks (600, 55.5%), and face shields (569, 52.6%). Professionals who performed procedures that generated aerosols reported shortages more frequently (p<0.05). Professionals working in the emergency department and primary care units reported more shortages than those working in intensive care units and hospital-based wards (p<0.001). Up to 556 (51.4%) participants reported the lack of sufficient knowledge about using PPE. Professionals working in public institutions felt less prepared, received less training, and had no protocols compared with their peers in working private institutions (p<0.001). Although the study sample corresponded to different hospital centers in different cities from the participating countries, sampling was non-random. Healthcare professionals in Latin America may face more difficulties than those from other countries, with 7 out of 10 professionals reporting that they did not have the necessary resources to care for patients with COVID-19. Technical and logistical difficulties should be addressed in the event of a future outbreak, as they have a negative impact on healthcare workers. Clinical trial registration: NCT04486404., Competing Interests: Authors have declared no competing interest exist. This does not alter our adherence to PLOS ONE policies on sharing data and materials. CEMEDIP is a private institution based in Ecuador which provides academic training to healthcare related professionals and students. It has not been part of conception, design, data analysis or drafting the manuscript of this research. EV is part of CEMEDIP as partial-time professor for which he receives a salary. EV principal affiliation is with Santander Ophthalmologic Foundation FOSCAL where he currently in undergoing a fellow. We have updated the author affiliation. We attest that we have no commercial associations (e.g., equity ownership or interest, consultancy, patent and licensing agreements, or institutional and corporate associations) that might be a conflict of interest in relation to the submitted manuscript. All sources of funding in support of the work presented in the article are indicated.

Background: Prevalence of IgG antibodies against SARS-CoV-2 infection provides essential information for deciding disease prevention and mitigation measures. We estimate the seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar., Methods: 2906 persons >18 years of age selected from hospital visitors across District Srinagar participated in the study. We tested samples for the presence of SARS-CoV-2 specific IgG antibodies using a chemiluminescent microparticle immunoassay-based serologic test., Results: Age- and gender-standardized seroprevalence was 3.6% (95% CI 2.9% to 4.3%). Age 30-69 years, a recent history of symptoms of an influenza-like-illness, and a history of being placed under quarantine were significantly related to higher odds of the presence of SARS-CoV-2 specific IgG antibodies. The estimated number of SARS-CoV-2 infections during the two weeks preceding the study, adjusted for test performance, was 32602 with an estimated (median) infection-to-known-case ratio of 46 (95% CI 36 to 57)., Conclusions: The seroprevalence of SARS-CoV-2 specific IgG antibodies is low in the District. A large proportion of the population is still susceptible to the infection. A sizeable number of infections remain undetected, and a substantial proportion of people with symptoms compatible with COVID-19 are not tested., Competing Interests: The authors have declared that no competing interests exist.

COVID-19 emerged in November 2019 leading to a global pandemic that has not only resulted in widespread medical complications and loss of life, but has also impacted global economies and transformed daily life. The current rapid response study in a convenience online sample quickly recruited 2,065 participants across the United States, Canada, and Europe in late March and early April 2020. Cross-sectional findings indicated elevated anxiety and depressive symptoms compared to historical norms, which were positively associated with COVID-19 concern more strongly than epidemiological data signifying risk (e.g., world and country confirmed cases). Employment loss was positively associated with greater depressive symptoms and COVID-19 concern, and depressive symptoms and COVID-19 concern were significantly associated with more stringent self-quarantine behavior. The rapid collection of data during the early phase of this pandemic is limited by under-representation of non-White and middle age and older adults. Nevertheless, these findings have implications for interventions to slow the spread of COVID-19 infection., Competing Interests: All authors declare no competing interests.

Background: Available COVID-19 mortality indices are limited to acute inpatient data. Using nationwide medical administrative data available prior to SARS-CoV-2 infection from the US Veterans Health Administration (VA), we developed the VA COVID-19 (VACO) 30-day mortality index and validated the index in two independent, prospective samples., Methods and Findings: We reviewed SARS-CoV-2 testing results within the VA between February 8 and August 18, 2020. The sample was split into a development cohort (test positive between March 2 and April 15, 2020), an early validation cohort (test positive between April 16 and May 18, 2020), and a late validation cohort (test positive between May 19 and July 19, 2020). Our logistic regression model in the development cohort considered demographics (age, sex, race/ethnicity), and pre-existing medical conditions and the Charlson Comorbidity Index (CCI) derived from ICD-10 diagnosis codes. Weights were fixed to create the VACO Index that was then validated by comparing area under receiver operating characteristic curves (AUC) in the early and late validation cohorts and among important validation cohort subgroups defined by sex, race/ethnicity, and geographic region. We also evaluated calibration curves and the range of predictions generated within age categories. 13,323 individuals tested positive for SARS-CoV-2 (median age: 63 years; 91% male; 42% non-Hispanic Black). We observed 480/3,681 (13%) deaths in development, 253/2,151 (12%) deaths in the early validation cohort, and 403/7,491 (5%) deaths in the late validation cohort. Age, multimorbidity described with CCI, and a history of myocardial infarction or peripheral vascular disease were independently associated with mortality-no other individual comorbid diagnosis provided additional information. The VACO Index discriminated mortality in development (AUC = 0.79, 95% CI: 0.77-0.81), and in early (AUC = 0.81 95% CI: 0.78-0.83) and late (AUC = 0.84, 95% CI: 0.78-0.86) validation. The VACO Index allows personalized estimates of 30-day mortality after COVID-19 infection. For example, among those aged 60-64 years, overall mortality was estimated at 9% (95% CI: 6-11%). The Index further discriminated risk in this age stratum from 4% (95% CI: 3-7%) to 21% (95% CI: 12-31%), depending on sex and comorbid disease., Conclusion: Prior to infection, demographics and comorbid conditions can discriminate COVID-19 mortality risk overall and within age strata. The VACO Index reproducibly identified individuals at substantial risk of COVID-19 mortality who might consider continuing social distancing, despite relaxed state and local guidelines., Competing Interests: The authors have declared that no competing interests exist.

Ivermectin has recently shown efficacy against SARS-CoV-2 in-vitro. We retrospectively reviewed severe COVID-19 patients receiving standard doses of ivermectin and we compared clinical and microbiological outcomes with a similar group of patients not receiving ivermectin. No differences were found between groups. We recommend the evaluation of high-doses of ivermectin in randomized trials against SARS-CoV-2., Competing Interests: The authors have declared that no competing interests exist.

Background: The COVID-19 pandemic challenges societies in unknown ways, and individuals experience a substantial change in their daily lives and activities. Our study aims to describe these changes using population-based self-reported data about social and health behavior in a random sample of the Swiss population during the COVID-19 pandemic. The aim of the present article is two-fold: First, we want to describe the study methodology. Second, we want to report participant characteristics and study findings of the first survey wave to provide some baseline results for our study., Methods: Our study design is a longitudinal online panel of a random sample of the Swiss population. We measure outcome indicators covering general well-being, physical and mental health, social support, healthcare use and working state over multiple survey waves., Results: From 8,174 contacted individuals, 2,026 individuals participated in the first survey wave which corresponds to a response rate of 24.8%. Most survey participants reported a good to very good general life satisfaction (93.3%). 41.4% of the participants reported a worsened quality of life compared to before the COVID-19 emergency and 9.8% feelings of loneliness., Discussion: The COVID-19 Social Monitor is a population-based online survey which informs the public, health authorities, and the scientific community about relevant aspects and potential changes in social and health behavior during the COVID-19 emergency and beyond. Future research will follow up on the described study population focusing on COVID-19 relevant topics such as subgroup differences in the impact of the pandemic on well-being and quality of life or different dynamics of perceived psychological distress., Competing Interests: The authors have declared that no competing interests exist.

