Prevalence of persistent SARS-CoV-2 in a large community surveillance study.

Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1-5, give rise to highly divergent lineages6-8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. We refer to these as 'persistent infections' as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all. Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We estimate that 0.1-0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people11-14. This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution.

Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burden, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. By analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior exposure, viral burden was 44% lower among Alpha variant infections, compared to those with the predecessor strain, B.1.177. Vaccination reduced viral burden by 67%, and among vaccinated individuals, viral burden was 286% higher among Delta variant, compared to Alpha variant, infections. In addition, viral burden increased by 17% for every 10-year age increment of the infected individual. In summary, within-host viral burden increases with age, is reduced by vaccination, and is influenced by the interplay of vaccination status and viral variant.

Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

[This corrects the article DOI: 10.1371/journal.ppat.1011461.].

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors, although this was also accompanied by a gradual fall in average viral burdens from June 2021 to March 2023. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non-SGTF over time. Evolution was characterized by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens.

Diagnosing nephrogenic systemic fibrosis in the post-FDA restriction era.

The emergence of an association between gadolinium-based contrast agents (GBCA) and the rare condition nephrogenic systemic fibrosis (NSF) led to a warning in 2006 from the Food and Drug Administration (FDA) restricting the use of the GBCAs to patients with an estimated glomerular filtration rate of >30 mL/min/1.73m(2) . We discuss our experience with a post-FDA restriction presentation of NSF and subsequent patient death in which the prolonged lead-time of ∼5.5 years led to challenges in ensuring a secure diagnosis of NSF and establishing risk exposures. Accurate contemporary records of contrast administration and clinical factors alongside clinical and pathological expertise ensured that we were able to confidently diagnose NSF, despite the length of lead time and confounding factors.

Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.

HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participants in the Rakai Community Cohort Study and longitudinal deep-sequence viral phylogenetics to assess how HIV incidence and population groups driving transmission have changed from 2003 to 2018 in Uganda. We observed 1,117 individuals in the incidence cohort and 1,978 individuals in the transmission cohort. HIV viral suppression increased more rapidly in women than men, however incidence declined more slowly in women than men. We found that age-specific transmission flows shifted: whereas HIV transmission to girls and women (aged 15-24 years) from older men declined by about one-third, transmission to women (aged 25-34 years) from men that were 0-6 years older increased by half in 2003 to 2018. Based on changes in transmission flows, we estimated that closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018. This study suggests that HIV programmes to increase HIV suppression in men are critical to reduce incidence in women, close gender gaps in infection burden and improve men's health in Africa.

Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.

HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participants in the Rakai Community Cohort Study and longitudinal deep sequence viral phylogenetics to assess how HIV incidence and population groups driving transmission have changed from 2003 to 2018 in Uganda. We observed 1,117 individuals in the incidence cohort and 1,978 individuals in the transmission cohort. HIV viral suppression increased more rapidly in women than men, however incidence declined more slowly in women than men. We found that age-specific transmission flows shifted, while HIV transmission to girls and women (aged 15-24 years) from older men declined by about one third, transmission to women (aged 25-34 years) from men that were 0-6 years older increased by half in 2003 to 2018. Based on changes in transmission flows, we estimated that closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018. This study suggests that HIV programs to increase HIV suppression in men are critical to reduce incidence in women, close gender gaps in infection burden and improve men's health in Africa.

Estimating deaths from foodborne disease in the UK for 11 key pathogens.

OBJECTIVE: To estimate the number of deaths from foodborne disease in the UK from 11 key pathogens. DESIGN: Four different models were developed using data from a range of sources. These included enhanced surveillance, outbreaks, death certificates and hospital episode statistics data. For each model, median estimates were produced with 95% credible intervals (CrI). The results from the different models were compared. RESULTS: The estimates for foodborne deaths for each pathogen from the different models were consistent, with CrIs largely overlapping. Based on the preferred model for each pathogen, foodborne norovirus is estimated to cause 56 deaths per year (95% CrI 32 to 92), foodborne Salmonella 33 deaths (95% CrI 7 to 159), foodborne Listeria monocytogenes 26 deaths (95% CrI 24 to 28), foodborne Clostridium perfringens 25 deaths (95% CrI 1 to 163) and foodborne Campylobacter 21 deaths (95% CrI 8 to 47). The considerable overlap in the CrIs means it is not possible to make any firm conclusions on ranking. Most of these deaths occur in those aged over 75 years. Foodborne deaths from Shigella, Cryptosporidium, Giardia, adenovirus, astrovirus and rotavirus are all rare. CONCLUSIONS: We estimate that there are 180 deaths per year in the UK (95% CrI 113 to 359) caused by foodborne disease based on these 11 pathogens. While this is a small fraction of the estimated 2.4 million cases of foodborne illness per year it still illustrates the potential severity of these illnesses demonstrating the importance in continuing efforts to reduce these infections.

