Clinical Performance of Cas13a-based Point-of-Care Lateral Flow Assay for Detecting Neisseria gonorrhoeae

Background

Diagnosis of Neisseria (N.) gonorrhoeae is dependent on nucleic acid amplification testing (NAAT), which is not available in resource-limited settings where the prevalence of infection is highest. Recent advances in molecular diagnostics leveraging the high specificity of CRISPR enzymes can permit field-deployable, point-of-care lateral flow assays. We previously reported on the development and in vitro performance of a lateral flow assay for detecting N. gonorrhoeae. Here we aimed to pair that assay with point-of-care DNA extraction techniques and assess the performance on clinical urine specimens.

Methods

We collected an additional urine specimen among individuals enrolling in an ongoing clinical trial at the Massachusetts General Hospital Sexual Health Clinic who presented with symptoms of urethritis or cervicitis (urethral or vaginal discharge, dysuria, or dyspareunia). We then assessed thermal, detergent, and combination DNA extraction conditions, varying the duration of heat at 95°C and concentration of Triton X. We assessed the efficacy of the various DNA extraction methods by quantitative polymerase chain reaction (qPCR). Once an extraction method was selected, we incubated samples for 90 minutes to permit isothermal recombinase polymerase amplification. We then assessed the performance of lateral flow Cas13a-based detection using our previously designed porA probe and primer system for N. gonorrhoeae detection, comparing lateral flow results with NAAT results from clinical care.

Results

We assessed DNA extraction conditions on 3 clinical urine specimens. There was no consistent significant difference in copies per microliter of DNA obtained using more or less heat. On average, we noted that 0.02% triton combined with 5 minutes of heating to 95°C resulted in the highest DNA yield, however, 0.02% triton alone resulted in a quantity of DNA that was above the previously determined analytic sensitivity of the assay. Given that detergent-based extraction is more easily deployable, we selected that as our method for extraction. We treated 23 clinical specimens with 0.02% triton, which we added to the Cas13a detection system. We ran all lateral flow detections in duplicate. The Cas13a-based assay detected 8 of 8 (100%) positive specimens, and 0 of 15 negative specimens.

Conclusion

Using point-of-care DNA extraction, isothermal amplification, and Cas13a-based detection, our point-of-care lateral flow N. gonorrhoeae assay correctly identified 23 clinical urine specimens as either positive or negative. Further evaluation of this assay among larger samples and more diverse sample types is warranted.

Development of Cas13a-based assays for Neisseria gonorrhoeae detection and gyrase A determination

Neisseria gonorrhoeae is one of the most common bacterial sexually transmitted infections. The emergence of antimicrobial-resistant N. gonorrhoeae is an urgent public health threat. Currently, the diagnosis of N. gonorrhoeae infection requires expensive laboratory infrastructure, while antimicrobial susceptibility determination requires bacterial culture, both of which are infeasible in low-resource areas where the prevalence of infection is highest. Recent advances in molecular diagnostics, such as specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) using CRISPR-Cas13a and isothermal amplification, have the potential to provide low-cost detection of pathogen and antimicrobial resistance. We designed and optimized RNA guides and primer sets for SHERLOCK assays capable of detecting N. gonorrhoeae via the porA gene and of predicting ciprofloxacin susceptibility via a single mutation in the gyrase A (gyrA) gene. We evaluated their performance using both synthetic DNA and purified N. gonorrhoeae isolates. For porA, we created both a fluorescence-based assay and lateral flow assay using a biotinylated fluorescein reporter. Both methods demonstrated sensitive detection of 14 N. gonorrhoeae isolates and no cross-reactivity with 3 non-gonococcal Neisseria isolates. For gyrA, we created a fluorescence-based assay that correctly distinguished between 20 purified N. gonorrhoeae isolates with phenotypic ciprofloxacin resistance and 3 with phenotypic susceptibility. We confirmed the gyrA genotype predictions from the fluorescence-based assay with DNA sequencing, which showed 100% concordance for the isolates studied. We report the development of Cas13a-based SHERLOCK assays that detect N. gonorrhoeae and differentiate ciprofloxacin-resistant isolates from ciprofloxacin-susceptible isolates. IMPORTANCE Neisseria gonorrhoeae, the cause of gonorrhea, disproportionately affects resource-limited settings. Such areas, however, lack the technical capabilities for diagnosing the infection. The consequences of poor or absent diagnostics include increased disease morbidity, which, for gonorrhea, includes an increased risk for HIV infection, infertility, and neonatal blindness, as well as an overuse of antibiotics that contributes to the emergence of antibiotic resistance. We used a novel CRISPR-based technology to develop a rapid test that does not require laboratory infrastructure for both diagnosing gonorrhea and predicting whether ciprofloxacin can be used in its treatment, a one-time oral pill. With further development, that diagnostic test may be of use in low-resource settings.

