Resource-limited settings and supply chain difficulties faced throughout the COVID-19 pandemic prompted the development of rapid and alternative methods of detecting SARS-CoV-2. These methods include reverse-transcription loop-mediated isothermal amplification (RT-LAMP), reverse-transcription recombinase polymerase amplification (RT-RPA), and CRISPR-Cas12a fluorescence detection. We describe RT-LAMP, RT-RPA, and CRISPR-Cas12a assays for the detection of the N and E-gene amplicons of SARS-CoV-2 and the optimization of various assay components, including incubation temperatures, Cas12a enzymes, reporter molecules, and the use of a lyophilized RT-LAMP master mix. We also describe the testing of a one-tube RT-LAMP-CRISPR-Cas12a assay. The one-tube assay showed promise in reducing hands-on time and improving time-to-result. We found no improvements in assay sensitivity with RT-RPA, but did achieve detection at a lower copy number with the lyophilized RT-LAMP master mix compared to liquid reagent (50 vs. 100 copies at 20 min). When used to detect the presence of SARS-CoV-2 RNA in clinical saliva samples from 75 infected patients, the discriminatory ability of the optimized RT-LAMP-CRISPR Cas12a assay was found to be comparable with RT-qPCR, with a minor reduction in sensitivity.

The aims of this study were to evaluate the performance and workflow characteristics of a laboratory-developed test to detect Treponema pallidum on the Hologic Panther Fusion system compared with an existing commercial assay. A Hologic Panther Fusion-based real-time polymerase chain reaction assay was optimised for T. pallidum (TP RT-PCR) using previously published primer and probe sequences and validated with a simplified preprocessing protocol. A total of 124 clinical and external quality assurance (EQA) samples were tested in parallel by the new method and the Viasure T. pallidum RT-PCR (Certest Biotech). Cross reactivity, limit of detection, PCR efficiency and coefficient of variation (CV) were measured. Simplified preprocessing methods involving either concentration or vortexing were compared with the existing overnight chemical/enzymatic preprocessing method for a subset of positive samples. Workflow impacts were assessed before and after implementation. The Panther Fusion T. pallidum assay correctly detected 65 of 65 (100%) positive clinical and EQA samples and 33 of 33 (100%) negative samples. No cross reactivity was observed for 45 of 45 (100%) samples. The limit of detection was 15 copies/reaction, and intrarun CV was <1.66%. The simplest preprocessing protocol detected 34 of 34 (100%) positive samples with an average Delta cycle threshold (Ct) <0.82 compared with the Viasure workflow. The new workflow reduced median turnaround time from 3.83 to 1.73 days (p<0.001) and estimated costs from US$35,004.96 to US$19,390.15 in the 3 months post-implementation. The laboratory-developed Panther Fusion T. pallidum assay is a sensitive and specific method for detection of syphilis and a cost-effective option to help improve workflow and turnaround time in a diagnostic laboratory.

The World Health Organization declared mpox (formerly monkeypox) a Public Health Emergency of International Concern in July 2022. Aotearoa New Zealand has reported cases of mpox since July, with reports of locally acquired cases since October 2022. The 2022 global mpox outbreak highlights many features of the illness not previously described, including at-risk populations, mode of transmission, atypical clinical features, and complications. It is important that all clinicians are familiar with the variety of clinical manifestations, as patients may present to different healthcare providers, and taking lessons from the HIV pandemic, that all patients are managed without stigma or discrimination. There have been numerous publications since the outbreak began. Our narrative clinical review attempts to bring together the current clinical evidence for the New Zealand clinician.

