Background and objective

Exercise is a cornerstone of management for type 2 diabetes; however, little is known about the cardiovascular (CV) response to submaximal functional exercise in people with type 2 diabetes. The aim of this study was to compare performance and CV response during a 6-minute walk test (6MWT) between people with type 2 diabetes and matched control subjects.

Editor’s Note: This article was adapted from the address Dr. Snoek delivered as the recipient of the American Diabetes Association’s Richard R. Rubin Award for 2019. This award recognizes a behavioral researcher who has made outstanding, innovative contributions to the study and understanding of the behavioral aspects of diabetes in diverse populations. Dr. Snoek delivered the address in June 2019 at the Association’s 79th Scientific Sessions in San Francisco, CA.

Editor’s Note: This article is adapted from the address Ms. Valentine delivered as the recipient of the American Diabetes Association’s (ADA’s) Outstanding Educator in Diabetes Award for 2019. She delivered the address in June 2019 at the Association’s 79th Scientific Sessions in San Francisco, CA. A webcast of this speech is available for viewing at the ADA website (professional.diabetes.org/webcast/outstanding-educator-diabetes-award-lecture%E2%80%94-most-important-thing-we-give-people-hope).

A multidisciplinary endocrinologist-led shared medical appointment (SMA) model showed statistically significant reductions in A1C from baseline over 3 years that were not significantly different from appointments with endocrinologists or primary care providers alone within a resource-poor population. Similarly, the SMA model achieved clinical outcomes on par with endocrinologist-only visits with the added benefit of improving endocrine provider productivity and specialty access for patients. Greater patient engagement with the SMA model was associated with significantly lower A1C.

Background

Advances in information communications technology (ICT) provide opportunities for enhanced diabetes care. Knowledge of the more acceptable communication modalities in patients of different ages will help to inform the direction of future innovations.

Background

Diabetes is associated with poor oral health, as well as reduced access to dental care. A large percentage of patients hospitalized in the United States carry a diagnosis of diabetes; however, the oral health status of patients with diabetes who are hospitalized is unknown.

In the context of type 2 diabetes, the definition of therapeutic inertia should include the failure not only to intensify therapy, but also to deintensify treatment when appropriate and should be distinguished from appropriate inaction in cases justified by particular circumstances. Therapy should be intensified when glycemic control deteriorates to prevent long periods of hyperglycemia, which increase the risk of complications. Strategic plans to overcome therapeutic inertia must include actions focused on patients, prescribers, health systems, and payers. Therapeutic inertia affects the management of glycemia, hypertension, and lipid disorders, all of which increase the risk for cardiovascular diseases. Thus, multifactorial interventions that act on additional therapeutic goals beyond glycemia are needed.

Therapeutic inertia is a prevalent problem in people with type 2 diabetes in primary care and affects clinical outcomes. It arises from a complex interplay of patient-, clinician-, and health system–related factors. Ultimately, clinical practice guidelines have not made an impact on improving glycemic targets over the past decade. A more proactive approach, including focusing on optimal combination agents for early glycemic durability, may reduce therapeutic inertia and improve clinical outcomes.

Factors contributing to therapeutic inertia related to patients’ medication experiences include concerns about side effects and out-of-pocket costs, stigmatization for having diabetes, confusion about frequent changes in evidence-based guidelines, low health literacy, and social determinants of health. A variety of solutions to this multifactorial problem may be necessary, including integrating pharmacists into interprofessional care teams, using medication refill synchronization programs, maximizing time with patients to discuss fears and concerns, being cognizant of language used to discuss diabetes-related topics, and avoiding stigmatizing patients. Managing diabetes successfully is a team effort, and the full commitment of all team members (including patients) is required to achieve desired outcomes through an individualized approach.

Despite significant advances in therapies for pediatric type 1 diabetes, achievement of glycemic targets remains elusive, and management remains burdensome for patients and their families. This article identifies common challenges in diabetes management at the patient-provider and health care system levels and proposes practical approaches to overcoming therapeutic inertia to enhance health outcomes for youth with type 1 diabetes.

Diabetes educators can be challenged by therapeutic inertia, as has been documented with other health care providers. There are many contributing factors related to the educators themselves, their patients, and the health care system in which they operate. To address this potentially significant barrier to quality patient care, diabetes educators can adopt numerous strategies to maximize their impact and address the factors contributing to therapeutic inertia in their practices.

Many people with diabetes do not achieve individualized treatment targets. Therapeutic inertia, the underuse of effective therapies in preventing serious clinical end points, is a frequent, important contributor to this failure. Clinicians, patients, health systems, payors, and producers of medications, devices, and other products for those with diabetes all play a role in the development of therapeutic inertia and can all help to reduce it.