In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world., Competing Interests: The authors have declared that no competing interests exist.

The current COVID-19 pandemic raises concerns worldwide, leading to serious health, economic, and social challenges. The rapid spread of the virus at a global scale highlights the need for a more harmonized, less privacy-concerning, easily accessible approach to monitoring the human mobility that has proven to be associated with viral transmission. In this study, we analyzed over 580 million tweets worldwide to see how global collaborative efforts in reducing human mobility are reflected from the user-generated information at the global, country, and U.S. state scale. Considering the multifaceted nature of mobility, we propose two types of distance: the single-day distance and the cross-day distance. To quantify the responsiveness in certain geographic regions, we further propose a mobility-based responsive index (MRI) that captures the overall degree of mobility changes within a time window. The results suggest that mobility patterns obtained from Twitter data are amenable to quantitatively reflect the mobility dynamics. Globally, the proposed two distances had greatly deviated from their baselines after March 11, 2020, when WHO declared COVID-19 as a pandemic. The considerably less periodicity after the declaration suggests that the protection measures have obviously affected people's travel routines. The country scale comparisons reveal the discrepancies in responsiveness, evidenced by the contrasting mobility patterns in different epidemic phases. We find that the triggers of mobility changes correspond well with the national announcements of mitigation measures, proving that Twitter-based mobility implies the effectiveness of those measures. In the U.S., the influence of the COVID-19 pandemic on mobility is distinct. However, the impacts vary substantially among states., Competing Interests: The authors have declared that no competing interests exist.

The ongoing COVID-19 pandemic has overwhelmingly demonstrated the need to accurately evaluate the effects of implementing new or altering existing nonpharmaceutical interventions. Since these interventions applied at the societal level cannot be evaluated through traditional experimental means, public health officials and other decision makers must rely on statistical and mathematical epidemiological models. Nonpharmaceutical interventions are typically focused on contacts between members of a population, and yet most epidemiological models rely on homogeneous mixing which has repeatedly been shown to be an unrealistic representation of contact patterns. An alternative approach is individual based models (IBMs), but these are often time intensive and computationally expensive to implement, requiring a high degree of expertise and computational resources. More often, decision makers need to know the effects of potential public policy decisions in a very short time window using limited resources. This paper presents a computation algorithm for an IBM designed to evaluate nonpharmaceutical interventions. By utilizing recursive relationships, our method can quickly compute the expected epidemiological outcomes even for large populations based on any arbitrary contact network. We utilize our methods to evaluate the effects of various mitigation measures in the District of Columbia, USA, at various times and to various degrees. Rcode for our method is provided in the supplementry material, thereby allowing others to utilize our approach for other regions., Competing Interests: The authors have declared that no competing interests exist.

The SARS-CoV-2 virion responsible for the current world-wide pandemic COVID-19 has a characteristic Spike protein (S) on its surface that embellishes both a prefusion state and fusion state. The prefusion Spike protein (S) is a large trimeric protein where each protomer may be in a so-called Up state or Down state, depending on the configuration of its receptor binding domain (RBD) within its distal, prefusion S1 domain. The Up state is believed to allow binding of the virion to ACE-2 receptors on human epithelial cells, whereas the Down state is believed to be relatively inactive or reduced in its binding behavior. We have performed detailed all-atom, dominant energy landscape mappings for noncovalent interactions (charge, partial charge, and van der Waals) of the SARS-CoV-2 Spike protein in its static prefusion state based on two recent and independent experimental structure publications. We included both interchain interactions and intrachain (domain) interactions in our mappings in order to determine any telling differences (different so-called "glue" points) between residues in the Up and Down state protomers. The S2 proximal, fusion domain demonstrated no appreciable energetic differences between Up and Down protomers, including interchain as well as each protomer's intrachain, S1-S2 interactions. However, the S1 domain interactions across neighboring protomers, which include the RBD-NTD cross chain interactions, showed significant energetic differences between Up-Down and Down-Down neighboring protomers. This included, for example, a key RBD residue ARG357 in the Up-Down interaction and a three residue sequence ALA520-PRO521-ALA522, associated with a turn structure in the RBD of the Up state protomer, acting as a stabilizing interaction with the NTD of its neighbor protomer. Additionally, our intra chain dominant energy mappings within each protomer, identified a significant "glue" point or possible "latch" for the Down state protomer between the S1 subdomain, SD1, and the RBD domain of the same protomer that was completely missing in the Up state protomer analysis. Ironically, this dominant energetic interaction in the Down state protomer involved the backbone atoms of the same three residue sequence ALA520-PRO521-ALA522 of the RBD with the amino acid R-group of GLN564 in the SD1 domain. Thus, this same three residue sequence acts as a stabilizer of the RBD in the Up conformation through its interactions with its neighboring NTD chain and a kind of latch in the Down state conformation through its interactions with its own SD1 domain. The dominant interaction energy residues identified here are also conserved across reported variations of SARS-CoV-2, as well as the closely related virions SARS-Cov and the bat corona virus RatG13. We conducted preliminary molecular dynamics simulations across 0.1 μ seconds to see if this latch provided structural stability and indeed found that a single point mutation (Q564G) resulted in the latch releasing transforming the protomer from the Down to the Up state conformation. Full trimeric Spike protein studies of the same mutation across all protomers, however, did not exhibit latch release demonstrating the critical importance of interchain interactions across the S1 domain, including RBD-NTD neighboring chain interactions. Therapies aimed at disrupting these noncovalent interactions could be a viable route for the physico-chemical mitigation of this deadly virion., Competing Interests: V.C.U (M.H.P.) entered an exclusive licensing agreement for "ACE2 Decoy Peptides in the Treatment of COVID-19" with Hoth Therapeutics, NY.

The COVID-19 pandemic has had tremendous impact on Americans' lives including their personal and social behaviors. While people of all ages are affected in some way by the pandemic, older persons have been far more likely to suffer the most severe health consequences. For this reason, how people have responded to mitigating behaviors to COVID-19 may differ by age. Using a nationally representative sample from the longitudinal data of the Understanding America Study (UAS), we examined differentials in behavioral responses to COVID-19 by age and how they changed over the first three months of the pandemic. Behavioral responses and changes in behavior over time differed by age, type of behaviors and time reference. At the beginning of the pandemic (March, 2020), older and younger people were similar in their likelihood of engaging in preventive personal behaviors when controlling for other influences. As the pandemic progressed, however, older people adopted mitigating personal behavioral changes more than younger people, such that about 1-2 months after the pandemic started, older people were more likely to comply with suggested behaviors and regulations including practicing better hygiene, quarantining, and social distancing. One month into the pandemic, older people were less likely than younger people to engage in two of four risky behaviors. The change in risky behavior over time did not differ by age; but both younger and older people were more likely to engage in risky behaviors after two months. Being female, a member of a racial/ethnic minority group, higher socioeconomic status, having more COVID-19 cases in one's state of residence, a higher perceived risk for infection and dying, and a more left-leaning political orientation were related to adopting more pandemic mitigating behaviors., Competing Interests: The authors have declared that no competing interests exist.

