Throat Samples Research Articles

Comparison of intestinal and pharyngeal microbiota in preterm infants on the first day of life and the characteristics of pharyngeal microbiota in infants delivered by cesarean section or vaginally.

This study aimed to explore the distribution of intestinal and pharyngeal microbiota on the first day of life in preterm infants and compare the composition of microbiota in infants delivered by cesarean section or vaginally. This study included 44 late preterm infants with a gestational age of 34-36 + 6 weeks. Stool and throat swab samples were collected from the preterm infants on the first day of life. The infants were divided into cesarean section and vaginal delivery groups. Illumina NovaSeq high-throughput sequencing technology was used to sequence the V3-V4 hypervariable region of the 16S rRNA gene of all bacteria in the samples. Venn diagram was used to identify shared operational taxonomic units (OTUs) in the intestines and pharynges. Microbial analysis was conducted at the phylum and genus levels, and α and β diversity comparisons were performed. (1) Gestational age may have significantly affected the microbial colonization of the intestines and pharynges of preterm infants on the first day after birth (p ≤ 0.001). (2) More OTUs were detected in the pharynx than in the intestines, both have a total of 819 shared OTUs. Proteobacteria, Firmicutes, and Bacteroidota were the dominant phyla in both. At the genus level, Streptococcus had a lower relative abundance in stool samples (0.5%) compared to throat samples (0.5% vs. 22.2%, p = 0.003). 3) The relative abundance of Streptococcus in pharyngeal samples was 26.2% in the cesarean section group much higher than the 3.8% in the vaginal delivery group (p = 0.01). The early postnatal period is a critical time for the establishment of an infant's microbiota. Gestational age at birth may influence microbial colonization, while birth weight, gender, and mode of delivery do not. The intestinal and pharyngeal microbiota composition of preterm infants on the first day after birth showed high similarity, but larger samples are needed for further validation.

Antibacterial and antibiofilm effect of Zinc Oxide nanoparticles on P. aeruginosa variants isolated from young patients with cystic fibrosis

BackgroundP. aeruginosa, a biofilm-forming bacteria, is the main cause of pulmonary infection in CF patients. We applied ZnO-np as a therapeutic agent for eradicating multi-drug resistance and biofilm-forming P. aeruginosa isolated from young CF patients. MethodsA total of 73 throat and sputum samples taken from young CF patients were inquired. ZnO-np was synthesized and characterized in terms of size, shape, and structure for anti-bacterial activity. The antibiotic susceptibility of isolates before and after the addition of 16 μg/ml of ZnO was evaluated using disc diffusion and microtiter methods, respectively. The gene expression level of QS genes was assessed after treatment with 16 μg/ml ZnO-np. ResultsThe optimum concentration of ZnO-np with a higher inhibitory zone was 16 μg/ml (MIC) and 32 μg/ml (MBC). All isolates were resistant to applied antibiotics, and about 45 % of isolates were strong biofilm-forming bacteria. After treatment with 16 μg/ml ZnO-np, all strains became susceptible to the applied antibiotic except for amikacin, which confers an intermediate pattern. About 63 % and 20 % of isolates were, respectively, non-biofilm and weak biofilm-forming bacteria following the addition of ZnO-np. Relative gene expression of gacA, lasR, and rhlR genes were downregulated significantly (P < 0.001). Although the retS did not have a significant reduction (P = 0.2) ConclusionZnO-np at a concentration of 16 μg/ml could significantly reduce the P. aeruginosa infection by altering the antibiotic susceptibility pattern and inhibiting biofilm formation. Due to their photocatalytic properties and their ability to penetrate the extracellular polysaccharide layer, ZnO nanoparticles can produce ROS, which increases their susceptibility to antibiotics. Nasal delivery of ZnO-np in the form of aerosol can be considered a potential strategy to decrease the mortality rate in CF patients at an early age.

Terminal Ileitis as the Exclusive Manifestation of COVID-19 in Children.