Background and objectives

The effects of active case finding (ACF) models that mobilise community networks for early identification and treatment of tuberculosis (TB) remain unknown. We investigated and compared the effect of community-based ACF using a seed-and-recruit model with one-off roving ACF and passive case finding (PCF) on the time to treatment initiation and identification of bacteriologically confirmed TB.

Management of cystic fibrosis has been revolutionised by the introduction of cystic fibrosis transmembrane conductance regulator (CFTR) modulators. These compounds treat the underlying molecular basis of the disease by increasing activity of defective CFTR channels, which improves many clinical parameters and enhances patient quality of life [1]. Next-generation modulators, also known as triple combination therapy, promise to be highly efficacious in up to 90% of patients [2] and will likely dramatically change the landscape of cystic fibrosis disease. Studies examining individuals before and after initiation of CFTR modulators have revealed novel functions of CFTR and shown that CFTR modulators do not reverse all disease manifestations [3–5]. Thus, knowledge of the post-modulator cystic fibrosis disease state is crucial for understanding what continued therapies will be needed for people with cystic fibrosis and what new challenges may arise.

Background

The increasing incidence of life-threatening Pneumocystis pneumonia (PCP) in non-HIV immunocompromised patients is a global concern. Yet, no reports have examined the prognostic significance of pre-existing interstitial lung disease (ILD) in non-HIV PCP.

Chronic cough is a common complaint in the general population but there are no precise data on the incidence of, and prospectively examined risk factors for chronic cough in a population-based setting. Therefore, we investigated the period prevalence, incidence and risk factors for chronic cough in adult subjects.

In a prospective population-based cohort study among subjects aged ≥45 years, data on chronic cough were collected on two separate occasions using a standardised questionnaire. Chronic cough was defined as daily coughing for at least 3 months duration during the preceding 2 years. Potential risk factors were gathered by interview, physical examination and several investigations.

Of the 9824 participants in this study, 1073 (10.9%) subjects had chronic cough at baseline. The prevalence of chronic cough increased with age and peaked in the eighth decade. In subjects aged <70 years, chronic cough was more common in women. During an average follow-up of 6 years, 439 incident cases of chronic cough occurred with an overall incidence rate of 11.6 per 1000 person-years (95% CI 10.6–12.8). In current smokers, the incidence of chronic cough was higher in men. In the multivariable analysis, current smoking, gastro-oesophageal reflux disease (GORD), asthma and COPD were identified as risk factors for chronic cough.

Chronic cough is common among adults and highly prevalent in the older population. Current smoking, GORD, asthma and COPD are independent risk factors for chronic cough. Individuals at risk of developing chronic cough may benefit from smoking cessation and control of the underlying disease.

Objective

We aimed to assess adherence to the Australian national guideline (COPD-X) against audited practice, and to document the outcomes of patients hospitalised with an acute exacerbation of chronic obstructive pulmonary disease (COPD) at discharge and 28 days after.

Inhaled corticosteroid/long-acting β₂-agonist combination therapy is a recommended treatment option for patients with chronic obstructive pulmonary disease (COPD) and increased exacerbation risk, particularly those with elevated blood eosinophil levels. SOPHOS (NCT02727660) evaluated the efficacy and safety of two doses of budesonide/formoterol fumarate dihydrate metered dose inhaler (BFF MDI) versus formoterol fumarate dihydrate (FF) MDI, each delivered using co-suspension delivery technology, in patients with moderate-to-very severe COPD and a history of exacerbations.

In this phase 3, randomised, double-blind, parallel-group, 12–52-week, variable length study, patients received twice-daily BFF MDI 320/10 µg or 160/10 µg, or FF MDI 10 µg. The primary endpoint was change from baseline in morning pre-dose trough forced expiratory volume in 1 s (FEV₁) at week 12. Secondary and other endpoints included assessments of moderate/severe COPD exacerbations and safety.

The primary analysis (modified intent-to-treat) population included 1843 patients (BFF MDI 320/10 µg, n=619; BFF MDI 160/10 µg, n=617; and FF MDI, n=607). BFF MDI 320/10 µg and 160/10 µg improved morning pre-dose trough FEV₁ at week 12 versus FF MDI (least squares mean differences 34 mL [p=0.0081] and 32 mL [p=0.0134], respectively), increased time to first exacerbation (hazard ratios 0.827 [p=0.0441] and 0.803 [p=0.0198], respectively) and reduced exacerbation rate (rate ratios 0.67 [p=0.0001] and 0.71 [p=0.0010], respectively). Lung function and exacerbation benefits were driven by patients with blood eosinophil counts ≥150 cells·mm^–3. The incidence of adverse events was similar, and pneumonia rates were low (≤2.4%) across treatments.

SOPHOS demonstrated the efficacy and tolerability of BFF MDI 320/10 µg and 160/10 µg in patients with moderate-to-very severe COPD at increased risk of exacerbations.