DNA damage in human spermatozoa is highly correlated with the efficiency of chromatin remodeling and the formation of 8-hydroxy-2'-deoxyguanosine, a marker of oxidative stress.

DNA damage in human spermatozoa has been associated with a range of adverse clinical outcomes, including infertility, abortion, and disease in the offspring. We have advanced a two-step hypothesis to explain this damage involving impaired chromatin remodeling during spermiogenesis followed by a free radical attack to induce DNA strand breakage. The objective of the present study was to test this hypothesis by determining whether impaired chromatin protamination is correlated with oxidative base damage and DNA fragmentation in human spermatozoa. DNA fragmentation, chromatin protamination, mitochondrial membrane potential, and formation of the oxidative base adduct, 8-hydroxy-2'-deoxyguanosine (8OHdG), were monitored by flow cytometry/fluorescence microscopy. Impairment of DNA protamination during late spermatogenesis was highly correlated (P < 0.001) with DNA damage in human spermatozoa. The disruption of chromatin remodeling also was associated with a significant elevation in the levels of 8OHdG (P < 0.001), and the latter was itself highly correlated with DNA fragmentation (P < 0.001). The significance of oxidative stress in 8OHdG formation was demonstrated experimentally using H2O2/Fe2+ and by the correlation observed between this base adduct and superoxide generation (P < 0.001). That 8OHdG formation was inversely associated with mitochondrial membrane potential (P < 0.001) suggested a possible role for these organelles in the creation of oxidative stress. These results clearly highlight the importance of oxidative stress in the induction of sperm DNA damage and carry significant implications for the clinical management of this condition.

Paracrine effects of PAMP and adrenomedullin on the human adrenal H295R cell line: PAMP but not adrenomedullin stimulates DHEA secretion.

It has previously been shown, by this laboratory and others, that adrenal cells actively secrete adrenomedullin. Here it is demonstrated that human adrenal cells also secrete the related peptide, proadrenomedullin N-terminal 20 peptide (PAMP). The actions of adrenomedullin and PAMP on adrenal steroid secretion were determined by measuring the aldosterone, cortisol and dehydroepiandrosterone (DHEA) content of cell culture medium after exposure of the human adrenal H295R cells to either PAMP or adrenomedullin. While PAMP was found to cause a dose-dependent increase in release of all the steroids into the medium, adrenomedullin only increased aldosterone and cortisol and had no effect on DHEA. These data suggest that both adrenomedullin and PAMP may be autocrine regulators of adrenal steroid secretion.

Pierre Robin sequence in a patient with ectrodactyly-ectodermal dysplasia-clefting syndrome: a case report and review of the literature.

Ectrodactyly-ectodermal dysplasia-clefting (EEC) syndrome is a rare condition first identified in 1970. The majority of cases are reported to be autosomal dominant with variable expression and penetrance. The most common clinical feature is ectodermal dysplasia. Ectrodactyly, cleft lip with or with out cleft palate and urogenital anomalies are also main clinical features of EEC syndrome. Pierre Robin (PR) sequence has the clinical findings of micro-retrognathia, retroposed tongue (glossoptosis), cleft of the secondary palate, and upper airway obstruction. Etiologically PR sequence is heterogeneous. It has been reported that less than 20% of cases are isolated, non-syndromic PR sequence. We present a case of a newborn male who was referred to our craniofacial clinic with EEC syndrome and PR sequence. This case represents a unique clinical association. We found no other reports in the literature of these two clinical entities occurring together. Upper airway obstruction of PR sequence, secondary to glossoptosis and micro-retrognathia, gives this association clinical relevance. In addition, this clinical association may represent a new gene locus associated with EEC syndrome.

Oxidative deoxyribonucleic acid damage in sperm has a negative impact on clinical pregnancy rate in intrauterine insemination but not intracytoplasmic sperm injection cycles.