Chemoradiotherapy versus radiotherapy in patients with advanced nasopharyngeal cancer: phase III randomized Intergroup study 0099

PURPOSE

The Southwest Oncology Group (SWOG) coordinated an Intergroup study with the participation of Radiation Therapy Oncology Group (RTOG), and Eastern Cooperative Oncology Group (ECOG). This randomized phase III trial compared chemoradiotherapy versus radiotherapy alone in patients with nasopharyngeal cancers.

MATERIALS AND METHODS

Radiotherapy was administered in both arms: 1.8- to 2.0-Gy/d fractions Monday to Friday for 35 to 39 fractions for a total dose of 70 Gy. The investigational arm received chemotherapy with cisplatin 100 mg/m2 on days 1, 22, and 43 during radiotherapy; postradiotherapy, chemotherapy with cisplatin 80 mg/m2 on day 1 and fluorouracil 1,000 mg/m2/d on days 1 to 4 was administered every 4 weeks for three courses. Patients were stratified by tumor stage, nodal stage, performance status, and histology.

RESULTS

Of 193 patients registered, 147 (69 radiotherapy and 78 chemoradiotherapy) were eligible for primary analysis for survival and toxicity. The median progression-free survival (PFS) time was 15 months for eligible patients on the radiotherapy arm and was not reached for the chemo-radiotherapy group. The 3-year PFS rate was 24% versus 69%, respectively (P < .001). The median survival time was 34 months for the radiotherapy group and not reached for the chemo-radiotherapy group, and the 3-year survival rate was 47% versus 78%, respectively (P = .005). One hundred eighty-five patients were included in a secondary analysis for survival. The 3-year survival rate for patients randomized to radiotherapy was 46%, and for the chemoradiotherapy group was 76% (P < .001).

CONCLUSION

We conclude that chemoradiotherapy is superior to radiotherapy alone for patients with advanced nasopharyngeal cancers with respect to PFS and overall survival.

Development of Cas13a-based Assays for Neisseria gonorrhoeae Detection and Gyrase A Determination

Background

Neisseria gonorrhoeae is one of the most common bacterial sexually transmitted infections. The emergence of antimicrobial-resistant N. gonorrhoeae is an urgent public health threat. Currently, diagnosis of N. gonorrhoeae infection requires expensive laboratory infrastructure, while antimicrobial susceptibility determination requires bacterial culture, both of which are infeasible in low-resource areas where prevalence is highest. Recent advances in molecular diagnostics, such as Specific High-sensitivity Enzymatic Reporter unLOCKing (SHERLOCK) using CRISPR-Cas13a and isothermal amplification, have the potential to provide low-cost detection of pathogen and antimicrobial resistance.

Methods and Results

We designed and optimized RNA guides and primer-sets for SHERLOCK assays capable of detecting N. gonorrhoeae via the por A gene and of predicting ciprofloxacin susceptibility via a single mutation in the gyrase A ( gyr A) gene. We evaluated their performance using both synthetic DNA and purified N. gonorrhoeae isolates. For por A, we created both a fluorescence-based assay and lateral flow assay using a biotinylated FAM reporter. Both methods demonstrated sensitive detection of 14 N. gonorrhoeae isolates and no cross-reactivity with 3 non-gonococcal Neisseria isolates. For gyr A, we created a fluorescence-based assay that correctly distinguished between 20 purified N. gonorrhoeae isolates with phenotypic ciprofloxacin resistance and 3 with phenotypic susceptibility. We confirmed the gyr A genotype predictions from the fluorescence-based assay with DNA sequencing, which showed 100% concordance for the isolates studied.

Conclusion

We report the development of Cas13a-based SHERLOCK assays that detect N. gonorrhoeae and differentiate ciprofloxacin-resistant isolates from ciprofloxacin-susceptible isolates.

The 2022 RSV surge was driven by multiple viral lineages

The US experienced an early and severe respiratory syncytial virus (RSV) surge in autumn 2022. Despite the pressure this has put on hospitals and care centers, the factors promoting the surge in cases are unknown. To investigate whether viral characteristics contributed to the extent or severity of the surge, we sequenced 105 RSV-positive specimens from symptomatic patients diagnosed with RSV who presented to the Massachusetts General Hospital (MGH) and its outpatient practices in the Greater Boston Area. Genomic analysis of the resulting 77 genomes (54 with >80% coverage, and 23 with >5% coverage) demonstrated that the surge was driven by multiple lineages of RSV-A (91%; 70/77) and RSV-B (9%; 7/77). Phylogenetic analysis of all US RSV-A revealed 12 clades, 4 of which contained Massachusetts and Washington genomes. These clades individually had times to most recent common ancestor (tMRCA) between 2014 and 2017, and together had a tMRCA of 2009, suggesting that they emerged well before the COVID-19 pandemic. Similarly, the RSV-B genomes had a tMRCA between 2016 and 2019. We found that the RSV-A and RSV-B genomes in our sample did not differ statistically from the estimated clock rate of the larger phylogenetic tree (10.6 and 12.4 substitutions per year, respectively). In summary, the polyphyletic nature of viral genomes sequenced in the US during the autumn 2022 surge is inconsistent with the emergence of a single, highly transmissible causal RSV lineage.