Background

COPD patients account for a large proportion of lung transplants; lung transplantation survival benefit for COPD patients is not well established.

Introduction

Immunotherapy has become the standard of care in advanced non-small cell lung cancer (NSCLC). We aimed to quantify the economic impact, in France, of anti-PD-1 therapy for NSCLC.

Background

We aimed to investigate the epidemiological and clinical features, and medical care-seeking process of patients with the 2019 coronavirus disease (COVID-19) in Wuhan, China, to provide useful information to contain COVID-19 in other places with similar outbreaks of the virus.

Background

Positive serology for cytomegalovirus (CMV) has been associated with all-cause mortality risk but its role in COPD mortality is unknown. The objective of the present study was to assess the relationship between CMV serology and COPD mortality.

Electronic cigarettes (e-cigarettes) have been used in many countries for >10 years and in this time, there has been a division of opinions amongst both the general public and health professionals regarding the benefit or harms of e-cigarettes. Prior to the reporting of a new phenomenon known as vaping-associated pulmonary injury (VAPI), public opinion about the relative harm of e-cigarettes were increasing but they were perceived as less harmful than cigarettes by one third of people [1]. The recent cases of severe illness and death attributable to VAPI were first described in September 2019 [2]. VAPI appears to be related to either the addition of cannabis/cannabis derivates or vitamin E acetate [3], and as such has not caused radical swing away from the use of e-cigarettes without cannabis or cannabis derivates.

Eligibility criteria for a biologic treatment for severe asthma include poor disease control despite a full medication plan according to Global Initiative for Asthma steps 4–5 [1]. Adherence to inhaled therapy should be verified as part of that prescription requirement [2]. In fact, it has been demonstrated that poor adherence is a major cause of uncontrolled asthma, regardless of its severity [3]. Furthermore, biologics do not exert a disease-modifying effect [4]; in contrast to allergen immunotherapy, which is able to permanently modulate the way the immune system reacts to allergens beyond the immunotherapy treatment course [5], biologic therapy withdrawal usually leads to asthma relapse [4]. Thus, a low adherence rate to inhaled treatment in patients undergoing biologic therapy raises some issues related to sustainability.

ABSTRACT

Academics in non-tenure-track positions encounter a unique set of challenges on the road toward tenure. Institutionalized policies and lack of mentors are additional burdens for foreign scientists, resulting in representation differences. Becoming a scientist has been a personal and moving journey in which my multiple selves intersect and clash every now and again. My identity as a scientist is a life project and has intersected with my other identities: a young Latina immigrant in Western Europe. This crossroad has molded, and at times, challenged my participation in science.

ABSTRACT

Interspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species. Candida orthopsilosis is an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight into the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ~4% of the genes studied. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ~9.5% of the heterozygous genes in the hybrids. This effect was larger in the hybrid with more extensive loss of heterozygosity, which may indicate a tendency to avoid loss of heterozygosity in these genes. Consistently, the number of shared genes with allele-specific expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. Some of the imbalanced genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence in C. orthopsilosis hybrids.

IMPORTANCE How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence.

ABSTRACT

Bezlotoxumab is a human monoclonal antibody against Clostridium difficile toxin B, indicated to prevent recurrence of C. difficile infection (rCDI) in high-risk adults receiving antibacterial treatment for CDI. An exploratory genome-wide association study investigated whether human genetic variation influences bezlotoxumab response. DNA from 704 participants who achieved initial clinical cure in the phase 3 MODIFY I/II trials was genotyped. Single nucleotide polymorphisms (SNPs) and human leukocyte antigen (HLA) imputation were performed using IMPUTE2 and HIBAG, respectively. A joint test of genotype and genotype-by-treatment interaction in a logistic regression model was used to screen genetic variants associated with response to bezlotoxumab. The SNP rs2516513 and the HLA alleles HLA-DRB1*07:01 and HLA-DQA1*02:01, located in the extended major histocompatibility complex on chromosome 6, were associated with the reduction of rCDI in bezlotoxumab-treated participants. Carriage of a minor allele (homozygous or heterozygous) at any of the identified loci was related to a larger difference in the proportion of participants experiencing rCDI versus placebo; the effect was most prominent in the subgroup at high baseline risk for rCDI. Genotypes associated with an improved bezlotoxumab response showed no association with rCDI in the placebo cohort. These data suggest that a host-driven, immunological mechanism may impact bezlotoxumab response. Trial registration numbers are as follows: NCT01241552 (MODIFY I) and NCT01513239 (MODIFY II).