BACKGROUND:Syphilis is a sexually transmitted bacterial infection caused by Treponema pallidum subspecies pallidum. Since 2012, syphilis rates have risen dramatically in many high-income countries, including England. Although this increase in syphilis prevalence is known to be associated with high-risk sexual activity in gay, bisexual, and other men who have sex with men (GBMSM), cases are rising in heterosexual men and women. The transmission dynamics within and between sexual networks of GBMSM and heterosexual people are not well understood. We aimed to investigate if whole genome sequencing could be used to supplement or enhance epidemiological insights around syphilis transmission. METHODS:We linked national patient demographic, geospatial, and behavioural metadata to whole T pallidum genome sequences previously generated from patient samples collected from across England between Jan 1, 2012, and Oct 31, 2018, and performed detailed phylogenomic analyses. FINDINGS:Of 497 English samples submitted for sequencing, we recovered 240 genomes (198 from the UK Health Security Agency reference laboratory and 42 from other laboratories). Three duplicate samples (same patient and collection date) were included in the main phylogenies, but removed from further analyses of English populations, leaving 237 genomes. 220 (92·8%) of 237 samples were from men, nine (3·8%) were from women, and eight (3·4%) were of unknown gender. Samples were mostly from London (n=118 [49·8%]), followed by southeast England (n=29 [12·2%]), northeast England (n=24 [10·1%]), and southwest England (n=15 [6·3%]). 180 (76·0%) of 237 genomes came from GBMSM, compared with 25 (10·5%) from those identifying as men who have sex with women, 15 (6·3%) from men with unrecorded sexual orientation, nine (3·8%) from those identifying as women who have sex with men, and eight (3·4%) from people of unknown gender and sexual orientation. Phylogenomic analysis and clustering revealed two dominant T pallidum sublineages in England. Sublineage 1 was found throughout England and across all patient groups, whereas sublineage 14 occurred predominantly in GBMSM older than 34 years and was absent from samples sequenced from the north of England. These different spatiotemporal trends, linked to demography or behaviour in the dominant sublineages, suggest they represent different sexual networks. By focusing on different regions of England we were able to distinguish a local heterosexual transmission cluster from a background of transmission in GBMSM. INTERPRETATION:These findings show that, despite extremely close genetic relationships between T pallidum genomes globally, genomics can still be used to identify putative transmission clusters for epidemiological follow-up. This could be of value for deconvoluting putative outbreaks and for informing public health interventions. FUNDING:Wellcome funding to the Sanger Institute, UK Research and Innovation, National Institute for Health and Care Research, European and Developing Countries Clinical Trials Partnership, and UK Health Security Agency.

Background Syphilis is a sexually transmitted bacterial infection caused by Treponema pallidum subspecies pallidum , with approximately 6.3 million annual cases globally. Over the last decade, syphilis rates have risen dramatically in many high-income countries, including in England, which has seen a greater than 150% increase. Although this increase is known to be associated with high risk sexual activity in gay, bisexual and other men who have sex with men (GBMSM), cases are rising in heterosexual men and women, and congenital syphilis cases are now seen annually. The transmission dynamics within and between sexual networks of GBMSM and heterosexuals are not well understood. Methods To determine if whole genome sequencing could be used to identify discrete patterns of transmission, we linked national patient demographic, geospatial and behavioural metadata to whole T. pallidum genome sequences previously generated from 237 patient samples collected from across England between 2012 and 2018. Findings Phylogenomic analysis and clustering revealed two of the eight T. pallidum sublineages detected in England dominated. These dominant sublineages exhibited different spatiotemporal trends linked to demography or behaviour, suggesting they represent different sexual networks: sublineage 1 was found throughout England and across all patient groups, whereas sublineage 14 occurred predominantly in older GBMSM and was absent from samples sequenced from the North of England. By focussing on different regions of England we were able to distinguish a local heterosexual transmission cluster from a background of transmission amongst GBMSM. Interpretation These findings demonstrate that despite extremely close genetic relationships between T. pallidum genomes globally, genomics can still be used to identify putative transmission clusters for epidemiological follow-up, and therefore has a role to play in informing public health interventions. Funding Wellcome funding to the Sanger Institute (#206194 and 108413/A/15/D), UKRI and NIHR (COV0335; MR/V027956/1, NIHR200125), the EDCTP (RIA2018D-249), and UKHSA. Evidence before this study Detailed phylogenomic analyses investigating the epidemiology and transmission dynamics of Treponema pallidum are challenging due to low bacterial loads in clinical specimens, and difficulty in culturing the bacteria. We searched PubMed until August 9th 2022 using the search terms “Syphilis” or “ Treponema pallidum ” and “genomic” or “genome(s)” or “sequencing”, finding 23 studies describing whole genome sequencing of T. pallidum subspecies pallidum , of which two used whole genome phylogenies to investigate sexual network epidemiology, with one large study of sexual networks conducted primarily in Victoria, Australia which characterised two major circulating sublineages in that setting, as well as putative sexual transmission networks with distinct sexual behavioural characteristics and potential bridging between networks. Added value of this study In this study, we linked national surveillance data to T. pallidum genomes, and characterised the transmission dynamics of syphilis using samples from across a whole country, in a European setting (England). Integration of national-level sociodemographic, spatiotemporal and genomic data allowed the delineation of putative sexual networks at both the national and region levels, and revealed patterns not previously detected using epidemiological or genomic data alone. Implications of all the available evidence Our findings are consistent with findings in Australia that demonstrate genomics can identify putative sociodemographic transmission clusters. However, in that study genomic clusters included samples separated by multiple single nucleotide polymorphisms, which could represent several years of evolution. Our study explored the value of linking identical genomes, and highlights that despite technical constraints, whole genome sequencing can be used to enable outbreak exclusion and identify putative local transmission clusters for epidemiological follow-up. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement MAB and NRT were supported by Wellcome funding to the Sanger Institute (#206194 and 108413/A/15/D). MM was funded by the UKRI and NIHR (COV0335; MR/V027956/1, NIHR200125) and the EDCTP (RIA2018D-249). Staff time for LT, MJC, RP, HC, KS, HF, patient metadata retrieval and analyses were funded internally by UKHSA. This research was funded in whole, or in part, by the Wellcome Trust (#206194 and 108413/A/15/D). For the purpose of open access, the authors have applied a CC-BY public copyright licence to any author-accepted manuscript version arising from this submission. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical approval for all clinical samples was granted by the London School of Hygiene and Tropical Medicine Observational Research Ethics Committee (REF#16014) and the National Health Service (UK) Health Research Authority and Health and Care Research Wales (UK; 19/HRA/0112). UKHSA has permission to process confidential patient data under Regulation 3 (Control of Patient Information) of the Health Service Regulations 2002. Information governance advice and ethics approval for this study were granted by the PHE (now UKHSA) Research Ethics and Governance Group. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Sequencing reads for all genomes used in this study have been previously published and described, and are available at the European Nucleotide Archive () in BioProjects PRJEB28546, PRJEB33181 and PRJNA701499. All accessions, corresponding sample identifiers and related metadata are available in Supplementary Data 1. Patient metadata for the UK genomes is available in pseudonymised form in Supplementary Data 2. UK shape files for Public Health (UKHSA) region boundaries were downloaded from the UK Office for National Statistics, available at . All sample metadata and intermediate analysis files are available at and [https://github.com/matbeale/Syphilis\_Genomic\_Epi\_England\_2022-23][1]. [https://github.com/matbeale/Syphilis\_Genomic\_Epi\_England\_2022-23][1] [1]: https://github.com/matbeale/Syphilis_Genomic_Epi_England_2022-23