Anti-inflammatory, procollagen, and wound repair properties of topical insulin gel

Diabetes mellitus is associated with impaired wound healing. The topical use of insulin is a promising therapy because it may favor all phases of the wound healing process. This study aimed to investigate the therapeutic outcomes of insulin gel in wounds of hyperglycemic mice. After diabetes induction, a 1-cm2 full-thickness wound was created on each animal's dorsum. The lesions were treated daily for 14 days with insulin gel (insulin group) or vehicle gel without insulin (vehicle group). Tissue samples were extracted on days 4, 7, 10, and 14 after the creation of the lesion. The samples were analyzed with hematoxylin/eosin and Sirius red staining, immunohistochemistry, Bio-Plex immunoassays, and western blotting. Insulin gel favored re-epithelialization at day 10 and increased the organization and deposition of collagen. Additionally, it modulated the expression of cytokines (interleukin (IL)-4 and IL-10) and increased the expression of arginase I, VEGF receptor 1, and VEGF on day 10. Activation of the insulin signaling pathway occurred via IRβ, IRS1, and IKK on day 10 and activation of Akt and IRS1 on day 14. These results suggested that insulin gel improved wound healing in hyperglycemic mice by modulating the expression of inflammatory factors, growth factors, and proteins of the insulin signaling pathway.

The reproducibility of remotely piloted aircraft systems to monitor seasonal variation in submerged seagrass and estuarine habitats

Seasonal variation in seagrass growth and senescence affects the provision of ecosystem services and restoration efforts, requiring seasonal monitoring. Remotely piloted aircraft systems (RPAS) enable frequent high-resolution surveys at full-meadow scales. However, the reproducibility of RPAS surveys is challenged by varying environmental conditions, which are common in temperate estuarine systems. We surveyed three eelgrass ( Zostera marina) meadows in Newfoundland, Canada, using an RPAS equipped with a three-color band (red, green, blue [RGB]) camera, to evaluate the seasonal reproducibility of RPAS surveys and assess the effects of flight altitude (30–115 m) on classification accuracy. Habitat percent cover was estimated using supervised image classification and compared to corresponding estimates from snorkel quadrat surveys. Our results revealed inconsistent misclassification due to environmental variability and low spectral separability between habitats. This rendered differentiating between model misclassification versus actual changes in seagrass cover infeasible. Conflicting estimates in seagrass and macroalgae percent cover compared to snorkel estimates could not be corrected by decreasing the RPAS altitude. Instead, higher altitude surveys may be worth the trade-off of lower image resolution to avoid environmental conditions shifting mid-survey. We conclude that RPAS surveys using RGB imagery alone may be insufficient to discriminate seasonal changes in estuarine subtidal vegetated habitats.

Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework

BACKGROUND

Universities are vulnerable to infectious disease outbreaks, making them ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures. Here, we analyze multimodal COVID-19-associated data collected during the 2020-2021 academic year at Colorado Mesa University and introduce a SARS-CoV-2 surveillance and response framework.

METHODS

We analyzed epidemiological and sociobehavioral data (demographics, contact tracing, and WiFi-based co-location data) alongside pathogen surveillance data (wastewater and diagnostic testing, and viral genomic sequencing of wastewater and clinical specimens) to characterize outbreak dynamics and inform policy. We applied relative risk, multiple linear regression, and social network assortativity to identify attributes or behaviors associated with contracting SARS-CoV-2. To characterize SARS-CoV-2 transmission, we used viral sequencing, phylogenomic tools, and functional assays.

FINDINGS

Athletes, particularly those on high-contact teams, had the highest risk of testing positive. On average, individuals who tested positive had more contacts and longer interaction durations than individuals who never tested positive. The distribution of contacts per individual was overdispersed, although not as overdispersed as the distribution of phylogenomic descendants. Corroboration via technical replicates was essential for identification of wastewater mutations.

CONCLUSIONS

Based on our findings, we formulate a framework that combines tools into an integrated disease surveillance program that can be implemented in other congregate settings with limited resources.

FUNDING

This work was supported by the National Science Foundation, the Hertz Foundation, the National Institutes of Health, the Centers for Disease Control and Prevention, the Massachusetts Consortium on Pathogen Readiness, the Howard Hughes Medical Institute, the Flu Lab, and the Audacious Project.

1079 USE OF AN ADVANCE CARE PLAN CHECKLIST TO IMPROVE COMMUNICATION AND ASSESSMENT OF THE IMPACT ON HOSPITAL READMISSIONS

Introduction

Advance care planning (ACP) is a vital part of holistic and person-centred care. It allows formalising of an individual’s wishes and best interests, and avoids unnecessary or unwanted interventions including, potentially, hospital admissions. It is crucial that any decisions or recommendations are communicated to all relevant healthcare professionals to ensure peoples’ wishes are upheld. We developed this project to review and improve documentation and communication on discharge when a decision had been made to limit care to the community and avoid admission.