IMPORTANCE Clostridium difficile infection is associated with significant clinical morbidity and mortality; antibacterial treatments are effective, but recurrence of C. difficile infection is common. In this genome-wide association study, we explored whether host genetic variability affected treatment responses to bezlotoxumab, a human monoclonal antibody that binds C. difficile toxin B and is indicated for the prevention of recurrent C. difficile infection. Using data from the MODIFY I/II phase 3 clinical trials, we identified three genetic variants associated with reduced rates of C. difficile infection recurrence in bezlotoxumab-treated participants. The effects were most pronounced in participants at high risk of C. difficile infection recurrence. All three variants are located in the extended major histocompatibility complex on chromosome 6, suggesting the involvement of a host-driven immunological mechanism in the prevention of C. difficile infection recurrence.

ABSTRACT

The prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine whether the fetal and placental tissues of rhesus macaques harbor bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor (~130/166 days gestation). The presence of bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profiles of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony of Cutibacterium acnes. This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profiles of fetal and placental tissues did not exceed or differ from those of background technical controls. By contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of bacterial communities in the fetal and placental tissues of rhesus macaques.

IMPORTANCE Microbial invasion of the amniotic cavity (i.e., intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low-biomass microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g., microbial load and community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of the in utero colonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e., culture, quantitative real-time PCR [qPCR], and DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placental and fetal tissues of rhesus macaques.

ABSTRACT

Members of family Coronaviridae cause a variety of diseases in birds and mammals. Porcine hemagglutinating encephalomyelitis virus (PHEV), a lesser-researched coronavirus, can infect naive pigs of any age, but clinical disease is observed in pigs ≤4 weeks of age. No commercial PHEV vaccines are available, and neonatal protection from PHEV-associated disease is presumably dependent on lactogenic immunity. Although subclinical PHEV infections are thought to be common, PHEV ecology in commercial swine herds is unknown. To begin to address this gap in knowledge, a serum IgG antibody enzyme-linked immunosorbent assay (ELISA) based on the S1 protein was developed and evaluated on known-status samples and then used to estimate PHEV seroprevalence in U.S. sow herds. Assessment of the diagnostic performance of the PHEV S1 ELISA using serum samples (n = 924) collected from 7-week-old pigs (n = 84; 12 pigs per group) inoculated with PHEV, porcine epidemic diarrhea virus, transmissible gastroenteritis virus, porcine respiratory coronavirus, or porcine deltacoronavirus showed that a sample-to-positive cutoff value of ≥0.6 was both sensitive and specific, i.e., all PHEV-inoculated pigs were seropositive from days postinoculation 10 to 42, and no cross-reactivity was observed in samples from other groups. The PHEV S1 ELISA was then used to estimate PHEV seroprevalence in U.S. sow herds (19 states) using 2,756 serum samples from breeding females (>28 weeks old) on commercial farms (n = 104) with no history of PHEV-associated disease. The overall seroprevalence was 53.35% (confidence interval [CI], ±1.86%) and herd seroprevalence was 96.15% (CI, ±3.70%).

IMPORTANCE There is a paucity of information concerning the ecology of porcine hemagglutinating encephalomyelitis virus (PHEV) in commercial swine herds. This study provided evidence that PHEV infection is endemic and highly prevalent in U.S. swine herds. These results raised questions for future studies regarding the impact of endemic PHEV on swine health and the mechanisms by which this virus circulates in endemically infected populations. Regardless, the availability of the validated PHEV S1 enzyme-linked immunosorbent assay (ELISA) provides the means for swine producers to detect and monitor PHEV infections, confirm prior exposure to the virus, and to evaluate the immune status of breeding herds.

ABSTRACT

Aspergillus flavus, a ubiquitous and saprophytic fungus, is the second most common cause of aspergillosis worldwide. Several mechanisms contribute to the establishment of the fungal infection. Extracellular vesicles (EVs) have been described as "virulence factor delivery bags" in several fungal species, demonstrating a crucial role during the infection. In this study, we evaluated production of A. flavus EVs and their immunomodulatory functions. We verified that A. flavus EVs induce macrophages to produce inflammatory mediators, such as nitric oxide, tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), and IL-1β. Furthermore, the A. flavus EVs enhance phagocytosis and killing by macrophages and induce M1 macrophage polarization in vitro. In addition, a prior inoculation of A. flavus EVs in Galleria mellonella larvae resulted in a protective effect against the fungal infection. Our findings suggest that A. flavus EVs are biologically active and affect the interaction between A. flavus and host immune cells, priming the innate immune system to eliminate the fungal infection. Collectively, our results suggest that A. flavus EVs play a crucial role in aspergillosis.

IMPORTANCE Immunocompromised patients are susceptible to several fungal infections. The genus Aspergillus can cause increased morbidity and mortality. Developing new therapies is essential to understand the fungal biology mechanisms. Fungal EVs carry important virulence factors, thus playing pivotal roles in fungal pathophysiology. No study to date has reported EV production by Aspergillus flavus, a fungus considered to be the second most common cause of aspergillosis and relevant food contaminator found worldwide. In this study, we produced A. flavus EVs and evaluated the in vitro immunomodulatory effects of EVs on bone marrow-derived macrophages (BMDMs) and in vivo effects in a Galleria mellonella model.