AIM:To compare detection of SARS-CoV-2 from paired nasopharyngeal swabs (NPS) and saliva using molecular methods in common use for testing swabs in New Zealand. METHOD:Samples from individuals testing positive for SARS-CoV-2 in Auckland, Wellington and Dunedin were tested at the local laboratories using methods previously established for these sample types. RESULTS:One hundred and ninety-six paired samples from unique individuals were tested, with 46 (23%) positive from either sample type, of which 43/46 (93%) tested positive from NPS, and 42/46 (91%) from saliva, indicating no significant difference in performance between sample types (p=0.69). The average Δ Ct between saliva and nasopharyngeal swabs overall across the sample set was 0.22 cycles, indicating excellent concordance; however, the difference between NPS and saliva collected from the same individual was quite variable with up to 19 cycles difference between the sample types. CONCLUSION:We found that saliva is an equivalent sample type to nasopharyngeal swab for the detection of SARS-CoV-2 in our laboratories using multiple assay combinations and is suitable for use as a diagnostic and surveillance test for selected groups of individuals.

AIM: To assess the sensitivity and potential utility of five RATs and the IDNow, Liat and Oxsed nucleic acid amplification tests (NAATs) in our population. METHOD: 39 retrospective and contrived SARS-CoV-2 positive samples were tested in parallel by standard RT-PCR and RAT. A second group of 44 samples was tested by standard RT-PCR, rapid RT-PCR and two isothermal NAAT assays. Limit of detection was compared at RT-PCR cycle thresholds for all assays. RESULTS: We found that the Cobas Liat RT-PCR had 100% concordance with conventional RT-PCR, whereas the sensitivity of other rapid NAAT assays was less at lower viral loads indicated by Cts >30 (p=0.042) and the RATs at Cts >25 (p <0.001). When applied to New Zealand testing scenarios, IDNow or Oxsed NAAT could miss up to 12% and RATs up to 44.3% of COVI D-19 cases compared with the RT-PCR currently used at our laboratory. CONCLUSION: We found that the POC Cobas Liat, a platform that delivers a sample answer in 20 minutes, demonstrated equivalent performance to standard RT-PCR. However, the RATs and isothermal NAAT assays demonstrated reduced sensitivity, limiting their utility in New Zealand's currently very low prevalence setting.