Method

A checklist was developed comprising 11 criteria to be documented in the discharge letter and actions to disseminate information including; updating the ReSPECT form and alerting the hospital frailty and community out of hours teams. We carried out a closed loop audit of patients where admission should be avoided and reviewed discharge letters against the criteria. Where patients were readmitted we reviewed the notes to determine whether the admission was appropriate.

Results

We compared patients discharged between February 2020–February 2021 and then from March–September 2021. 161 and 27 patients were identified respectively. Average age was 84.6 and 87.3 years respectively. In cohort 2 48.1% of patients were readmitted, up from 8.7% during the previous cycle. 33% of admissions in cohort 2 and 38.9% of readmissions in cohort 1 were deemed appropriate. Documentation improved in 10 of the 11 criteria. Average length of stay for readmissions was reduced from 16.7 to 5.7 days.

Conclusion

As evidenced by our study utilising a checklist has improved documentation and dissemination of ACPs to the Community. This did not lead to a reduction in hospital admissions but this may have been skewed by factors relating to the Covid-19 pandemic. We did find a significant reduction in length of stay for those subsequently readmitted.

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant's respective emergence period, finding that Delta emerged 1.37-2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%-167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1-10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta's enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability.

Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows

The global spread and continued evolution of SARS-CoV-2 has driven an unprecedented surge in viral genomic surveillance. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine laboratory processes and results. This challenge will increase with the expanding global production of sequences across a variety of laboratories for epidemiological and clinical interpretation, as well as for genomic surveillance of emerging diseases in future outbreaks. We present SDSI + AmpSeq, an approach that uses 96 synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination throughout the sequencing workflow. We apply SDSIs to the ARTIC Consortium's amplicon design, demonstrate their utility and efficiency in a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases and validate them across 6,676 diagnostic samples at multiple laboratories. We establish that SDSI + AmpSeq provides increased confidence in genomic data by detecting and correcting for relatively common, yet previously unobserved modes of error, including spillover and sample swaps, without impacting genome recovery.

Demand for regional level III neonatal services is not reduced during national COVID lockdowns

Following the first peak of the COVID-19 pandemic, reports from around the world suggested a reduction in preterm deliveries during lockdown periods. We reviewed preterm admissions to a large tertiary neonatal unit in inner North East London during two United Kingdom (UK) national lockdowns in 2020 and 2021. We found no evidence of difference in admissions during two national lockdowns compared to previous years. Based on these findings, we recommend that neonatal services remain as vigilant and prepared as ever for the unpredictable nature of preterm birth, and their staff protected to provide this highly specialist care.

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta's infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ∼6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta's enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations.

Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis

Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.

Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay

Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.

DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing

The rapid global spread and continued evolution of SARS-CoV-2 has highlighted an unprecedented need for viral genomic surveillance and clinical viral sequencing. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine lab processes and results. This challenge will only increase with expanding global production of sequences by diverse research groups for epidemiological and clinical interpretation. We present an approach which uses synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination through a sequencing workflow. Applying this approach to the ARTIC Consortium's amplicon design, we define a series of best practices for Illumina-based sequencing and provide a detailed characterization of approaches to increase sensitivity for low-viral load samples incorporating the SDSIs. We demonstrate the utility and efficiency of the SDSI method amidst a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases.

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

Analysis of 772 complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from early in the Boston-area epidemic revealed numerous introductions of the virus, a small number of which led to most cases. The data revealed two superspreading events. One, in a skilled nursing facility, led to rapid transmission and significant mortality in this vulnerable population but little broader spread, whereas other introductions into the facility had little effect. The second, at an international business conference, produced sustained community transmission and was exported, resulting in extensive regional, national, and international spread. The two events also differed substantially in the genetic variation they generated, suggesting varying transmission dynamics in superspreading events. Our results show how genomic epidemiology can help to understand the link between individual clusters and wider community spread.

Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2

The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. SHINE's results can be visualized with an in-tube fluorescent readout - reducing contamination risk as amplification reaction tubes remain sealed - and interpreted by a companion smartphone application. We validate SHINE on 50 nasopharyngeal patient samples, demonstrating 90% sensitivity and 100% specificity compared to RT-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay

Developing and deploying new diagnostic tests is difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important for an effective response. In the early stages of a pandemic, laboratories play a key role in helping health care providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, polymerase chain reaction (PCR) remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility, and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to fast and accurate diagnostic testing in crisis conditions.

Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events

SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.

Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events

SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.

Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2

The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (SHERLOCK and HUDSON Integration to Navigate Epidemics), a sensitive and specific integrated diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We combine the steps of SHERLOCK into a single-step reaction and optimize HUDSON to accelerate viral inactivation in nasopharyngeal swabs and saliva. SHINE's results can be visualized with an in-tube fluorescent readout - reducing contamination risk as amplification reaction tubes remain sealed - and interpreted by a companion smartphone application. We validate SHINE on 50 nasopharyngeal patient samples, demonstrating 90% sensitivity and 100% specificity compared to RT-PCR with a sample-to-answer time of 50 minutes. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

123 Nerve growth factor-induced ovulation in llamas: Evidence of hypothalamic refractoriness to nerve growth factor during the declining phase of the luteinising hormone surge

Nerve growth factor (NGF) in semen is responsible for triggering ovulation after copulation in camelids. Interaction of NGF with its cognate receptors results in a preovulatory luteinising hormone (LH) surge that leads to ovulation, but the pharmacokinetics of NGF and the mechanism by which it mediates LH release are unknown. In an effort to elucidate the site and mechanism of action involved, the objective of this study was to determine whether the decline in the LH surge occurs as a result of pituitary depletion (i.e. diminished response to gonadotrophin-releasing hormone (GnRH)) or as an obtunded response at the level of the hypothalamus (diminished GnRH). Adult nonpregnant, nonlactating llamas (n=18) were synchronized by the administration of an ovulatory dose of a GnRH analogue (100μg IM; Fertiline, Vetoquinol). At 10 to 14 days later, the ovaries were examined to confirm the presence of a dominant follicle measuring ≥ 7mm, and a jugular catheter was put in place. The following day, a pretreatment blood sample was taken, and llamas were treated intravenously with 1mg of purified NGF from llama seminal plasma. Blood samples were taken every 30min for 7h from the time of NGF treatment. After the last blood sample was taken, llamas were treated with NGF (n=6; 1mg IV), GnRH (n=5; 100μg IV), or saline (Sal; IV; n=6), and blood samples were taken every 30min for another 7h. The ovaries were examined 48h after initial NGF treatment, via transrectal ultrasonography, to detect ovulation. Plasma was harvested and stored for analysis of LH concentration by radioimmunoassay. Data were compared using ANOVA for repeated measures, and single-point data were analysed using paired t-tests. As expected, most llamas ovulated in response to the initial NGF treatment (5 out of 5 in NGF-GnRH; 5 of 6 in NGF-NGF; 5 of 6 in NGF-Sal). Compared with pretreatment values, all llamas showed a 4-fold increase in plasma LH concentrations within 2h of the initial NGF treatment (P&lt;0.05). Plasma LH concentrations peaked at 3h after initial NGF treatment and began to decline 4.5 to 5h after treatment (P&lt;0.05). Plasma LH concentrations continued to decline following the second dose of NGF or Sal, whereas a transient elevation of LH was detected in llamas treated with GnRH (P&lt;0.05). The LH concentration returned to basal levels (pretreatment) 8, 12, and 13h after NGF treatment in llamas treated with NGF-Sal, NGF-GnRH, and NGF-NGF, respectively. We conclude that the lack of LH response to the second dose of NGF is not because of pituitary depletion but rather due to diminished GnRH. The latter may be attributed to either a downregulation of NGF receptors within the hypothalamus or to temporary depletion of GnRH at the nerve terminals within the median eminence. Research was supported by the Natural Sciences and Engineering Research Council of Canada.

175 Use of equine chorionic gonadotrophin in a minimum-handling protocol for oocyte collection in bison

Wood bison (Bison bison athabascae) and plains bison (Bison bison bison) are threatened subspecies native to North America. The creation of a germplasm biobank will connect valuable and inaccessible genetics from geographically distant herds in a biosecure manner. Protocols that are feasible in field conditions are required for cumulus-oocyte complex (COC) collection for the purpose of invitro embryo production (IVP). The efficacy of a single dose of equine chorionic gonadotrophin (ECG) was tested in an effort to develop a minimum-handling ovarian superstimulation protocol for bison. The experimental design enabled comparison between ECG-treated and non-superstimulated bison. Transvaginal ultrasound-guided follicle ablation was performed in mature wood bison (n=24) during May (anovulatory season) to induce follicular wave emergence the following day. Immediately after ablation, the bison were assigned to one of three groups (n=8 per group) and treated intramuscularly with 5000IU of ECG (Folligon, Merck), 2500IU of ECG, or saline (control). Transvaginal COC collection was performed 5 days later. Follicular and COC data were recorded, and only grade 1 and 2 COC were used for IVP. The COC were matured invitro for 25-28h at 38.8°C, fertilised (2×106 spermmL−1), and co-incubated at 38.8°C in 5% O2, 5% CO2, and 90% N2 for 18h. Presumptive zygotes were denuded and cultured at 38.8°C in 5% O2, 5% CO2, and 90% N2. Nominal data were compared among groups using analysis of variance, and proportional data were compared using GLIMMIX. The total number of follicles ≥3mm on the day of COC collection was greater in the 5000-IU ECG group than in the 2500-IU ECG and control groups (37.5±6.9, 17.5±2.0, and 16.9±2.0, respectively; P&lt;0.005). The number of follicles 5-8mm was also greater in the 5000-IU ECG group than in the 2500-IU ECG and control groups (12.5±2.1, 7.6±1.0, and 5.8±0.9, respectively; P&lt;0.01), as was the number of follicles &gt;8mm (21.1±5.4, 3.3±1.2, and 0.9±0.2, respectively; P&lt;0.0005). The proportion of grade 1 and 2 COC/total COC recovered was greater in the 5000-IU ECG group than in the 2500-IU ECG and control groups (84/124 (68%), 39/76 (51%), and 37/75 (49%), respectively; P&lt;0.05). The proportion of cleaved zygotes/number of COC matured, assessed at 56h after fertilisation, was similar among the 5000-IU ECG, 2500-IU ECG, and control groups (42/84 (50%), 27/39 (69%), and 21/37 (57%), respectively; P=0.20). The proportion of embryos of IETS grades 1-3/number of COC matured was also similar among the 5000-IU ECG, 2500-IU ECG, and control groups (15/84 (17.9%), 8/39 (20.5%), and 7/37 (18.9%), respectively; P=0.94), but the bison in the 5000-IU ECG group produced twice as many embryos than those in the other groups. In summary, a single dose of 5000IU of ECG increased the number and size of follicles available for COC collection, more than doubled the number of COC collected for IVP, and resulted in the production of more embryos than the other groups. A single dose of 5000IU of ECG is effective in a minimum-handling protocol for ovarian superstimulation and IVP in bison. This research was supported by NSERC.