ABSTRACT

The chemical structures of soluble fiber carbohydrates vary from source to source due to numerous possible linkage configurations among monomers. However, it has not been elucidated whether subtle structural variations might impact soluble fiber fermentation by colonic microbiota. In this study, we tested the hypothesis that subtle structural variations in a soluble polysaccharide govern the community structure and metabolic output of fermenting microbiota. We performed in vitro fecal fermentation studies using arabinoxylans (AXs) from different classes of wheat (hard red spring [AX_HRS], hard red winter [AX_HRW], and spring red winter [AX_SRW]) with identical initial microbiota. Carbohydrate analyses revealed that AX_SRW was characterized by a significantly shorter backbone and increased branching compared with those of the hard varieties. Amplicon sequencing demonstrated that fermentation of AX_SRW resulted in a distinct community structure of significantly higher richness and evenness than those of hard-AX-fermenting cultures. AX_SRW favored OTUs within Bacteroides, whereas AX_HRW and AX_HRS favored Prevotella. Accordingly, metabolic output varied between hard and soft varieties; higher propionate production was observed with AX_SRW and higher butyrate and acetate with AX_HRW and AX_HRS. This study showed that subtle changes in the structure of a dietary fiber may strongly influence the composition and function of colonic microbiota, further suggesting that physiological functions of dietary fibers are highly structure dependent. Thus, studies focusing on interactions among dietary fiber, gut microbiota, and health outcomes should better characterize the structures of the carbohydrates employed.

IMPORTANCE Diet, especially with respect to consumption of dietary fibers, is well recognized as one of the most important factors shaping the colonic microbiota composition. Accordingly, many studies have been conducted to explore dietary fiber types that could predictably manipulate the colonic microbiota for improved health. However, the majority of these studies underappreciate the vastness of fiber structures in terms of their microbial utilization and omit detailed carbohydrate structural analysis. In some cases, this causes conflicting results to arise between studies using (theoretically) the same fibers. In this investigation, by performing in vitro fecal fermentation studies using bran arabinoxylans obtained from different classes of wheat, we showed that even subtle changes in the structure of a dietary fiber result in divergent microbial communities and metabolic outputs. This underscores the need for much higher structural resolution in studies investigating interactions of dietary fibers with gut microbiota, both in vitro and in vivo.

ABSTRACT

In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic data set can be readily queried using web-based tools, meta-searches through all such data sets are less accessible. In this brief communication, we demonstrate such a meta-metagenomic approach, examining close matches to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in all high-throughput sequencing data sets in the NCBI Sequence Read Archive accessible with the "virome" keyword. In addition to the homology to bat coronaviruses observed in descriptions of the SARS-CoV-2 sequence (F. Wu, S. Zhao, B. Yu, Y. M. Chen, et al., Nature 579:265–269, 2020, https://doi.org/10.1038/s41586-020-2008-3; P. Zhou, X. L. Yang, X. G. Wang, B. Hu, et al., Nature 579:270–273, 2020, https://doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in metavirome data sets generated from the lungs of deceased pangolins reported by Liu et al. (P. Liu, W. Chen, and J. P. Chen, Viruses 11:979, 2019, https://doi.org/10.3390/v11110979). While analysis of these reads indicates the presence of a similar viral sequence in pangolin lung, the similarity is not sufficient to either confirm or rule out a role for pangolins as an intermediate host in the recent emergence of SARS-CoV-2. In addition to the implications for SARS-CoV-2 emergence, this study illustrates the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences.

IMPORTANCE Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.

Molar element ratio analysis of element concentrations consists of four basic tools that provide substantial insight into the lithogeochemistry (and mineralogy) of rocks under examination. These tools consist of: (1) conserved element ratio analysis; (2) Pearce element ratio analysis; (3) general element ratio analysis; and (4) lithogeochemical mineral mode analysis. Conserved element ratio analysis is useful in creating a chemostratigraphic model for the host rocks to mineral deposits, whereas Pearce element ratio analysis and general element ratio analysis are primarily used to identify mineralogical and metasomatic controls on rock compositions and to investigate and quantify the extent of the material transfers that formed the host rocks and mineralization. Lithogeochemical mineral mode analysis converts element concentrations into mineral concentrations using a matrix-based change-of-basis operation, allowing lithogeochemical data to be interpreted in terms of mineral modes. It can be used to provide proper names to rocks, an important activity for an exploration geologist because of the implications that rock names have on genetic processes and mineral deposit models.