The Coronavirus Disease 2019 (COVID-19) has fast spread to over 200 countries and regions worldwide since its outbreak, while in March, Europe became the emerging epicentre. In this study, we aimed to model the epidemic trends and estimate the essential epidemic features of COVID-19 in Italy, Spain, Germany, and France at the initial stage. The numbers of daily confirmed cases and total confirmed cases were extracted from the Coronavirus disease (COVID-19) situation reports of WHO. We applied an extended Susceptible-Exposed-Infectious-Removed (SEIR) model to fit the epidemic trend and estimated corresponding epidemic features. The transmission rate estimates were 1.67 (95% credible interval (CrI), 1.64-1.71), 2.83 (2.72-2.85), 1.91 (1.84-1.98), and 1.89 (1.82-1.96) for Italy, Spain, Germany, and France, corresponding to the basic reproduction numbers (R0) 3.44 (3.35-3.54), 6.25 (5.97-6.55), 4.03 (3.84-4.23), and 4.00 (3.82-4.19), respectively. We found Spain had the lowest ascertainment rate of 0.22 (0.19-0.25), followed by France, Germany, and Italy of 0.45 (0.40-0.50), 0.46 (0.40-0.52), and 0.59 (0.55-0.64). The peaks of daily new confirmed cases would reach on April 16, April 5, April 21, and April 19 for Italy, Spain, Germany, and France if no action was taken by the authorities. Given the high transmissibility and high covertness of COVID-19, strict countermeasures, such as national lockdown and social distancing, were essential to be implemented to reduce the spread of the disease., Competing Interests: The authors have declared that no competing interests exist.

Coronavirus Disease 2019 (COVID-19) has recently become a public emergency and a worldwide pandemic. However, the information on the risk factors associated with the mortality of COVID-19 and of their prognostic potential is limited. In this retrospective study, the clinical characteristics, treatment and outcome data were collected and analyzed from 676 COVID-19 patients stratified into 140 non-survivors and 536 survivors. We found that the levels of Dimerized plasmin fragment D (D-dimer), C-reactive protein (CRP), lactate dehydrogenase (LDH), procalcitonin (PCT) were significantly higher in non-survivals on admission (non-survivors vs. survivors: D-Dimer ≥ 0.5 mg/L, 83.2% vs. 44.9%, P<0.01; CRP ≥10 mg/L, 50.4% vs. 6.0%, P<0.01; LDH ≥ 250 U/L, 73.8% vs. 20.1%, P<0.01; PCT ≥ 0.5 ng/ml, 27.7% vs. 1.8%, P<0.01). Moreover, dynamic tracking showed D-dimer kept increasing in non-survivors, while CRP, LDH and PCT remained relatively stable after admission. D-dimer has the highest C-index to predict in-hospital mortality, and patients with D-dimer levels ≥0.5 mg/L had a higher incidence of mortality (Hazard Ratio: 4.39, P<0.01). Our study suggested D-dimer could be a potent marker to predict the mortality of COVID-19, which may be helpful for the management of patients., Competing Interests: The authors have declared that no competing interests exist.

Background: In December 2019, the COVID-19 outbreak began in China and quickly spread throughout the world and was reclassified as a pandemic in March 2020. The first case of COVID-19 was declared in Togo on March 5. Two months later, few data were available to describe the circulation of the new coronavirus in the country., Objective: This survey aimed to estimate the prevalence of SARS-CoV-2 in high-risk populations in Lomé., Materials and Methods: From April 23, 2020, to May 8, 2020, we recruited a sample of participants from five sectors: health care, air transport, police, road transport and informal. We collected oropharyngeal swabs for direct detection through real-time reverse transcription polymerase chain reaction (rRT-PCR) and blood for antibody detection by serological tests. The overall prevalence (current and past) of infection was defined by positivity for both tests., Results: A total of 955 participants with a median age of 36 (IQR 32-43) were included, and 71.6% (n = 684) were men. Approximately 22.1% (n = 212) were from the air transport sector, 20.5% (n = 196) were from the police sector, and 38.7% (n = 370) were from the health sector. Seven participants (0.7%, 95% CI: 0.3-1.6%) had a positive rRT-PCR test result at the time of recruitment, and nine (0.9%, 95% CI: 0.4-1.8%) were seropositive for IgM or IgG against SARS-CoV-2. We found an overall prevalence of 1.6% (n = 15), 95% CI: 0.9-2.6%., Conclusion: The prevalence of SARS-CoV-2 infection among high-risk populations in Lomé was relatively low and could be explained by the various measures taken by the Togolese government. Therefore, we recommend targeted screening., Competing Interests: The authors have declared that no competing interests exist

In March of this year, COVID-19 was declared a pandemic, and it continues to threaten public health. This global health crisis imposes limitations on daily movements, which have deteriorated every sector in our society. Understanding public reactions to the virus and the non-pharmaceutical interventions should be of great help to fight COVID-19 in a strategic way. We aim to provide tangible evidence of the human mobility trends by comparing the day-by-day variations across the U.S. from January 2020 to early April 2020. Large-scale public mobility at an aggregated level is observed by leveraging mobile device location data and the measures related to social distancing. Our study captures spatial and temporal heterogeneity as well as the sociodemographic variations and teleworking trends regarding the pandemic propagation and the non-pharmaceutical mobility interventions. All metrics adapted capture decreased public movements after the national emergency declaration. The population staying home has increased in all states before the stay-at-home mandates implemented and becomes more stable after the order with a smaller range of fluctuation. The public had been taking active responses, voluntarily staying home more, to the in-state confirmed cases while the stay-at-home orders stabilize the variations. As the estimated teleworking rates also continue to incline throughout the study period, the teleworking trend can be another driving factor for the growing stay-at-home population. We confirm that there exists overall mobility heterogeneity between the income or population density groups. The study suggests that public mobility trends are in line with the government message urging to stay home. We anticipate our data-driven analysis offers integrated perspectives and serves as evidence to raise public awareness and, consequently, reinforce the importance of social distancing while assisting policymakers., Competing Interests: The authors have declared that no competing interests exist.

Evidence-based models may assist Mexican government officials and health authorities in determining the safest plans to respond to the coronavirus disease 2019 (COVID-19) pandemic in the most-affected region of the country, the Mexico City Metropolitan Area. This study aims to present the potential impacts of COVID-19 in this region and to model possible benefits of mitigation efforts. The COVID-19 Hospital Impact Model for Epidemics was used to estimate the probable evolution of COVID-19 in three scenarios: (i) no social distancing, (ii) social distancing in place at 50% effectiveness, and (iii) social distancing in place at 60% effectiveness. Projections of the number of inpatient hospitalizations, intensive care unit admissions, and patients requiring ventilators were made for each scenario. Using the model described, it was predicted that peak case volume at 0% mitigation was to occur on April 30, 2020 at 11,553,566 infected individuals. Peak case volume at 50% mitigation was predicted to occur on June 1, 2020 with 5,970,093 infected individuals and on June 21, 2020 for 60% mitigation with 4,128,574 infected individuals. Occupancy rates in hospitals during peak periods at 0%, 50%, and 60% mitigation would be 875.9%, 322.8%, and 203.5%, respectively, when all inpatient beds are included. Under these scenarios, peak daily hospital admissions would be 40,438, 13,820, and 8,650. Additionally, 60% mitigation would result in a decrease in peak intensive care beds from 94,706 to 23,116 beds and a decrease in peak ventilator need from 67,889 to 17,087 units. Mitigating the spread of COVID-19 through social distancing could have a dramatic impact on reducing the number of infected people and minimize hospital overcrowding. These evidence-based models may enable careful resource utilization and encourage targeted public health responses., Competing Interests: The authors have declared that no competing interests exist.