Rapid Detection of Powassan Virus in a Patient With Encephalitis by Metagenomic Sequencing

We describe a patient with severe and progressive encephalitis of unknown etiology. We performed rapid metagenomic sequencing from cerebrospinal fluid and identified Powassan virus, an emerging tick-borne flavivirus that has been increasingly detected in the United States.

868. Prospective Pathogen Detection in Patients With Central Nervous System Inflammation Using Metagenomic Sequencing

Background

Metagenomic sequencing can identify pathogens in patients with central nervous system (CNS) inflammation, who often have no diagnosis achieved despite extensive clinical testing.

Methods

This prospective study enrolled patients with CNS inflammation at a tertiary hospital from 2016 to 2017. Total nucleic acid was extracted from cerebrospinal fluid (CSF). Libraries were constructed by random primer cDNA synthesis from RNA, and Nextera XT preparation from both cDNA and DNA. Sequencing was performed on an Illumina platform. Reads from human and environmental contaminants were removed. Metagenomic analysis was performed with Kraken and confirmed with viral-ngs. The Institutional Review Board approved the study, and informed consent was obtained.

Results

Of 68 subjects enrolled, 63% were men and 84% were white. The median age was 58 years. The median CSF pleocytosis was 80 cells/mm³ [IQR 17–132]. A median of 2.4 million RNA and 6.8 million DNA sequencing reads were generated per sample. Twenty-five subjects had no diagnosis achieved by routine clinical testing; metagenomic sequencing identified enterovirus in 2 of these subjects, and no pathogen in 23. Thirty-six subjects were clinically diagnosed with an infection. In 12 of these, pathogen nucleic acid was detected in CSF by clinical polymerase chain reaction (PCR); metagenomic sequencing detected the expected pathogen in 10 subjects (83%). The other 24 subjects were clinically diagnosed with infection by serology or PCR from blood. Among these, metagenomic sequencing detected the CSF presence of HIV and locally important tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. Four subjects with West Nile Virus (WNV) infection did not have WNV RNA detected in CSF by sequencing or clinical PCR testing. Among 7 subjects diagnosed with malignancy or autoimmune disease, no pathogens were detected by metagenomic sequencing.

Conclusion

When applied broadly to patients with CNS inflammation, metagenomic sequencing identified known and unexpected pathogens in CSF, including emerging tick-borne pathogens, highlighting its potential as a diagnostic tool. Patients in whom no pathogen nucleic acid was detected could have had an infection with low pathogen burden or short duration in CSF, or a noninfectious syndrome.

Disclosures

All authors: No reported disclosures.