This paper provides a review of the theoretical foundations of each of these four tools and then illustrates how these techniques have been used in a variety of exploration applications to assist in the search for, evaluation and planning of, and the mining of mineral deposits. Examples include the evaluation of total digestion lithogeochemical datasets from mineral deposits hosted by igneous and sedimentary rocks and formed by hydrothermal and igneous processes. In addition, this paper illustrates a more recent geometallurgical application of these methods, whereby the mineral proportions determined by lithogeochemical mineral mode analysis are used to predict rock properties and obtain the ore body knowledge critical for resource evaluation, mine planning, mining and mine remediation.

Thematic collection: This article is part of the Exploration 17 collection available at: https://www.lyellcollection.org/cc/exploration-17

Multi-element geochemical surveys of rocks, soils, stream/lake/floodplain sediments and regolith are typically carried out at continental, regional and local scales. The chemistry of these materials is defined by their primary mineral assemblages and their subsequent modification by comminution and weathering. Modern geochemical datasets represent a multi-dimensional geochemical space that can be studied using multivariate statistical methods from which patterns reflecting geochemical/geological processes are described (process discovery). These patterns form the basis from which probabilistic predictive maps are created (process validation). Processing geochemical survey data requires a systematic approach to effectively interpret the multi-dimensional data in a meaningful way. Problems that are typically associated with geochemical data include closure, missing values, censoring, merging, levelling different datasets and adequate spatial sample design. Recent developments in advanced multivariate analytics, geospatial analysis and mapping provide an effective framework to analyse and interpret geochemical datasets. Geochemical and geological processes can often be recognized through the use of data discovery procedures such as the application of principal component analysis. Classification and predictive procedures can be used to confirm lithological variability, alteration and mineralization. Geochemical survey data of lake/till sediments from Canada and of floodplain sediments from Australia show that predictive maps of bedrock and regolith processes can be generated. Upscaling a multivariate statistics-based prospectivity analysis for arc-related Cu–Au mineralization from a regional survey in the southern Thomson Orogen in Australia to the continental scale, reveals a number of regions with a similar (or stronger) multivariate response and hence potentially similar (or higher) mineral potential throughout Australia.

Thematic collection: This article is part of the Exploration 17 collection available at: https://www.lyellcollection.org/cc/exploration-17

This paper focuses on handheld and top-of-hole techniques which have appeared since 2007 or have undergone major improvements, and discusses their benefits, challenges and pitfalls, why we use them and what to expect from them. There is an ongoing need to be innovative with the way we undertake mineral exploration. Recent technological advances that have been applied to successful mineral exploration include on-site or portable instruments, on-site laboratory technologies, various core scanners, and technologies for fluid analysis. Portable or field technologies such as pXRF, pXRD, pNIR-SWIR, µRaman and LIBS aid in obtaining chemical and mineralogical information. Spectral gamma tools, a well-known technology, recently took advantage of improved ground and airborne (drone) instruments, to complement hyperspectral imagery. At mine and exploration sites, top-of-hole sensing technologies, such as Lab-at-Rig® and various core scanners (both spectral- and XRF-based) have become useful tools to analyse metres of core as it is being drilled. Fluid analyses are not as common as analyses of solid materials, but there are advances in such technologies as anodic stripping voltammetry, polarography and ion-exchange electrodes aiming for analysis of commodity or environmentally important elements.

Field-portable geochemical techniques and on-site technologies now offer instant response and flexibility for most exploration tasks. By providing relevant data within minutes, they allow safer field decisions and focus on the most promising finds, while saving valuable resources in sampling grids or drilling. More efficient laboratory analysis programs are supported by sample screening and homogeneity checking on-site. Field analyses are not always as accurate as laboratory ones, but most of the time can be correlated with them, enabling reliable decisions. The level of confidence in field-made decisions needs to be compared between later and less numerous laboratory analyses, and less precise but more abundant and immediate field analyses. It may be demonstrated that, in many cases, the fit–for-purpose nature of the latter allows a better confidence level. Quality compromises associated with field analyses can be reduced by the application of better sample preparation and quality assurance/quality control (QA/QC) procedures. Most of the further development of on-site chemical analysis is expected to be based on its integration with lab methods and on sound QA/QC practice, allowing a precise evaluation of its confidence level and uncertainties. Mineralogical analyses are constrained by our ability to interpret the data in near-real time but offer promising approaches in both surface and drilling exploration campaigns.