OBJECTIVE: To determine the level of DNA damage, both fragmentation and oxidative, in the sperm population used for intrauterine insemination (IUI) and intracytoplasmic sperm injection (ICSI) and its impact on fertilization and clinical pregnancy rates. DESIGN: A prospective clinical study. SETTING: A tertiary care fertility clinic. PATIENT(S): Couples undergoing ICSI (n = 48) and couples undergoing IUI cycles (n = 53). INTERVENTION(S): Assessment of both sperm DNA fragmentation using the TUNEL assay and oxidative DNA damage using the biomarker 8-hydroxy-2'-deoxyguanosine (8-OHdG) in the samples prepared and used for insemination. MAIN OUTCOME MEASURE(S): Achievement of a clinical pregnancy. RESULT(S): Sperm DNA fragmentation and 8-OHdG were highly correlated (r = 0.55) and 8-OHdG was significantly lower in those who achieved a clinical pregnancy after IUI (8.9% vs. 20.2%). A threshold value of 11.5% 8-OHdG was identified as a useful predictor of IUI success. No differences were found in sperm DNA fragmentation or 8-OHdG between pregnant and nonpregnant couples in ICSI cycles. CONCLUSION(S): 8-Hydroxy-2'-deoxyguanosine, a biomarker of oxidative DNA damage highly correlated with sperm DNA fragmentation, in human sperm DNA has significant value in predicting the chance of a clinical pregnancy after IUI but not ICSI in assisted reproductive technology.

Acute portal vein thrombosis: an important mimic of malignancy on FDG PET/CT.

The authors report a case of portal vein thrombosis, with no underlying malignant cause identified, which was initially detected by fludeoxyglucose positron emission tomography/CT (FDG PET/CT) and subsequently confirmed by both contrast enhanced CT and MRI. The multimodality imaging findings are outlined, the potential clinical implications discussed and note made of the possible FDG PET/CT mimics of this disorder.

The effect of repeated freezing and thawing on human sperm DNA fragmentation.

OBJECTIVE: To investigate the effects of repeated freezing and thawing on human sperm motility, vitality, and DNA integrity. DESIGN: A prospective clinical study. SETTING: Tertiary care fertility clinic. PATIENT(S): Twenty men presenting for infertility investigations. INTERVENTION(S): Each sample was subjected to three cycles of freezing and thawing both with and without washing steps and the addition of fresh cryoprotectant between each cycle. MAIN OUTCOME MEASURE(S): Percentage sperm DNA fragmentation, motility, and vitality before and following repeated freezing and thawing. RESULT(S): The percentage sperm DNA fragmentation rose significantly following each freeze-thaw cycle; however, samples that were not washed and to which fresh cryoprotectant was not added after each cycle fared significantly better than their washed counterparts. Both motility and vitality decreased steadily following each cycle but cell survival was significantly greater in the unwashed samples. CONCLUSION(S): In terms of the level of sperm DNA fragmentation, up to three cycles of freezing and thawing can be performed with a level of risk comparable to that following a single cycle of freezing and thawing. This is provided that samples are refrozen in their original cryoprotectant and not washed or altered in any way in between, and provided that they are separated by density gradient centrifugation or swim-up before use in assisted reproduction technology.

The DNA integrity of cryopreserved spermatozoa separated for use in assisted reproductive technology is unaffected by the type of cryoprotectant used but is related to the DNA integrity of the fresh separated preparation.

OBJECTIVE: To investigate and compare seven different commercially available cryoprotectant media in terms of the DNA integrity of spermatozoa recovered after cryopreservation and separation using density gradient centrifugation (DGC). DESIGN: A prospective clinical study. SETTING: Tertiary care fertility clinic. PATIENT(S): Three hundred twenty men presenting for infertility investigations. INTERVENTION(S): Each sample was randomly assigned to one of seven commercially available cryoprotectants or to no cryoprotectant. MAIN OUTCOME MEASURE(S): Percentage sperm DNA fragmentation after cryopreservation and preparation using DGC. RESULT(S): The mean percentage fragmentation was significantly higher post-thaw and post-DGC; however, some patients (26.3%) demonstrated a lower percentage fragmentation post-thaw. No single cryoprotectant was identified as the best at preserving DNA integrity. The difference in fragmentation after thawing and DGC was found to be highly dependent on the prefreeze fragmentation. Motility was also significantly correlated with the difference in fragmentation post-thaw (r = -0.161). CONCLUSION(S): Neither the presence nor type of cryoprotectant affects the DNA integrity of spermatozoa after cryopreservation and DGC. Individuals with lower prefreeze fragmentation in DGC-prepared spermatozoa have larger increases in fragmentation and are less likely to exhibit lower levels of fragmentation post-thaw. The reverse effect observed in those with higher prefreeze fragmentation gives rise to a possible novel method of reducing fragmentation in sperm used for assisted reproductive technology treatment cycles without the need for testicular sperm retrievals.

Interactive approach to optical tweezers control.

We have developed software with an interactive user interface that can be used to generate phase holograms for use with spatial light modulators. The program utilizes different hologram design techniques, allowing the user to select an appropriate algorithm. The program can be used to generate multiple beams and can be used for beam steering. We see a major application of the program to be in optical tweezers to control the position, number, and type of optical traps.