202 ANTRAL FOLLICULAR COUNTS AND SUPERSTIMULATORY RESPONSE IN PREPUBERTAL CALVES

The number of follicles recruited in successive waves are consistent in postpubertal cattle (Singh et al. 2004 Theriogenology 62, 227), but ovarian response to gonadotropin stimulation is highly variable among animals. We tested the hypotheses that the number of follicles present at wave emergence are repeatable and are predictive of superstimulatory response in prepubertal calves; therefore, we expected that calves with higher antral follicular counts (AFC; follicles = 1mm) at wave emergence will result in a greater number of follicles available for oocyte collection after a conventional 4-day gonadotropin treatment. Hereford crossbreed calves (n = 52; 5.1 to 6.8 months of age) were ranked according to the number of follicles = 1 mm detected in transrectal ultrasound video recordings of both ovaries at the time of wave emergence (First AFC; range: 12 to 53 follicles). Calves in the bottom (Low AFC; <20 follicles; n = 6) and top (High AFC; >32 follicles; n = 5) quartiles were selected for ovarian superstimulation. Emergence of a new follicular wave (Day 0) was induced by transvaginal follicle ablation (14 to 57 days after first AFC; 5.7 to 7.1 months of age), AFC were performed again (Second AFC), and calves were given eight 12-hourly IM injections of 25 mg of pFSH (Folltropin-V®, Bioniche Animal Health Inc., Belleville, Canada) beginning on Day 0.5. All calves were given 12.5 mg of pLH (Lutropin-V®, Bioniche Animal Health Inc.) IM 12 h after the last FSH and number of follicles equal to 3, 3 to 5, 6 to 8, and equal to 6 and 9 were counted 24 h after LH treatment (at the time of oocyte collection). A t-test was used to compare the number of follicles and ovarian response (Low v. High AFC). Values of Pearson (0.8; P < 0.001) and Spearman (0.9; P < 0.001) correlation coefficients between First and Second AFC indicate strong repeatability of numbers of follicles present at the time of wave emergence. As expected, mean number of follicles were greater (P = 0.01) in the High- than Low-AFC group (24.2 ± 2.0 v. 15.7 ± 1.0) at the Second AFC. The High-AFC group had a greater number of follicles at oocyte collection than Low AFC for 6 to 8 mm (13.4 ± 2.1 v. 5.3 ± 1.7; P = 0.01), but not for 3 to 5 mm (9.4 ± 2.5 v. 5.3 ± 2.1; P = 0.2) or 9 mm (7.6 ± 2.9 v. 4.8 ± 2.0; P = 0.4) size categories. However, High AFC resulted in a greater total number of follicles 3 (30.4 ± 3.1 v. 15.5 ± 3.2; P = 0.009) and 6 mm (21.0 ± 4.1 v. 10.2 ± 2.9; P = 0.05). The number of 6-mm follicles at the end of superstimulation represented 80 and 60% of 1-mm follicles at wave emergence in the High- and Low-AFC groups (P = 0.3). In conclusion, the number of follicles at the beginning of a wave are predictive of follicles recruited into subsequent waves in 7-month-old calves, and higher AFC at wave emergence resulted in a greater number of 3- and 6-mm follicles available for oocyte collection. Research was supported by the Natural Science and Engineering Council of Canada (NSERC). Hormones provided by Vetoquinol Inc. ARTK funded by CNPq-Science Without Borders, Brazil.

121 THREE-DIMENSIONAL ASSESSMENT OF EARLY CORPUS LUTEUM VASCULARITY IN BUFFALO (BUBALUS BUBALIS)

The aim of the study was to develop an objective method to assess the vascular flow to the early corpus luteum (CL) in buffaloes using colour Doppler ultrasound data. Our hypothesis was that 3-dimensional (3D) volumetric analysis of vascularity would demonstrate lower variability between animals compared with conventional 2-dimensional (2D) analysis of single images. Wave emergence and ovulation was synchronized in buffalo (n = 16) using prostaglandin-GnRH based protocols. Colour Doppler ultrasonography (MyLab5, 7.5-MHz linear array, colour gain 65%) was performed daily from Day −2 to 4 (Day 0 = ovulation). Video clips of the ovaries (20 s at 18–28 frames per second, AVI) were recorded by slow and uniform free-hand movement of the transducer. Day 4 CL was used for analysis of vascular area and volume. For 2D vascularity assessment, 3 images (800 × 652 pixels, RGB, BMP) of each CL (at maximum apparent vascularity) were acquired through the clip image function on the ultrasound machine and analysed by ImageJ (Fiji) software (NIH, Bethesda, MD, USA). For 3D vascularity assessment, a portion of the video clip encompassing an entire ovary was identified and exported as a series of 2D TIFF images using Videomach software. The ultrasound scale bar was used to calculate the number of pixels per millimetre and to calibrate the X (horizontal) and Y (vertical) dimensions. For 2D analyses, the CL boundary was drawn using the free-hand manual selection tool in Fiji, the area of the CL (mm2) was recorded, and the border was then enlarged by 1.5 mm to include the peripheral vascular region of the CL. The colour threshold was adjusted to select the vascular region. The 2D vascularity score was calculated as the ratio of the coloured area to the enlarged luteal area. For 3D volumetric analyses, each series of TIFF images was imported as an image sequence in Fiji and colour thresholding (similar to 2D analysis) was applied to save a second TIFF series containing luteal vascular regions (coloured areas) only. The remaining volumetric analyses were completed in Imaris software using the ovarian volume (original TIFF series) and luteal vascular volume (second TIFF series) as separate channels. The Z-dimension thickness of each image was estimated by using the dimensions of a follicle within the same ovary (Z-axis diameter = mean diameter along X- and Y-axes). Similar to 2D analyses, the volume of the CL was obtained by drawing a border along the edge of the CL, the CL border was enlarged by 1.5 mm, and a 3D vascularity score was obtained by building a surface on the luteal vascular image and calculating the vascular to luteal volume ratio. The 2D vascularity score differed from 3D vascularity score (0.21 ± 0.02 v. 0.13 ± 0.02, paired t-test P < 0.01); however, variance did not differ (Bartlett’s test P = 0.32). Our initial results support the notion that the described technique of quantifying vascular volume of the corpus luteum may decrease the technical variability during image assessment and therefore better reflect the true vascularity compared with 2D image analyses. Research was supported by a grant from the Natural Sciences and Engineering Research Council of Canada.