The clinical presentation, organ involvement, and severity of disease caused by SARS-CoV-2 are highly variable, ranging from asymptomatic or mild infection to respiratory or multi-organ failure and, in children and young adults, the life-threatening multisystemic inflammatory disease (MIS-C). SARS-CoV-2 enters cells via the angiotensin-converting enzyme-2 receptor (ACE-2), which is expressed on the cell surfaces of all organ systems, including the gastrointestinal tract. GI manifestations have a high prevalence in children with COVID-19. However, isolated terminal ileitis without other manifestations of COVID-19 is rare. In March 2023, two previously healthy boys (aged 16 months and 9 years) without respiratory symptoms presented with fever and diarrhea, elevated C-reactive protein levels, and low procalcitonin levels. Imaging studies revealed marked terminal ileitis in both cases. SARS-CoV-2 (Omicron XBB.1.9 and XBB.1.5 variants) was detected by nucleic acid amplification in throat and stool samples. Both patients recovered fast with supportive measures only. A differential diagnosis of acute abdominal pain includes enterocolitis, mesenteric lymphadenitis, appendicitis, and more. During SARS-CoV-2 epidemics, this virus alone may be responsible for inflammation of the terminal ileum, as demonstrated. Coinfection with Campylobacter jejuni in one of our patients demonstrates the importance of a complete microbiological workup.

Upper Airway Alarmin Cytokine Expression in Asthma of Different Severities.

Background: The secretion of alarmin cytokines by epithelial cells, including thymic stromal lymphopoietin (TSLP), interleukin (IL)-25, and IL-33, initiates inflammatory cascades in asthma. However, alarmin cytokine expression in the upper airways in asthma remains largely unknown. Methods: We recruited 40 participants with asthma into four groups as per the Global Initiative for Asthma (GINA) steps (10 in each group of GINA 1/2, 3, 4, and 5). Cells were derived from nasal, buccal, and throat brushings. Intracellular cytokine expression (TSLP, IL-25, and IL-33) was assessed by flow cytometry in cytokeratin 8+ (Ck8+) epithelial cells immediately following collection. Results: TSLP was significantly increased (p < 0.001) in GINA 5 patients across nasal, buccal, and throat Ck8+ epithelial cells, while IL-25 was elevated in nasal and throat samples (p < 0.003), and IL-33 levels were variable, compared with GINA 1-4 patients. Individual GINA subgroup comparison showed that TSLP levels in nasal samples from GINA 5 patients were significantly (p = 0.03) elevated but did not differ between patients with and without nasal comorbidities. IL-25 and IL-33 (obtained from nasal, buccal, and throat samples) were not significantly different in individual groups. Conclusions: Our study demonstrates for the first time that Ck8+ nasal epithelial cells from GINA 5 asthma patients express elevated levels of TSLP.

Throat microbiota drives alterations in pulmonary alveolar microbiota in patients with septic ARDS

ABSTRACT Objectives The translocation of intestinal flora has been linked to the colonization of diverse and heavy lower respiratory flora in patients with septic ARDS, and is considered a critical prognostic factor for patients. Methods On the first and third days of ICU admission, BALF, throat swab, and anal swab were collected, resulting in a total of 288 samples. These samples were analyzed using 16S rRNA analysis and the traceability analysis of new generation technology. Results On the first day, among the top five microbiota species in abundance, four species were found to be identical in BALF and throat samples. Similarly, on the third day, three microbiota species were found to be identical in abundance in both BALF and throat samples. On the first day, 85.16% of microorganisms originated from the throat, 5.79% from the intestines, and 9.05% were unknown. On the third day, 83.52% of microorganisms came from the throat, 4.67% from the intestines, and 11.81% were unknown. Additionally, when regrouping the 46 patients, the results revealed a significant predominance of throat microorganisms in BALF on both the first and third day. Furthermore, as the disease progressed, the proportion of intestinal flora in BALF increased in patients with enterogenic ARDS. Conclusions In patients with septic ARDS, the main source of lung microbiota is primarily from the throat. Furthermore, the dynamic trend of the microbiota on the first and third day is essentially consistent.It is important to note that the origin of the intestinal flora does not exclude the possibility of its origin from the throat.

Expanded Access Programme for the use of tecovirimat for the treatment of monkeypox infection: A study protocol for an Expanded Access Programme.