The coronavirus disease 2019 (Covid-19) pandemic, caused by SARS-CoV-2, has resulted in a global testing supply shortage. In response, pooled testing has emerged as a promising strategy that can immediately increase testing capacity. In pooled sample testing, multiple samples are combined (or pooled) together and tested as a single unit. If the pool is positive, the individual samples can then be individually tested to identify the positive case(s). Here, we provide support for the adoption of sample pooling with the point-of-care Cepheid Xpert® Xpress SARS-CoV-2 molecular assay. Corroborating previous findings, the limit of detection of this assay was comparable to laboratory-developed reverse-transcription quantitative PCR SARS-CoV-2 tests, with observed detection below 100 copies/mL. The Xpert® Xpress assay detected SARS-CoV-2 after samples with minimum viral loads of 461 copies/mL were pooled in groups of six. Based on these data, we recommend the adoption of pooled testing with the Xpert® Xpress SARS-CoV-2 assay where warranted based on public health needs. The suggested number of samples per pool, or the pooling depth, is unique for each point-of-care testing site and can be determined by the positive test rates. To statistically determine appropriate pooling depth, we have calculated the pooling efficiency for numerous combinations of pool sizes and test rates. This information is included as a supplemental dataset that we encourage public health authorities to use as a guide to make recommendations that will maximize testing capacity and resource conservation., Competing Interests: The authors have declared that no competing interests exist.

Fatigue is a common symptom in those presenting with symptomatic COVID-19 infection. However, it is unknown if COVID-19 results in persistent fatigue in those recovered from acute infection. We examined the prevalence of fatigue in individuals recovered from the acute phase of COVID-19 illness using the Chalder Fatigue Score (CFQ-11). We further examined potential predictors of fatigue following COVID-19 infection, evaluating indicators of COVID-19 severity, markers of peripheral immune activation and circulating pro-inflammatory cytokines. Of 128 participants (49.5 ± 15 years; 54% female), more than half reported persistent fatigue (67/128; 52.3%) at median of 10 weeks after initial COVID-19 symptoms. There was no association between COVID-19 severity (need for inpatient admission, supplemental oxygen or critical care) and fatigue following COVID-19. Additionally, there was no association between routine laboratory markers of inflammation and cell turnover (leukocyte, neutrophil or lymphocyte counts, neutrophil-to-lymphocyte ratio, lactate dehydrogenase, C-reactive protein) or pro-inflammatory molecules (IL-6 or sCD25) and fatigue post COVID-19. Female gender and those with a pre-existing diagnosis of depression/anxiety were over-represented in those with fatigue. Our findings demonstrate a significant burden of post-viral fatigue in individuals with previous SARS-CoV-2 infection after the acute phase of COVID-19 illness. This study highlights the importance of assessing those recovering from COVID-19 for symptoms of severe fatigue, irrespective of severity of initial illness, and may identify a group worthy of further study and early intervention., Competing Interests: The authors have declared that no competing interests exist.

Background: A recent cluster of pneumonia cases in Wuhan, China, has been caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We propose the protocol described below to perform an individual-patient data (IPD) network meta-analysis (NMA) in order to evaluate the efficacies of different antiviral drugs to treat patients with coronavirus disease 2019 (COVID-19)., Materials and Methods: We will search the Medline, EMBASE, Cochrane Library, SinoMed, CNKI and VIP databases from their inceptions through July 2020. There will be no restrictions on language, publication year, or publication type. Randomized clinical trials (RCTs) and prospective cohort studies with antiviral treatments for COVID-19 will be considered. Two reviewers will independently select studies and collect data. Risk-of-bias assessments will be completed using the Cochrane risk-of-bias scale. Primary outcome will be the COVID-19 recovery rate. We will combine aggregated data from IPD with the NMA in a single model, compare the effects of different antiviral drugs on patient-relevant efficacy, and rank the results to decide which is the most effective., Trial Registration: PROSPERO registration number: CRD42020167038., Competing Interests: There are no conflicts of interest in relation to this study.

Transmission pathways of SARS-CoV-2 are aerosol, droplet and touching infected material. The diffusion of the virus contagion among people is easier in indoor location, but direct detection of SARS-CoV-2 in air or on surfaces is quite sparse, especially regarding public transport, while it would be important to know how and if it is safe to use them. To answer these questions we analysed the air and the surfaces most usually touched by passengers inside a city bus during normal operation, in order to understand the possible spreading of the virus and the effectiveness of the protective measures. The measurements were carried out across the last week of the lockdown and the first week when, gradually, all the travel restrictions were removed. The air and surface samples were analysed with the RT-PCR for the detection of SARS-CoV-2 virus. After two weeks of measurements and more than 1100 passenger travelling on the bus the virus was never detected both on surfaces and on air, suggesting that the precautions adopted on public transportation are effective in reducing the COVID-19 spreading., Competing Interests: The authors have declared that no competing interests exist.

Competing Interests: The authors have declared that no competing interests exist.

Background: The study objective was to conduct a systematic review and meta-analysis on the proportion of asymptomatic infection among coronavirus disease 2019 (COVID-19) positive persons and their transmission potential., Methods: We searched Embase, Medline, bioRxiv, and medRxiv up to 22 June 2020. We included cohorts or cross-sectional studies which systematically tested populations regardless of symptoms for COVID-19, or case series of any size reporting contact investigations of asymptomatic index patients. Two reviewers independently extracted data and assessed quality using pre-specified criteria. Only moderate/high quality studies were included. The main outcomes were proportion of asymptomatic infection among COVID-19 positive persons at testing and through follow-up, and secondary attack rate among close contacts of asymptomatic index patients. A qualitative synthesis was performed. Where appropriate, data were pooled using random effects meta-analysis to estimate proportions and 95% confidence intervals (95% CI)., Results: Of 6,137 identified studies, 71 underwent quality assessment after full text review, and 28 were high/moderate quality and were included. In two general population studies, the proportion of asymptomatic COVID-19 infection at time of testing was 20% and 75%, respectively; among three studies in contacts it was 8.2% to 50%. In meta-analysis, the proportion (95% CI) of asymptomatic COVID-19 infection in obstetric patients was 95% (45% to 100%) of which 59% (49% to 68%) remained asymptomatic through follow-up; among nursing home residents, the proportion was 54% (42% to 65%) of which 28% (13% to 50%) remained asymptomatic through follow-up. Transmission studies were too heterogenous to meta-analyse. Among five transmission studies, 18 of 96 (18.8%) close contacts exposed to asymptomatic index patients were COVID-19 positive., Conclusions: Despite study heterogeneity, the proportion of asymptomatic infection among COVID-19 positive persons appears high and transmission potential seems substantial. To further our understanding, high quality studies in representative general population samples are required., Competing Interests: We declare no competing interests or conflicts of interest.

Background: Epidemiological differences between men and women have been reported with regards to sepsis, influenza and severe coronavirus infections including SARS-CoV and MERS-CoV., Aim: To systematically review the literature relating to men versus women on SARS-CoV-2 in order to seek differences in disease characteristics (e.g. infectivity, severity) and outcomes (e.g. mortality)., Methods: We searched 3 electronic databases up or observational studies reporting differences between men and women in the SARS-CoV-2 disease characteristics stated. We identified and included 47 studies, reporting data for 21,454 patients mainly from China., Results: The unadjusted mortality rates of men were higher than those of women, with a mortality OR 0.51 [0.42, 0.61] (p<0.001) for women. The proportion of men presenting with severe disease and admitted to the intensive care unit (ICU) was also higher than that of women (OR 0.75 [0.60-0.93] p<0.001 and OR 0.45 [0.40-0.52] p<0.001 respectively). Adjusted analyses could not be conducted due to lack of data., Conclusion: COVID-19 may be associated with worse outcomes in males than in females. However, until more detailed data are provided in further studies enabling adjusted analysis, this remains an unproven assumption., Competing Interests: IL, DLP, SE and JLM have no conflict of interest to disclose. ML served as speaker for MSD, Pfizer and as consultant for Amomed, Aguettant and Gilead. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Objectives: The purpose is to assess the ability of low-dose CT (LDCT) to determine lung involvement in SARS-CoV-2 pneumonia and to describe a COVID19-LDCT severity score., Materials and Methods: Patients with SARS-CoV-2 infection confirmed by RT-PCR were retrospectively analysed. Clinical data, the National Early Warning Score (NEWS) and imaging features were recorded. Lung features included ground-glass opacities (GGO), areas of consolidation and crazy paving patterns. The COVID19-LDCT score was calculated by summing the score of each segment from 0 (no involvement) to 10 (severe impairment). Univariate analysis was performed to explore predictive factor of high COVID19-LDCT score. The nonparametric Mann-Whitney test was used to compare groups and a Spearman correlation used with p<0.05 for significance., Results: Eighty patients with positive RT-PCR were analysed. The mean age was 55 years ± 16, with 42 males (53%). The most frequent symptoms were fever (60/80, 75%) and cough (59/80, 74%), the mean NEWS was 1.7±2.3. All LDCT could be analysed and 23/80 (28%) were normal. The major imaging finding was GGOs in 56 cases (67%). The COVID19-LDCT score (mean value = 19±29) was correlated with NEWS (r = 0.48, p<0.0001). No symptoms were risk factor to have pulmonary involvement. Univariate analysis shown that dyspnea, high respiratory rate, hypertension and diabetes are associated to a COVID19-LDCT score superior to 50., Conclusions: COVID19-LDCT score did correlate with NEWS. It was significantly different in the clinical low-risk and high-risk groups. Further work is needed to validate the COVID19-LDCT score against patient prognosis., Competing Interests: The authors have declared that no competing interests exist.