Infection control link professionals' knowledge of Clostridium difficile

lostridium difficile is a common cause of diarrhoea in hospitalised patients. It can result in longer hospital stays and due to the need for strict isolation procedures can add significantly to nursing workload. Additionally, it can be very distressing for the patient and if patients are vulnerable to infection it can have serious health consequences. Cross-transmission can be limited by good infection prevention and control practices, however this relies on a sound knowledge base and support from the infection control team. This small-scale study reports on infection control link professionals' knowledge and assesses how they would utilise this knowledge in practice situations. Findings imply that the knowledge base concerning the microorganism was poor, but knowledge relating to general infection procedures was good.

The micro-architecture of human cancellous bone from fracture neck of femur patients in relation to the structural integrity and fracture toughness of the tissue

Osteoporosis is clinically assessed from bone mineral density measurements using dual energy X-ray absorption (DXA). However, these measurements do not always provide an accurate fracture prediction, arguably because DXA does not grapple with ‘bone quality’, which is a combined result of microarchitecture, texture, bone tissue properties, past loading history, material chemistry and bone physiology in reaction to disease. Studies addressing bone quality are comparatively few if one considers the potential importance of this factor. They suffer due to low number of human osteoporotic specimens, use of animal proxies and/or the lack of differentiation between confounding parameters such as gender and state of diseased bone. The present study considers bone samples donated from patients (n = 37) who suffered a femoral neck fracture and in this very well defined cohort we have produced in previous work fracture toughness measurements (FT) which quantify its ability to resist crack growth which reflects directly the structural integrity of the cancellous bone tissue. We investigated correlations between BV/TV and other microarchitectural parameters; we examined effects that may suggest differences in bone remodelling between males and females and compared the relationships with the FT properties. The data crucially has shown that TbTh, TbSp, SMI and TbN may provide a proxy or surrogate for BV/TV. Correlations between FT critical stress intensity values and microarchitecture parameters (BV/TV, BS/TV, TbN, BS/BV and SMI) for osteoporotic cancellous tissue were observed and are for the first time reported in this study. Overall, this study has not only highlighted that the fracture model based upon BMD could potentially be improved with inclusion of other microarchitecture parameters, but has also given us clear clues as to which of them are more influential in this role.

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first time ever study to relate microarchitecture to the fracture toughness of cancellous bone from the femoral head of FNF victims

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reduction in bone mass relates to a reduction in the number of trabeculae and trabecular thickness and an increase in trabeculae spacing

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bone loss observed appears to be a consequence of thinning of the trabeculae in males and perforation of the trabeculae in females

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study hints that TbTh, TbSp, SMI and TbN may provide a proxy or surrogate for BV/TV

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fracture models can be improved by including microarchitecture, BMD and the bone mineral quality of osteoporotic cancellous bone

287 EFFECT OF FOLLICULAR AGING ON THE ATP CONTENT AND DISTRIBUTION OF MITOCHONDRIA IN BOVINE OOCYTES

Our objective was to determine how follicular aging affects the distribution and content of mitochondrial population and ATP in in vivo-matured bovine oocytes. We hypothesised that in vivo-matured bovine oocytes obtained from aged follicles (84 h of gonadotropin starvation) have altered mitochondrial distribution and decreased cytoplasmic ATP content compared to those obtained immediately at the end of a superstimulatory protocol (no starvation). Follicular waves were synchronized by ablation 5 to 8 d after ovulation and a CIDR device was given. Starting on the day of wave emergence (Day 0), short FSH and FSH starvation groups (n = 5 heifers each) were given 8 doses of FSH im over 4 d and the long FSH group (n = 4) was given 14 doses over 7 d. Two doses of PGF were given on Day 4 (short FSH) or Day 7 (FSH starvation and long FSH groups), the CIDR was removed, and LH was given 24 h after second PGF treatment. The ovaries were removed 24 h later by colpotomy and cumulus-oocyte-complexes (COC) were collected from follicles ≥8 mm. Denuded oocytes were either stained with Mitotracker Deep Red FM and imaged by confocal microscopy or processed for ATP assay. Mitochondria numbers were assessed by segmentation of 3D datasets. Proportions of COC within each grade were compared using Fischer's exact test, and ATP and mitochondrial data were compared by analysis of variance. Short and long FSH groups had a greater proportion of Grade 1 expanded COC than the FSH starvation group (P = 0.02). The ATP content of oocytes (from expanded COC) tended to be higher in the long FSH group than short FSH (P = 0.09), and the FSH starvation group was intermediate. The ATP content of oocytes from compact COC did not differ among groups (P = 0.49). The proportion of mitochondrial clusters was highest (P = 0.01) and the proportion of individual mitochondria was lowest (P = 0.01) in the FSH starvation group compared to short and long FSH groups. Mitochondria from the long FSH and FSH starvation groups had twice the relative intensity compared to the short FSH group (P < 0.01). In conclusion, follicular aging (FSH starvation) was associated with a decrease in oocyte morphologic grade and marked clustering of mitochondria, which may be a reflection of oxidative stress and atresia.