Monkeypox is a viral zoonotic disease commonly reported in humans in parts of Central and West Africa. This protocol is for an Expanded Access Programme (EAP) to be implemented in the Central African Republic, where Clade I monkeypox virus diseases is primarily responsible for most monkeypox infections. The objective of the programme is to provide patients with confirmed monkeypox with access to tecovirimat, a novel antiviral targeting orthopoxviruses, and collect data on clinical and virological outcomes of patients to inform future research. The study will be conducted at participating hospitals in the Central African Republic. All patients who provide informed consent to enrol in the programme will receive tecovirimat. Patients will remain in hospital for the duration of treatment. Data on clinical signs and symptoms will be collected every day while the patient is hospitalised. Blood, throat and lesion samples will be collected at baseline and then on days 4, 8, 14 and 28. Patient outcomes will be assessed on Day 14 -end of treatment-and at Day 28. Adverse event and serious adverse event data will be collected from the point of consent until Day 28. This EAP is the first protocolised treatment programme in Clade I MPXV. The data generated under this protocol aims to describe the use of tecovirimat for Clade I disease in a monkeypox endemic region of Central Africa. It is hoped that this data can inform the definition of outcome measures used in future research and contribute to the academic literature around the use of tecovirimat for the treatment of monkeypox. The EAP also aims to bolster research capacity in the region in order for robust randomised controlled trials to take place for monkeypox and other diseases. {2a & 2b}: ISRCTN43307947.

Gut microbiome alterations in Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections (PANDAS) suggests variation in the gut-brain axis and gut metabolic potential

PANDAS, or Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections is a form of Children’s Post infectious Autoimmune Encephalopathy (CPAE), a neuropsychiatric condition characterized by the abrupt onset of diverse neuropsychiatric manifestations following streptococcal infection. It is an increasingly recognized neuropsychiatric disorder that affects a subset of children whose underlying etiology remains unclear. Gut microbiome plays a crucial role in its host brain development and is implicated throughout the life in neurobehavior and neurological disorders. Emerging evidence suggest gut dysbiosis resulting in altered intestinal flora can impair gut barrier and increase leakiness in the blood-brain barrier leading to inflammation. We aimed to investigate if the microbiome is altered in pediatric patients with PANDAS. Stool (n=19), oral (n=20) and nasal swabs (n=18) were collected from patients diagnosed with PANDAS or healthy controls (HC) and used for 16S analysis. 13 stool samples (7 HC and 6 PANDAS) samples were further used for shogun metagenomics and 17 for untargeted metabolomics (8 HC and 9 PANDAS). 16S rRNA gene sequencing identified significant difference in microbial α diversity, with lower Shannon H’ in PANDAS compared to HC (Welch’s t-test t(16.95)=-2.6, p=0.02), and in β-diversity (PERMANOVA R2=0.08 p=0.04) between PANDAS and HC fecal but not throat and nasal samples. Shotgun metagenomics identified a significant reduction in gene diversity (Welch’s t-test t(9.9)=-3.06, p=0.01) and changes in various KEGG ortholog modules involved in gut metabolism and gut-brain axis. Significant differences were also detected in metabolite composition (PERMANOVA R2=0.10, p=0.02). We also identified a set of microbial groups and metabolites enriched or depleted in CPAE patients, involved in different aspects of host physiology and gut metabolism. Our results show that PANDAS patients have an altered gut microbial community, which may exacerbate their behavioral symptoms and it should be taken into consideration in unveiling the complex pathogenesis and selection of treatment options. Arizona Department of Health Services RFGA2022-010-23 (PK) and ADHS17-00007403 (SR, MD); The Alex Manfull Fund (PK). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Effect of molnupiravir on SARS-CoV-2 evolution in immunocompromised patients: a retrospective observational study