SARS-CoV-2 is spreading globally with unprecedented consequences for modern societies. The early detection of infected individuals is a pre-requisite to contain the virus. Currently, purification of RNA from patient samples followed by RT-PCR is the gold standard to assess the presence of this single-strand RNA virus. However, these procedures are time consuming, require continuous supply of specialized reagents, and are prohibitively expensive in resource-poor settings. Here, we report an improved nucleic-acid-based approach to detect SARS-CoV-2 with the ability to detect as little as five viral genome equivalents. The approach delivers results without the need to purify RNA, reduces handling steps, minimizes costs, and allows evaluation by non-specialized equipment. The use of unprocessed swap samples is enabled by employing a heat-stable RNA- and DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. As results are obtained within 2 hours and can be read-out by a hand-held LED-screen, this novel protocol will be of particular importance for large-scale virus surveillance in economically constrained settings., Competing Interests: RK and AM are founders of myPOLS Biotec GmbH, manufacturer of Volcano3G polymerase used in this manuscript. AM is a shareholder of and RK is employed by myPOLS Biotec GmbH. This does not alter our adherence to PLOS ONE policies on sharing data and materials. All other authors declare that they have no conflict of interest.

Objective: Poor housing conditions have been linked with worse health outcomes and infectious disease spread. Since the relationship of poor housing conditions with incidence and mortality of COVID-19 is unknown, we investigated the association between poor housing condition and COVID-19 incidence and mortality in US counties., Methods: We conducted cross-sectional analysis of county-level data from the US Centers for Disease Control, US Census Bureau and John Hopkins Coronavirus Resource Center for 3135 US counties. The exposure of interest was percentage of households with poor housing conditions (one or greater of: overcrowding, high housing cost, incomplete kitchen facilities, or incomplete plumbing facilities). Outcomes were incidence rate ratios (IRR) and mortality rate ratios (MRR) of COVID-19 across US counties through 4/21/2020. Multilevel generalized linear modeling (with total population of each county as a denominator) was utilized to estimate relative risk of incidence and mortality related to poor housing conditions with adjustment for population density and county characteristics including demographics, income, education, prevalence of medical comorbidities, access to healthcare insurance and emergency rooms, and state-level COVID-19 test density. We report incidence rate ratios (IRRs) and mortality ratios (MRRs) for a 5% increase in prevalence in households with poor housing conditions., Results: Across 3135 US counties, the mean percentage of households with poor housing conditions was 14.2% (range 2.7% to 60.2%). On April 21st, the mean (SD) number of cases and deaths of COVID-19 were 255.68 (2877.03) cases and 13.90 (272.22) deaths per county, respectively. In the adjusted models standardized by county population, with each 5% increase in percent households with poor housing conditions, there was a 50% higher risk of COVID-19 incidence (IRR 1.50, 95% CI: 1.38-1.62) and a 42% higher risk of COVID-19 mortality (MRR 1.42, 95% CI: 1.25-1.61). Results remained similar using earlier timepoints (3/31/2020 and 4/10/2020)., Conclusions and Relevance: Counties with a higher percentage of households with poor housing had higher incidence of, and mortality associated with, COVID-19. These findings suggest targeted health policies to support individuals living in poor housing conditions should be considered in further efforts to mitigate adverse outcomes associated with COVID-19., Competing Interests: The authors have declared that no competing interests exist.

Background: Rapid and extensive testing of large parts of the population and specific subgroups is crucial for proper management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and decision-making in times of a pandemic outbreak. However, point-of-care (POC) testing in places such as emergency units, outpatient clinics, airport security points or the entrance of any public building is a major challenge. The need for thermal cycling and nucleic acid isolation hampers the use of standard PCR-based methods for this purpose., Methods: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK)., Results: Whilst specificity of standard RT-LAMP assays appears to be satisfactory, sensitivity does not reach the current gold-standard quantitative real-time polymerase chain reaction (qPCR) assays yet. We describe a novel multiplexed RT-LAMP approach and validate its sensitivity on primary samples. This approach allows for fast and reliable identification of infected individuals. Primer optimization and multiplexing helps to increase sensitivity significantly. In addition, we directly compare and combine our novel RT-LAMP assays with SHERLOCK., Conclusion: In summary, this approach reveals one-step multiplexed RT-LAMP assays as a prime-option for the development of easy and cheap POC test kits., Competing Interests: F.Z., O.O.A., J.S.G., J.J., and A.L. are inventors on patent applications related to SHERLOCK technology filed by the Broad Institute, with the specific aim of ensuring this technology can be made freely, widely, and rapidly available for research and deployment (US provisional application no. 62/975,743, "CRISPR Effector System Based Coronavirus Diagnostics"). This does not alter our adherence to PLOS ONE`s policies on sharing data and materials. O.O.A., J.S.G., and F.Z. are co-founders, scientific advisors, and hold equity interests in Sherlock Biosciences, Inc., and Pine Trees Health, Inc. F.Z. is also a co-founder of Editas Medicine, Beam Therapeutics, Pairwise Plants, and Arbor Biotechnologies. NAT is employed by New England Biolabs, Inc, manufacturer of the LAMP reagents and some additional enzymes described in this manuscript. All of the aforementioned does not alter our adherence to PLOS ONE`s policies on sharing data and materials. The remaining authors declare no competing financial interests.

There is an urgent need for an accurate antibody test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have developed 3 ELISA methods, trimer spike IgA, trimer spike IgG, and nucleocapsid IgG, for detecting anti-SARS-CoV-2 antibodies. We evaluated their performance along with four commercial ELISAs, EDI™ Novel Coronavirus COVID-19 ELISA IgG and IgM, Euroimmun Anti-SARS-CoV-2 ELISA IgG and IgA, and one lateral flow assay, DPP® COVID-19 IgM/IgG System (Chembio). Both sensitivity and specificity were evaluated and the probable causes of false-positive reactions were determined. The assays were evaluated using 300 pre-epidemic samples and 100 PCR-confirmed COVID-19 samples. The sensitivities and specificities of the assays were as follows: 90%/100% (in-house trimer spike IgA), 90%/99.3% (in-house trimer spike IgG), 89%/98.3% (in-house nucleocapsid IgG), 73.7%/100% (EDI nucleocapsid IgM), 84.5%/95.1% (EDI nucleocapsid IgG), 95%/93.7% (Euroimmun S1 IgA), 82.8%/99.7% (Euroimmun S1 IgG), 82.0%/91.7% (Chembio nucleocapsid IgM), 92%/93.3% (Chembio nucleocapsid IgG). The presumed causes of false positive results from pre-epidemic samples in commercial and in-house assays were mixed. In some cases, assays lacked reproducibility. In other cases, reactivity was abrogated by competitive inhibition (spiking the sample with the same antigen that was used for coating ELISAs prior to performing the assay), suggesting positive reaction could be attributed to the presence of antibodies against these antigens. In other cases, reactivity was consistently detected but not abrogated by the spiking, suggesting positive reaction was not attributed to the presence of antibodies against these antigens. Overall, there was wide variability in assay performance using our samples, with in-house tests exhibiting the highest combined sensitivity and specificity. The causes of "false positivity" in pre-epidemic samples may be due to plasma antibodies apparently reacting with the corresponding antigen, or spurious reactivity may be directed against non-specific components in the assay system. Identification of these targets will be essential to improving assay performance., Competing Interests: The authors have declared that no competing interests exist.