Thematic collection: This article is part of the Exploration 17 collection available at: https://www.lyellcollection.org/cc/exploration-17

Among the emerging techniques to detect the real footprint of buried ore deposits is isotope tracing. Novel and automated preparation systems such as continuous flow isotope ratio mass spectrometry, off-axis integrated cavity output spectroscopy for isotopic compositions of selected molecules, multi-collector inductively coupled-plasma mass spectrometry (ICP-MS), triple quadrupole ICP-MS, laser ablation ICP-MS, and a multitude of inline preparation systems have facilitated the use of isotopes as tracers in mineral exploration, as costs for isotope analyses have decreased and the time required for the analyses has improved. In addition, the isotope systems being used have expanded beyond the traditional light stable and Pb isotopes to include a multitude of elements that behave differently during processes that promote the mobilization of elements during both primary and secondary dispersion. Isotopes are also being used to understand barren areas that lack a critical process to form an ore deposit and to reveal precise redox mechanisms. The goal is to be able to use isotopes to reflect a definitive process that occurs in association with the deposit and not in barren systems, and then to relate these to something that is easier to measure, namely elemental concentrations. As new generations of exploration and environmental scientists are becoming more comfortable with the application of isotopes to effectively trace processes involved in geoscience, and new technologies for rapid and inexpensive analyses of isotopes are continually being developed, novel applications of isotope tracing are becoming more mainstream.

Thematic collection: This article is part of the Exploration 17 collection available at: https://www.lyellcollection.org/cc/exploration-17

There is a pressing need for new exploration tools to target and vector towards mineralization in covered terrains. Groundwater provides a valuable and under-utilized geochemical sampling medium, and represents an important and cost-effective tool to expose covered terrains to systematic exploration. For Au exploration, researchers agree the best hydrogeochemistry pathfinder is dissolved Au itself, with additional potential from other pathfinders (albeit non-unique) such as As, Ag, W and Mo. Despite Au's relatively low solubility, with rigorous field protocols and appropriate analytical methods, explorers can respond to dissolved Au directly with robust parts per trillion (ppt)-level analyses.

Even with ppt-level analyses, a practical implication of Au's low solubility is that a deposit's dissolved Au signature is generally weaker than seen in other more mobile pathfinders, producing a smaller detectable footprint, which must be considered when designing exploration programmes. Using purpose-drilled groundwater sampling bores, explorers can collect groundwater samples at the density required to respond to dissolved Au where existing borehole coverage is otherwise insufficient. In addition to its use at the regional scale, with even tighter sample density, hydrogeochemistry also shows promise at the project scale, allowing the 3D modelling of pathfinder dispersion.

For hydrogeochemistry to be widely adopted for Au exploration, explorers need confidence in ppt-level dissolved Au analyses, and the context to understand their significance. This paper aims to address these topics and provide a straightforward starting point for Au explorers interested in applying hydrogeochemistry by: (i) summarizing examples of regional sampling programmes and more focused case studies to illustrate how covered Au deposits create measurable dissolved Au footprints distinguishable from background; and (ii) sharing examples of dissolved Au analyses that are being integrated into exploration at the regional and project scales.

As seen in the results, the distributions of dissolved Au in the regional- and project-scale programmes show remarkably similar and easy to interpret high-contrast, low-frequency anomalies against relatively low backgrounds. These are desirable attributes of any geochemical pathfinder. When combined with the benefits of hydrogeochemistry v. other geochemical exploration tools (e.g. groundwater can create larger footprints requiring fewer samples to detect, and groundwater can recharge from depth to reflect deeper mineralization), dissolved Au is a powerful pathfinder ideally suited for Au exploration in covered terrains.

While this paper focuses on the use of dissolved Au, additional pathfinders can provide valuable information, including indications of lithological changes, hydrothermal alteration and different styles of mineralization, as well as opportunities to use secondary pathfinders when sample density or local conditions may not result in detectable dissolved Au signatures.

Thematic collection: This article is part of the Exploration 17 collection available at: https://www.lyellcollection.org/cc/exploration-17

In the past decade, significant research efforts have been devoted to mineral chemistry studies to assist porphyry exploration. These activities can be divided into two major fields of research: (1) porphyry indicator minerals (PIMs), which are used to identify the presence of, or potential for, porphyry-style mineralization based on the chemistry of magmatic minerals such as zircon, plagioclase and apatite, or resistate hydrothermal minerals such as magnetite; and (2) porphyry vectoring and fertility tools (PVFTs), which use the chemical compositions of hydrothermal minerals such as epidote, chlorite and alunite to predict the likely direction and distance to mineralized centres, and the potential metal endowment of a mineral district. This new generation of exploration tools has been enabled by advances in and increased access to laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), short-wave length infrared (SWIR), visible near-infrared (VNIR) and hyperspectral technologies. PIMs and PVFTs show considerable promise for exploration and are starting to be applied to the diversity of environments that host porphyry and epithermal deposits globally. Industry has consistently supported development of these tools, and in the case of PVFTs encouraged by several successful blind tests where deposit centres have successfully been predicted from distal propylitic settings. Industry adoption is steadily increasing but is restrained by a lack of the necessary analytical equipment and expertise in commercial laboratories, and also by the ongoing reliance on well-established geochemical exploration techniques (e.g. sediment, soil and rock chip sampling) that have aided the discovery of near-surface resources over many decades, but are now proving less effective in the search for deeply buried mineral resources and for those concealed under cover.