Since the first wave of coronavirus disease in March 2020, citizens and permanent residents returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days and mandatory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of October 20, 2020, of 62,698 arrivals, testing of persons in MIQ had identified 215 cases of SARS-CoV-2 infection. Among 86 passengers on a flight from Dubai, United Arab Emirates, that arrived in New Zealand on September 29, test results were positive for 7 persons in MIQ. These passengers originated from 5 different countries before a layover in Dubai; 5 had negative predeparture SARS-CoV-2 test results. To assess possible points of infection, we analyzed information about their journeys, disease progression, and virus genomic data. All 7 SARS-CoV-2 genomes were genetically identical, except for a single mutation in 1 sample. Despite predeparture testing, multiple instances of in-flight SARS-CoV-2 transmission are likely.

Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum , has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum , we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides.

During New Zealand's first outbreak in early 2020 the Southern Region had the highest per capita SARS-CoV-2 infection rate. Polymerase chain reaction (PCR) testing was initially limited by a narrow case definition and limited laboratory capacity, and cases may have been missed. Our objectives were to evaluate the Abbott SARS-CoV-2 IgG nucleocapsid assay, alongside spike-based assays, and to determine the frequency of antibodies among PCRconfirmed and probable cases, and higher risk individuals in the Southern Region of New Zealand. Pre-pandemic sera (n=300) were used to establish assay specificity and sera from PCR-confirmed SARS-CoV-2 patients (n=78) to establish sensitivity. For prevalence analysis, all samples (n=1214) were tested on the Abbott assay, and all PCR-confirmed cases (n=78), probable cases (n=9), and higher risk individuals with 'grey-zone' (n=14) or positive results (n=11) were tested on four additional SARS-CoV-2 serological assays. The median time from infection onset to serum collection for PCR-confirmed cases was 14 weeks (range 11-17 weeks). The Abbott assay demonstrated a specificity of 99.7% (95% CI 98.2-99.99%) and a sensitivity of 76.9% (95% CI 66.0-85.7%). Spike-based assays demonstrated superior sensitivity ranging 89.7-94.9%. Nine previously undiagnosed sero-positive individuals were identified, and all had epidemiological risk factors. Spike-based assays demonstrated higher sensitivity than the Abbott IgG assay, likely due to temporal differences in antibody persistence. No unexpected SARS-CoV-2 infections were found in the Southern Region of New Zealand, supporting the elimination status of the country at the time this study was conducted.

We describe three cases with viral strains that demonstrate impaired N2-gene detection on the Cepheid Xpert Xpress SARS-CoV-2 assay, with two previously undescribed single nucleotide polymorphisms (SNPs): C29197T and G29227T. We propose that these SNPs are likely responsible since they are in close proximity to the previously described C29200T/C29200A SNPs, already shown to abolish N2-gene detection by the Xpert assay. Whether these SNPs abolish N2-gene detection by the Xpert assay individually or only in combination requires more work to elucidate.

Background: Since the first wave of COVID-19 in March 2020, people returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days with mandatory testing for SARS-CoV-2. As of 20 October, testing in MIQ had identified 215 cases of SARS-CoV-2 from a total of 62,698 arrivals. While the majority of infections were likely obtained in the country of origin prior to departure, there have been possible reports of in-flight transmission. Methods: Seven people who arrived in New Zealand on the same flight on 29 September tested positive during their stay in MIQ (out of 86 passengers). The seven passengers originated from five different countries before travelling on the same flight from Dubai, United Arab Emirates (UAE) to Auckland, New Zealand. Information about their journeys, disease progression and virus genomic data was used to assess possible points of infection. Findings: All seven SARS-CoV-2 genomes were genetically identical, with the exception of a single mutation in one case, and all genomes had five signature mutations seen in only six other genomes from the >155,000 genomes sequenced globally. Four of these six related genome sequences were from Switzerland, the country of origin of the suspected index case. Interpretation: By combining information on disease progression, travel dynamics and genomic analysis, we conclude that at least four in-flight transmission events of SARS-CoV-2 likely took place.