Both polyester and foam nasal swabs were collected from convalescent COVID-19 patients at a single visit and stored in viral transport media (VTM), saline or dry. Sensitivity of each swab material and media combination were estimated, three by three tables were constructed to measure polyester and foam concordance, and cycle threshold (Ct) values were compared. 126 visits had polyester and foam swabs stored in viral transport media (VTM), 51 had swabs stored in saline, and 63 had a foam swab in VTM and a polyester swab stored in a dry tube. Polyester and foam swabs had an estimated sensitivity of 87.3% and 94.5% respectively in VTM, 87.5% and 93.8% respectively in saline, and 75.0% and 90.6% respectively for dry polyester and foam VTM. Polyester and foam Ct values were correlated, but polyester showed decreased performance for cases with a viral load near the detection threshold and higher Ct values on average., Competing Interests: Brian Hart, Rachel Jennings, Prateek Verma, Deneen Vojta, and Ethan Berke were employees of UnitedHealth Group during the design and analysis of the study and initial drafting of the manuscript. Yuan-Po Tu is an employee of The Everett Clinic, which is a subsidiary of UnitedHealth Group. Leah R. Padgett and Douglas Rains are employees of Quantigen Biosciences and have performed contract services for Thermo Fisher Scientific. The specific roles of these authors are articulated in the ‘author contributions’ section. The competing interests implied by the authors’ employer/employee relationships do not alter our adherence to PLOS ONE policies on sharing data and materials.

Background: There is increasing demand for post-acute care services, which is amplified by the COVID-19 pandemic., Aims: We studied the pattern of spatial association between post-acute care services and acute care facilities and evaluated how geographic variability could influence their use., Methods: We compiled data on CMS-certified acute care and critical access hospitals and post-acute health care services (nursing homes, home health care services, inpatient rehabilitation facilities, long-term care hospitals, and hospice facilities). We used the colocation quotient (CLQ) to measure the magnitude and direction of association (clustering or segregation) between post-acute care providers and hospitals. This metric allows pairwise comparison of categorical data; a value <1 indicates spatial segregation and a value >1 spatial clustering. Unity marks the lack of spatial dependence (random distribution)., Results: With the exception of nursing homes (CLQ 1.26), all other types of post-acute care providers are spatially segregated from rural critical access hospitals. Long-term care facilities ranked first (had the lowest global CLQ, 0.06), hospice facilities ranked last (had the highest global CLQ estimate, 0.54). Instead, post-acute care services either clustered with (inpatient rehabilitation 2.76, long-term care 2.10, nursing homes 1.37) or were only weakly segregated (home health care 0.86) from acute care hospitals. Home health care (1.44), hospice services (1.46), and nursing homes (1.08) spatially clustered with the same category of services. Results were robust in the sensitivity analysis and we provided illustrative examples of local variation for the states of MA and IA., Conclusion: Post-acute care services are isolated from critical access hospitals, and have a clustering pattern with the same category services and acute care hospitals. Such misdistribution of resources may result in both underuse and a substitution effect on the type of post-acute care between rural and urban areas and undermine public health during increasing demand, such as the COVID-19 pandemic., Competing Interests: The authors have declared that no competing interests exist. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Objectives: During the course of the Novel Coronavirus (SARS-CoV-2) pandemic, Italy has reported one of the highest number of infections. Nearly ten percent of reported coronavirus infections in Italy occurred in healthcare workers. This study aimed to understand physicians' access to personal protective equipment (PPE) and to information about their use, risk perception and strategies adopted to prevent contracting the infection., Methods: We undertook a cross-sectional, online self-reported survey implemented between March 31 and April 5 2020 of Italian physicians., Results: Responses were received from 516 physicians, only 13% of which reported to have access to PPE every time they need them. Approximately half of the physicians reported that the information received about the use of PPE was either clear (47%) or complete (54%). Risk perception about contracting the infection was influenced by receiving adequate information on the use of PPE. Access to adequate information on the use of PPE was associated with better ability to perform donning and doffing procedures [OR = 2.2 95% C.I. 1.7-2.8] and reduced perception of risk [OR = 0.5, 95% C.I. 0.4-0.6]., Conclusions: Results from this rapid survey indicate that while ramping up supplies on PPE for healthcare workers is certainly of mandatory importance, adequate training and clear instructions are just as important., Competing Interests: The authors have declared that no competing interests exist.

Background: After a COVID-19 diagnosis, vulnerable populations face considerable logistical and financial challenges to isolate and quarantine. We developed and evaluated a novel, community-based approach ('Test-to-Care' Model) designed to address these barriers for socioeconomically vulnerable Latinx individuals with newly diagnosed COVID-19 and their households., Methods: This three-week demonstration project was nested within an epidemiologic surveillance study in a primarily Latinx neighborhood in the Mission district of San Francisco, California. The Test-to-Care model was developed with input from community members and public health leaders. Key components included: (1) provision of COVID-19-related education and information about available community resources, (2) home deliveries of material goods to facilitate safe isolation and quarantine (groceries, personal protective equipment and cleaning supplies), and (3) longitudinal clinical and social support. Newly SARS-CoV-2 PCR-positive participants were eligible to participate. Components of the model were delivered by the Test-to-Care team, which was comprised of healthcare providers and community health workers (CHWs) who provided longitudinal clinic- and community-based support for the duration of the isolation period to augment existing services from the Department of Public Health (DPH). We evaluated the Test-to-Care Model using the Reach, Effectiveness, Adoption, Implementation, Maintenance (RE-AIM) Framework and drew upon multiple data sources including: programmatic data, informal interviews with participants and providers/CHWs and structured surveys among providers/CHWs., Results: Overall, 83 participants in the surveillance study were diagnosed with COVID-19, of whom 95% (79/83) were Latinx and 88% (65/74) had an annual household income <$50,000. Ninety-six percent (80/83) of participants were reached for results disclosure, needs assessment and DPH linkage for contact tracing. Among those who underwent an initial needs assessment, 45% (36/80) were uninsured and 55% (44/80) were not connected to primary care. Sixty-seven percent (56/83) of participants requested community-based CHW support to safely isolate at their current address and 65% (54/83) of all COVID-19 participants received ongoing community support via CHWs for the entire self-isolation period. Participants reported that the intervention was highly acceptable and that their trust increased over time-this resulted in 9 individuals who disclosed a larger number of household members than first reported, and 6 persons who requested temporary relocation to a hotel room for isolation despite initially declining this service; no unintended harms were identified. The Test-to-Care Model was found to be both acceptable and feasible to providers and CHWs. Challenges identified included a low proportion of participants linked to primary care despite support (approximately 10% after one month), and insufficient access to financial support for wage replacement., Conclusions: The Test-to-Care Model is a feasible and acceptable intervention for supporting self-isolation and quarantine among newly diagnosed COVID-19 patients and their households by directly addressing key barriers faced by socioeconomically vulnerable populations., Competing Interests: The authors have read the journal’s policy and have the following competing interests: Grocery Outlet donated groceries to support the participants of this demonstration project. This does not alter our adherence to PLOS ONE policies on sharing data and materials. There are no patents, products in development or marketed products associated with this research to declare.