Continued SARS-CoV-2 infection among immunocompromised individuals is likely to play a role in generating genomic diversity and the emergence of novel variants. Antiviral treatments such as molnupiravir are used to mitigate severe COVID-19 outcomes, but the extended effects of these drugs on viral evolution in patients with chronic infections remain uncertain. This study investigates how molnupiravir affects SARS-CoV-2 evolution in immunocompromised patients with prolonged infections. The study included five immunocompromised patients treated with molnupiravir and four patients not treated with molnupiravir (two immunocompromised and two non-immunocompromised). We selected patients who had been infected by similar SARS-CoV-2 variants and with high-quality genomes across timepoints to allow comparison between groups. Throat and nasopharyngeal samples were collected in patients up to 44 days post treatment and were sequenced using tiled amplicon sequencing followed by variant calling. The UShER pipeline and University of California Santa Cruz genome viewer provided insights into the global context of variants. Treated and untreated patients were compared, and mutation profiles were visualised to understand the impact of molnupiravir on viral evolution. Patients treated with molnupiravir showed a large increase in low-to-mid-frequency variants in as little as 10days after treatment, whereas no such change was observed in untreated patients. Some of these variants became fixed in the viral population, including non-synonymous mutations in the spike protein. The variants were distributed across the genome and included unique mutations not commonly found in global omicron genomes. Notably, G-to-A and C-to-T mutations dominated the mutational profile of treated patients, persisting up to 44 days post treatment. Molnupiravir treatment in immunocompromised patients led to the accumulation of a distinctive pattern of mutations beyond the recommended 5 days of treatment. Treated patients maintained persistent PCR positivity for the duration of monitoring, indicating clear potential for transmission and subsequent emergence of novel variants. Australian Research Council.

Development of a multiple cross displacement amplification combined with nanoparticles-based biosensor assay for rapid and sensitive detection of Streptococcus pyogenes

BackgroundS. pyogenes, is a primary pathogen that leads to pharyngitis and can also trigger severe conditions like necrotizing fasciitis and streptococcal toxic shock syndrome (STSS), often resulting in high mortality rates. Therefore, prompt identification and appropriate treatment of S. pyogenes infections are crucial in preventing the worsening of symptoms and alleviating the disease's impact. ResultsIn this study, a newly developed technique called multiple cross displacement amplification (MCDA) was employed to detect S. pyogenes,specifically targeting the speB gene, at a temperature of 63°C within 30 min. Then, an easily portable and user-friendly nanoparticles-based lateral flow biosensor (LFB) assay was introduced for the rapid analysis of MCDA products in just 2 min. The results indicated that the LFB offers greater objectivity compared to Malachite Green and is simpler than electrophoresis. The MCDA-LFB assay boasts a low detection limit of 200 fg and exhibits no cross-reaction with non-S. pyogenes strains. Among 230 clinical swab throat samples, the MCDA-LFB method identified 27 specimens as positive, demonstrating higher sensitivity compared to 23 samples detected positive by qPCR assay and 18 samples by culture. The only equipment needed for this assay is a portable dry block heater. Moreover, each MCDA-LFB test is cost-effective, priced at approximately $US 5.5.ConclusionThe MCDA-LFB assay emerges as a straightforward, specific, sensitive, portable, and user-friendly method for the rapid diagnosis of S. pyogenes in clinical samples.

MOSAIC: A cohort study of human mpox virus disease

Background Human mpox is a viral disease caused by an Orthopoxvirus, human mpox virus (hMPXV), typically causing fever and a rash. Mpox has historically been endemic to parts of Central and West Africa, with small numbers of imported cases reported elsewhere, but starting May 2022 an unprecedented global outbreak caused by clade IIb hMPXV was reported outside traditionally endemic countries. This prompted the initiation of MOSAIC, a cohort study implemented in Europe and Asia that aims to describe clinical and virologic outcomes of PCR-confirmed hMPXV disease, including those who receive antiviral therapy. The focus of this article, however, is on describing the study protocol itself with implementation process and operational challenges. Methods MOSAIC recruits participants of any age with laboratory-confirmed mpox disease who provide informed consent. Participants enrol in the cohort for a total of six months. Blood, lesion and throat samples are collected at several timepoints from the day of diagnosis or the first day of treatment (Day 1) until Day 28 for PCR detection of hMPXV. Clinical data are collected by clinicians and participants (via a self-completion questionnaire) for six months to characterize the signs and symptoms associated with the illness, as well as short- and more long-term outcomes. Discussion The design and prompt implementation of clinical research response is key in addressing emerging outbreaks. MOSAIC began enrolment within two months of the start of the international mpox epidemic. Enrolment has been stopped and the last follow-up visits are expected in January 2024. ICTRP registration EU CT number: 2022-501132-42-00 (22/06/2022)