Objectives: The aim of this study was to investigate associations between baseline characteristics and CD4 cell count response on first-line antiretroviral therapy and risk of virological failure (VF) with or without drug resistance. Methods: We conducted an analysis of UK Collaborative HIV Cohort data linked to the UK HIV Drug Resistance Database. Inclusion criteria were viral sequence showing no resistance prior to initiation of first-line efavirenz +tenofovir disoproxil fumarate +emtricitabine and virological suppression within 6 months. Outcomes of VF (>= 200 copies/mL) with or without drug resistance were assessed using a competing risks approach fitted jointly with a model for CD4 cell count recovery. Hazard ratios for each VF outcome were estimated for baseline CD4 cell count and viral load and characteristics of CD4 cell count response using latent variables on a standard normal scale. Results: A total of 3640 people were included with 338 VF events; corresponding viral sequences were available in 134 with >= 1 resistance mutation in 36. VF with resistance was associated with lower baseline CD4 (0.30, 0.09-0.62), lower CD4 recovery (0.04, 0.00-0.17) and higher CD4 variability (4.40, 1.22-12.68). A different pattern of associations was observed for VF without resistance, but the strength of these results was less consistent across sensitivity analyses. Cumulative incidence of VF with resistance was estimated to be <2% at 3 years for baseline CD4 350 cells/L. Conclusion: Lower baseline CD4 cell count and suboptimal CD4 recovery are associated with VF with drug resistance. People with low CD4 cell count before ART or with suboptimal CD4 recovery on treatment should be a priority for regimens with high genetic barrier to resistance.

Objectives This is a comparative review between using dried blood spot (DBS) and mini-tube (MT) HIV sampling kits as part of an online sexually transmitted infection (STI) postal testing service. England has recently seen increases in internet-based and postal (eHealth) STI services. Expanding accessibility and testing for patients, cost implications and narrowing the HIV undiagnosed margin are drivers for this. Methods In 2017, data were reviewed from an online postal STI kit requesting service at a time of transitioning from MT to DBS. We compared the STI postal kit and HIV blood sample return rates, and the successful processing/analysis rates of the DBS and MT kits. Descriptive statistics were applied to participant characteristics, with Pearson’s χ 2 or Fisher exact test used to demonstrate statistical differences. We also describe and calculate a ‘request-to-result ratio’ (RRR) for both kit types. The RRR is defined as the number of online kit requests required to produce one successfully analysed result. Results 550 STI postal kit requests from a North-West of England region were reviewed from 13 June 2017 to 22 September 2017 (275 MT, 275 DBS). Baseline characteristics between the two groups were comparable (63% woman, 90% white British and 86% heterosexual with a median age of 26 years). The successful processing rate for the DBS was 98.8% c.f. 55.7% for the MT (p<0.001). The RRR for MT was 2.96, c.f. 1.70 for DBS. There was a 5.4% false positive HIV rate in the MT c.f. none in the DBS. Conclusions This comparative analysis suggests that in this community setting, the use of postal HIV DBS kits resulted in a significantly improved RRR compared with MT. The biggest factor was the large number of MT samples not analysed due to inadequate blood volumes. The unexpected level of false positive results in the MT samples needs confirming in larger studies.

Objectives In subjects with transmitted thymidine analogue mutations (TAMs), boosted PIs (PI/b) are often chosen to overcome possible resistance to the NRTI backbone. However, data to guide treatment selection are limited. Our aim was to obtain firmer guidance for clinical practice using real-world cohort data. Methods We analysed 1710 subjects who started a PI/b in combination with tenofovir or abacavir plus emtricitabine or lamivudine, and compared their virological outcomes with those of 4889 patients who started an NNRTI (predominantly efavirenz), according to the presence of 1 TAM as the sole form of transmitted drug resistance. Results Participants with 1 TAM comprised predominantly MSM (213 of 269, 79.2%), subjects of white ethnicity (206 of 269, 76.6%) and HIV-1 subtype B infections (234 of 269, 87.0%). Most (203 of 269, 75.5%) had singleton TAMs, commonly a revertant of T215Y or T215F (112 of 269, 41.6%). Over a median of 2.5years of follow-up, 834 of 6599 (12.6%) subjects experienced viraemia (HIV-1 RNA >50 copies/mL). The adjusted HR for viraemia was 2.17 with PI/b versus NNRTI-based therapy (95% CI 1.88-2.51; P<0.001). Other independent predictors of viraemia included injecting drug use, black ethnicity, higher viral load and lower CD4 cell count at baseline, and receiving abacavir instead of tenofovir. Resistance showed no overall impact (adjusted HR 0.77 with 1 TAM versus no resistance; 95% CI 0.54-1.10; P=0.15). Conclusions In this cohort, patients harbouring 1 TAM as the sole form of transmitted drug resistance gained no apparent virological advantage from starting first-line ART with a PI/b.