In Bangladesh, an array of measures have been adopted to control the rapid spread of the COVID-19 epidemic. Such general population control measures could significantly influence perception, knowledge, attitudes, and practices (KAP) towards COVID-19. Here, we assessed KAP towards COVID-19 immediately after the lock-down measures were implemented and during the rapid rise period of the outbreak. Online-based cross-sectional study conducted from March 29 to April 19, 2020, involving Bangladeshi residents aged 12-64 years, recruited via social media. After consenting, participants completed an online survey assessing socio-demographic variables, perception, and KAP towards COVID-19. Of the 2017 survey participants, 59.8% were male, the majority were students (71.2%), aged 21-30 years (57.9%), having a bachelor's degree (61.0%), having family income >30,000 BDT (50.0%), and living in urban areas (69.8). The survey revealed that 48.3% of participants had more accurate knowledge, 62.3% had more positive attitudes, and 55.1% had more frequent practices regarding COVID-19 prevention. Majority (96.7%) of the participants agreed 'COVID-19 is a dangerous disease', almost all (98.7%) participants wore a face mask in crowded places, 98.8% agreed to report a suspected case to health authorities, and 93.8% implemented washing hands with soap and water. In multiple logistic regression analyses, COVID-19 more accurate knowledge was associated with age and residence. Sociodemographic factors such as being older, higher education, employment, monthly family income >30,000 BDT, and having more frequent prevention practices were the more positive attitude factors. More frequent prevention practice factors were associated with female sex, older age, higher education, family income > 30,000 BDT, urban area residence, and having more positive attitudes. To improve KAP of general populations is crucial during the rapid rise period of a pandemic outbreak such as COVID-19. Therefore, development of effective health education programs that incorporate considerations of KAP-modifying factors is needed., Competing Interests: The authors have declared that no competing interests exist.

Background: A greater understanding of the antibody response to SARS-CoV-2 in an infected population is important for the development of a vaccination., Aim: To investigate SARS-CoV-2 IgA and IgG antibodies in Thai patients with differing severities of COVID-19., Methods: Plasma from the following patient groups was examined: 118 adult patients with confirmed SARS-CoV-2 infections, 49 patients under investigation (without confirmed infections), 20 patients with other respiratory infections, and 102 healthy control patients. Anti-SARS-CoV-2 enzyme-linked immunosorbent assay (ELISA) from EUROIMMUN was performed to assess for IgA and IgG antibodies. The optical density (OD) ratio cutoff for a positive result was 1.1 for IgA and 0.8 for IgG. Additionally, the association of the antibody response with both the severity of disease and the date after onset of symptoms was analyzed., Results: A total of 289 participants were enrolled and 384 samples analyzed from March 10 to May 31, 2020. Patients were categorized, based on their clinical manifestations, as mild (n = 59), moderate (n = 27), or severe (n = 32). The overall sensitivity of IgA and IgG from the samples collected after day 7 of the symptoms was 87.9% (95% CI: 79.8-93.6) and 84.8% (95% CI: 76.2-91.3), respectively. Compared to the mild group, the severe group had significantly higher levels of spike 1 (S1) antigen-specific IgA and IgG. All patients in the moderate and severe groups had S1-specific IgG, while 20% of the patients in the mild group did not have any IgG detected after two weeks after the onset of symptoms. Interestingly, in the severe group, the SARS-CoV-2 IgG level was significantly higher in males than females (p = 0.003)., Conclusion: The serological test for SARS-CoV-2 has a high sensitivity more than two weeks after the onset of illness. Additionally, the serological response differs among patients based on sex as well as the severity of infection., Competing Interests: The authors have declared that no competing interests exist.

Little is known about the SARS-CoV-2 contamination of environmental surfaces and air in non-health care settings among COVID-19 cases. We explored the SARS-CoV-2 contamination of environmental surfaces and air by collecting air and swabbing environmental surfaces among 39 COVID-19 cases in Guangzhou, China. The specimens were tested on RT-PCR. The information collected for COVID-19 cases included basic demographic, clinical severity, symptoms at onset, radiological testing, laboratory testing and hospital admission. A total of 641 environmental surfaces and air specimens were collected among 39 COVID-19 cases before disinfection. Among them, 20 specimens (20/641, 3.1%) were tested positive from 9 COVID-19 cases (9/39, 23.1%), with 5 (5/101, 5.0%) positive specimens from 3 asymptomatic cases, 5 (5/220, 2.3%) from 3 mild cases, and 10 (10/374, 2.7%) from 3 moderate cases. All positive specimens were collected within 3 days after diagnosis, and 10 (10/42, 23.8%) were found in toilet (5 on toilet bowl, 4 on sink/faucet/shower, 1 on floor drain), 4 (4/21, 19.0%) in anteroom (2 on water dispenser/cup/bottle, 1 on chair/table, 1 on TV remote), 1 (1/8, 12.5%) in kitchen (1 on dining-table), 1 (1/18, 5.6%) in bedroom (1 on bed/sheet pillow/bedside table), 1 (1/5, 20.0%) in car (1 on steering wheel/seat/handlebar) and 3 (3/20, 21.4%) on door knobs. Air specimens in room (0/10, 0.0%) and car (0/1, 0.0%) were all negative. SARS-CoV-2 was found on environmental surfaces especially in toilet, and may survive for several days. We provided evidence of potential for SARS-CoV-2 transmission through contamination of environmental surfaces., Competing Interests: The authors have declared that no competing interests exist.

This study analyzes the effects of COVID-19 confinement on the autonomous learning performance of students in higher education. Using a field experiment with 458 students from three different subjects at Universidad Autónoma de Madrid (Spain), we study the differences in assessments by dividing students into two groups. The first group (control) corresponds to academic years 2017/2018 and 2018/2019. The second group (experimental) corresponds to students from 2019/2020, which is the group of students that had their face-to-face activities interrupted because of the confinement. The results show that there is a significant positive effect of the COVID-19 confinement on students' performance. This effect is also significant in activities that did not change their format when performed after the confinement. We find that this effect is significant both in subjects that increased the number of assessment activities and subjects that did not change the student workload. Additionally, an analysis of students' learning strategies before confinement shows that students did not study on a continuous basis. Based on these results, we conclude that COVID-19 confinement changed students' learning strategies to a more continuous habit, improving their efficiency. For these reasons, better scores in students' assessment are expected due to COVID-19 confinement that can be explained by an improvement in their learning performance., Competing Interests: The authors have declared that no competing interests exist.

In this study we present the first comprehensive analysis of the spatio-temporal differences in excess mortality during the COVID-19 pandemic in Italy. We used a population-based design on all-cause mortality data, for the 7,904 Italian municipalities. We estimated sex-specific weekly mortality rates for each municipality, based on the first four months of 2016-2019, while adjusting for age, localised temporal trends and the effect of temperature. Then, we predicted all-cause weekly deaths and mortality rates at municipality level for the same period in 2020, based on the modelled spatio-temporal trends. Lombardia showed higher mortality rates than expected from the end of February, with 23,946 (23,013 to 24,786) total excess deaths. North-West and North-East regions showed one week lag, with higher mortality from the beginning of March and 6,942 (6,142 to 7,667) and 8,033 (7,061 to 9,044) total excess deaths respectively. We observed marked geographical differences also at municipality level. For males, the city of Bergamo (Lombardia) showed the largest percent excess, 88.9% (81.9% to 95.2%), at the peak of the pandemic. An excess of 84.2% (73.8% to 93.4%) was also estimated at the same time for males in the city of Pesaro (Central Italy), in stark contrast with the rest of the region, which does not show evidence of excess deaths. We provided a fully probabilistic analysis of excess mortality during the COVID-19 pandemic at sub-national level, suggesting a differential direct and indirect effect in space and time. Our model can be used to help policy-makers target measures locally to contain the burden on the health-care system as well as reducing social and economic consequences. Additionally, this framework can be used for real-time mortality surveillance, continuous monitoring of local temporal trends and to flag where and when mortality rates deviate from the expected range, which might suggest a second wave of the pandemic., Competing Interests: The authors have declared that no competing interests exist.