Thematic collection: This article is part of the Exploration 17 collection available at: https://www.lyellcollection.org/cc/exploration-17

There have been several advances in inductively coupled plasma-mass spectrometer (ICP-MS) analytical technologies in the last decade. Collision/reaction cell ICP-MS and triple quadrupole ICP-MS techniques can produce lower detection limits for select elements that experience interferences with a standard quadrupole (e.g. Se and As). Triple quadrupole ICP-MS, in particular, can eliminate virtually all polyatomic or isobaric interferences for highly accurate measurements of some element isotopes systematics that are of great interest in mineral exploration, namely Pb/Pb. Laser ablation ICP-MS has become more popular as an effective analytical tool to measure mineral grain trace elements, which could assist in vectoring to mineralization or exploration drill targets. The ablation of a spot on a Li-borate fused glass disk paired with XRF analysis has also gained popularity as an alternative to total whole rock characterization packages that employ several separate digestions and analytical methods. While there have been several advancements in ICP-MS technologies in exploration geochemistry, they have not been widely accepted or implemented. This slow adaptation could be due to the extended recession in the mining industry between 2012 and 2017. It is also possible that standard ICP-MS data (i.e. no collision/reaction cell) is still fit for purpose. This stands in stark contrast to implementation of ICP-MS in the previous decade (1997–2007), which was transformational for the industry.

Consideration of all elements from large multi-element ICP-MS analytical suites for mineral exploration can be an extremely powerful tool in the exploration toolkit. The discovery of the White Gold District, Yukon, is a prime example of how the utilization of soil geochemical data, when plotted spatially, can vector to gold mineralization. The presence of Au + As + Sb soil anomalies were key to delineating mineralization, especially when accompanied by publicly available geological, geographical and geophysical data. Additionally, elements and element ratios not typically considered in Au exploration, including Ni and U, were utilized to determine the lithological and structural controls on mineralization. The availability of multi-element ICP-MS data was also useful in the discovery of the Cascadero Copper Taron Caesium deposit. Ore-grade Cs was discovered only because Cs was included in the multi-element ICP-MS exploration geochemistry suite. Before the availability of ICP-MS, it is unlikely that this deposit would have been discovered.

Thematic collection: This article is part of the Exploration 17 collection available at: https://www.lyellcollection.org/cc/exploration-17

Mineral exploration under relatively young, exotic cover still presents a major challenge to discovery. Advances and future developments can be categorized in four key areas, (1) understanding metal mobility and mechanisms, (2) rapid geochemical analyses, (3) data access, integration and interoperability and (4) innovation in laboratory-based methods.

Application of ‘regolith-style' surface mapping in covered terrains outside of conventional lateritic terrains is achieving success in terms of reducing background noise and improving geochemical contrasts. However, process models for anomaly generation are still uncertain and require further research. The interaction between the surface environment, microbes, hydrocarbons and chemistry is receiving greater attention. While significant progress has been achieved in understanding the role of vegetation, interaction with the water table and cycling of metals in the near surface environment in Australia, other regions of the world, for example, the till-covered terrains in the northern hemisphere and arid colluvium-covered areas of South America, have seen less progress. In addition to vegetation, the influence of bacteria, fungi and invertebrates is not as well studied with respect to metal mobilization in cover. Field portable XRF has become a standard field technique, though more often used in a camp setting. Apart from a tweaking of analytical quality, instruments have probably reached their peak of analytical development with add-ons, such as cameras, beam-limiters, wireless transmission and GPS as the main differences between instrument suppliers. Their future rests in automated application in unconventional configurations, for example, core scanning and better integration of analytical data with other information such as spectral analyses. Pattern drilling that persists in industry, however, has benefited from innovative application of field-portable tools along with rock and mineral chemistry to provide near real-time results and assist in a shift toward more flexible and targeted drilling in greenfields settings.

Innovation in the laboratory continues to progress. More selective geochemical analysis, imaging of fine particle size fractions and resistate mineral phases and isotope analysis are faster and more accessible than ever before. The application of genomics (and data analysis) as mineral exploration tools is on the horizon. A continuing problem in geoscience, the supply to industry of suitably trained geochemists, persists although some needs, particularly at junior level, will be met by recent initiatives at various universities at graduate level. Unfortunately, the current economic climate has had a significant impact on R&D and retention of geochemistry skills by the industry. Whilst the future is positive, significant investment is required to develop the next generation of geochemical exploration tools and concepts.

Thematic collection: This article is part of the Exploration 17 collection available at: https://www.lyellcollection.org/cc/exploration-17

Thematic collection: This article is part of the Exploration 17 collection available at: https://www.lyellcollection.org/cc/exploration-17