Primary effusion lymphoma (PEL) is a serious sequel to Human Herpes Virus 8 (HHV8) infection in the immunosuppressed host. Usually requiring a cytological diagnosis, body cavity effusions are often referred for investigation for possible PEL. Although absence of HHV8 effectively refutes this, the presence of HHV8 DNA, though indicative is not diagnostic. Referred effusion and plasma samples from 10 patients with HHV8-related pleural and pericardial effusions were submitted for quantitative investigations. HHV8 DNA and human DNA from unseparated effusion extracts have been quantified allowing estimation of virus-to-cell ratios in effusion fluid. These ratios varied widely between 0.003 and 700. Five fluids had in excess of 106 HHV-8 DNA genome equivalents per ML (GEq/ML), ranging between 18 and 300 million GEq/ML. Four of these five effusions were from patients with cytologically proven PEL and had virus to cell (V:C) ratios between 100 and 700 to 1. The remaining high load effusion exhibited a ratio of 1.6 to 1 and came from a patient with extensive thoracic Kaposi's sarcoma. Five effusion fluids with low viral loads exhibited virus to cell ratios between 0.003 and 0.5. High effusion HHV8 load, though supportive of a diagnosis of PEL is less accurate than using virus to cell ratios.

Background. Drug-resistant minority variants (DRMinVs) detected in patients who recently acquired human immunodeficiency virus type 1 (HIV-1) can be transmitted, generated de novo through virus replication, or technical errors. The first form is likely to persist and result in treatment failure, while the latter two could be stochastic and transient. Methods. Ultradeep sequencing of plasma samples from 835 individuals with recent HIV-1 infection in the United Kingdom was performed to detect DRMinVs at a mutation frequency between 2% and 20%. Sequence alignments including >110 000 HIV-1 partial pol consensus sequences from the UK HIV Drug Resistance Database (UK-HDRD), linked to epidemiological and clinical data from the HIV and AIDS Reporting System, were used for transmission cluster analysis. Transmission clusters were identified using Cluster Picker with a clade support of >90% and maximum genetic distances of 4.5% or 1.5%, the latter to limit detection to likely direct transmission events. Results. Drug-resistant majority variants (DRMajVs) were detected in 66 (7.9%) and DRMinVs in 84 (10.1%) of the recently infected individuals. High levels of clustering to sequences in UK-HDRD were observed for both DRMajV (n = 48; 72.7%) and DRMinV (n = 63; 75.0%) sequences. Of these, 43 (65.2%) with DRMajVs were in a transmission cluster with sequences that harbored the same DR mutation compared to only 3 (3.6%) sequences with DRMinVs (P < .00001, Fisher exact test). Evidence of likely direct transmission of DRMajVs was observed for 25/66 (37.9%), whereas none were observed for the DRMinVs (P < .00001). Conclusions. Using a densely sampled HIV-infected population, we show no evidence of DRMinV transmission among recently infected individuals.

Background Persistent hepatitis E virus genotype 3 (HEV G3) infections affect solid organ transplant (SOT) recipients and hematopoietic stem cell transplant (HSCT) recipients, but the burden in these cohorts in the United Kingdom is unknown. We established an audit to determine the point prevalence of HEV viremia in SOT and HSCT patients in the United Kingdom and compare different testing approaches to inform screening strategies. Methods Between January 5, 2016, and September 21, 2016, 3044 patients undergoing therapeutic drug monitoring at a single transplant center were screened for HEV ribonucleic acid (RNA) in minipools. A total of 2822 patients who could be characterized included 2419 SOT patients, 144 HSCT patients and 259 patients with no available transplant history. HEV RNA-positive samples were characterized by serology and genomic phylogeny. HEV antigen (HEV-Ag) testing was performed on RNA-positive samples, 420 RNA-negative samples and 176 RNA-negative blood donor samples. Results Nineteen of 2822 patients were viremic with G3 HEV giving a prevalence of 0.67%. The median alanine aminotransferase was significantly higher in the HEV viremic patients (P < 0.0001); however, 2 viremic patients had an alanine aminotransferase value within the normal range at the time of screening. The HEV-Ag assay identified 18/19 viremic patients and all those patients with proven viremia longer than 4 weeks. Conclusions Transplant recipients in the United Kingdom are at a low but significant risk of HEV infection. HEV-Ag detection could be an alternative to RNA detection where the goal is to identify established persistent HEV infection, particularly where expertise, facilities, or cost prohibit RNA testing.