About 50% of individuals infected with the novel Coronavirus (SARS-CoV-2) suffer from intestinal infection as well as respiratory infection. They shed virus in their stool. Municipal sewage systems carry the virus and its genetic remnants. These viral traces can be detected in the sewage entering a wastewater treatment plant (WTP). Such virus signals indicate community infections but not locations of the infection within the community. In this paper, we frame and formulate the problem in a way that leads to algorithmic procedures homing in on locations and/or neighborhoods within the community that are most likely to have infections. Our data source is wastewater sampled and real-time tested from selected manholes. Our algorithms dynamically and adaptively develop a sequence of manholes to sample and test. The algorithms are often finished after 5 to 10 manhole samples, meaning that-in the field-the procedure can be carried out within one day. The goal is to provide timely information that will support faster more productive human testing for viral infection and thus reduce community disease spread. Leveraging the tree graph structure of the sewage system, we develop two algorithms, the first designed for a community that is certified at a given time to have zero infections and the second for a community known to have many infections. For the first, we assume that wastewater at the WTP has just revealed traces of SARS-CoV-2, indicating existence of a "Patient Zero" in the community. This first algorithm identifies the city block in which the infected person resides. For the second, we home in on a most infected neighborhood of the community, where a neighborhood is usually several city blocks. We present extensive computational results, some applied to a small New England city., Competing Interests: No authors have competing interests.

Given the global spread of coronavirus disease (COVID-19), strict discharge standard is of great significance for the prevention and control of the epidemic, thus, the purpose of this study is to formulate more strict and scientific discharge standards. A total of 845 patients with mild and general COVID-19 who were considered to be discharged from hospital were included in this study. The median time from the onset of COVID-19 to the occurrence of two consecutive negative nucleic acid tests of these patients was 21 days. 223 of the 845 patients were tested again after two consecutive negative nucleic acid tests and 17.49% of the patients were positive. Moreover, 82.51% (184 of 223) of these patients experienced negative results from three consecutive nucleic acid tests, the median time from the onset of COVID-19 to the occurrence of three consecutive negative nucleic acid tests was 23 days (range: 3-56 days), and 38 of which were further tested after three consecutive negative nucleic acid tests, while about 5.26% (2 of 38) patients showed positive nucleic acid test results. Thus, we suggested that the patient should be negative for at least 3 consecutive nucleic acid tests before discharge, and the test time should be no earlier than the 23rd day since the onset of the disease., Competing Interests: The authors have declared that no competing interests exist.

Background: The SARS-CoV-2 (Severe Acute Respiratory Syndrome CoronaVirus 2) is responsible for the infectious respiratory disease called COVID-19 (COronaVIrus Disease 2019). In response to the growing COVID-19 pandemic, point-of-care (POC) tests have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. We conducted a prospective observational study to evaluate the performance of two POC tests, COVID-PRESTO® and COVID-DUO®, compared to the gold standard, RT-PCR (real-time reverse transcriptase polymerase chain reaction)., Methods: RT-PCR testing of SARS-Cov-2 was performed from nasopharyngeal swab specimens collected in adult patients visiting the infectious disease department at the hospital (Orléans, France). Capillary whole blood (CWB) samples from the fingertip taken at different time points after onset of the disease were tested with POC tests. The specificity and sensitivity of the rapid test kits compared to test of reference (RT-PCR) were calculated., Results: Among 381 patients with symptoms of COVID-19 who went to the hospital for a diagnostic, 143 patients were RT-PCR negative. Results of test with POC tests were all negative for these patients, indicating a specificity of 100% for both POC tests. In the RT-PCR positive subgroup (n = 238), 133 patients were tested with COVID-PRESTO® and 129 patients were tested with COVID-DUO® (24 patients tested with both). The further the onset of symptoms was from the date of collection, the greater the sensitivity. The sensitivity of COVID-PRESTO® test ranged from 10.00% for patients having experienced their 1st symptoms from 0 to 5 days ago to 100% in patients where symptoms had occurred more than 15 days before the date of tests. For COVID-DUO® test, the sensitivity ranged from 35.71% [0-5 days] to 100% (> 15 days)., Conclusion: COVID-PRESTO® and DUO® POC tests turned out to be very specific (none false positive) and to be sensitive enough after 15 days from onset of symptom. These easy to use IgG/IgM combined test kits are the first ones allowing a screening with CWB sample, by typing from a finger prick. These rapid tests are particularly interesting for screening in low resource settings., Competing Interests: The point-of-care tests were provided free of charge by AAZ-LMB. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Until treatment and vaccine for coronavirus disease-2019 (COVID-19) becomes widely available, other methods of reducing infection rates should be explored. This study used a retrospective, observational analysis of deidentified tests performed at a national clinical laboratory to determine if circulating 25-hydroxyvitamin D (25(OH)D) levels are associated with severe acute respiratory disease coronavirus 2 (SARS-CoV-2) positivity rates. Over 190,000 patients from all 50 states with SARS-CoV-2 results performed mid-March through mid-June, 2020 and matching 25(OH)D results from the preceding 12 months were included. Residential zip code data was required to match with US Census data and perform analyses of race/ethnicity proportions and latitude. A total of 191,779 patients were included (median age, 54 years [interquartile range 40.4-64.7]; 68% female. The SARS-CoV-2 positivity rate was 9.3% (95% C.I. 9.2-9.5%) and the mean seasonally adjusted 25(OH)D was 31.7 (SD 11.7). The SARS-CoV-2 positivity rate was higher in the 39,190 patients with "deficient" 25(OH)D values (<20 ng/mL) (12.5%, 95% C.I. 12.2-12.8%) than in the 27,870 patients with "adequate" values (30-34 ng/mL) (8.1%, 95% C.I. 7.8-8.4%) and the 12,321 patients with values ≥55 ng/mL (5.9%, 95% C.I. 5.5-6.4%). The association between 25(OH)D levels and SARS-CoV-2 positivity was best fitted by the weighted second-order polynomial regression, which indicated strong correlation in the total population (R2 = 0.96) and in analyses stratified by all studied demographic factors. The association between lower SARS-CoV-2 positivity rates and higher circulating 25(OH)D levels remained significant in a multivariable logistic model adjusting for all included demographic factors (adjusted odds ratio 0.984 per ng/mL increment, 95% C.I. 0.983-0.986; p<0.001). SARS-CoV-2 positivity is strongly and inversely associated with circulating 25(OH)D levels, a relationship that persists across latitudes, races/ethnicities, both sexes, and age ranges. Our findings provide impetus to explore the role of vitamin D supplementation in reducing the risk for SARS-CoV-2 infection and COVID-19 disease., Competing Interests: HWK, JKN, MHK, and CB are employees of Quest Diagnostics. HWK, MHK and CB own stock in Quest Diagnostics. MFH is a consultant to Quest Diagnostics and was on the speakers’ bureau for Abbott Inc. and Hyatt Pharmaceutical Industries Company PLC.