The course of COVID-19 with the development of “shock organs — lungs and heart”

The article presents a clinical and morphological description of a case involving death upon admission to a hospital, marked by developed sepsis and septic shock caused by the addition of bacterial flora. It also presents a clinical and morphological description of the development of shock organs lungs and heart after infection with SARS-CoV-2.&#x0D; A 38-year-old patient was hospitalized diagnosed with severe coronavirus infection, leading to shock. Complications arising from the underlying disease included bilateral viral interstitial pneumonia. Virological analysis of throat and nose swap samples confirmed SARS-CoV-2 coronavirus RNA. The patients condition, evaluated on the NEWS2 scale, scored 18 points. C-reactive protein levels were measured at 117 mg/l, and procalcitonin level was 9 ng/ml. Despite treatment efforts, the patient did not survive. Sectional examination in the lungs showed focal atelectasis of various sizes, edema with a large number of red blood cells. In the alveoli, there are fibrin threads and hyaline membranes blood stasis in the microcirculatory bed. In the heart, uneven blood filling in vessels, subendocardial hemorrhages, dystrophic and necrobiotic changes in cardiomyocytes, small foci of necrosis, fragmentation of cardiomyocytes, and intermuscular edema were noted. In the described case, the patient developed an infectious-toxic shock with severe changes in the lungs and heart attributed to a SARS-CoV-2 infection. These changes were intensified because of the addition and activation of bacterial flora due to a violation of the barrier function of the lung epithelium, leading to its complete destruction.

MOSAIC: A cohort study of human mpox virus disease.

Human mpox is a viral disease caused by an Orthopoxvirus, human mpox virus (hMPXV), typically causing fever and a rash. Mpox has historically been endemic to parts of Central and West Africa, with small numbers of imported cases reported elsewhere, but starting May 2022 an unprecedented global outbreak caused by clade IIb hMPXV was reported outside traditionally endemic countries. This prompted the initiation of MOSAIC, a cohort study implemented in Europe and Asia that aims to describe clinical and virologic outcomes of PCR-confirmed hMPXV disease, including those who receive antiviral therapy. The focus of this article, however, is on describing the study protocol itself with implementation process and operational challenges. MOSAIC recruits participants of any age with laboratory-confirmed mpox disease who provide informed consent. Participants enrol in the cohort for a total of six months. Blood, lesion and throat samples are collected at several timepoints from the day of diagnosis or the first day of treatment (Day 1) until Day 28 for PCR detection of hMPXV. Clinical data are collected by clinicians and participants (via a self-completion questionnaire) for six months to characterize the signs and symptoms associated with the illness, as well as short- and more long-term outcomes. The design and prompt implementation of clinical research response is key in addressing emerging outbreaks. MOSAIC began enrolment within two months of the start of the international mpox epidemic. Enrolment has been stopped and the last follow-up visits are expected in January 2024. EU CT number: 2022-501132-42-00 (22/06/2022).

Antibiotic susceptibility and plasmid profiling of selected multi-drug resistant bacteria (M.D.R.B.) isolated from ear, nose and throat (E.N.T.) samples in two different hospitals in Cross River State

Antibiotic susceptibility and plasmid profiling of selected multi-drug resistant bacteria (M.D.R.B.) isolated from ear, nose and throat (E.N.T.) samples in two different hospitals in Cross River State

A-253 Overcoming Pre-Analytical and Analytical Challenges Associated with Home Collected STI Specimens

Abstract Introduction Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are common sexually transmitted infections (STIs) that are often asymptomatic, delaying diagnosis and treatment which can cause health consequences and increased transmission. The CDC suggests that self-collected (SC) samples (urine; vaginal, rectal, oropharyngeal swabs) are reasonable alternatives to provider-collected (PC) samples. However, only urine and vaginal swabs are commercially offered for within-clinic self-collection leaving a gap for (1)detecting extra-genital infections (common among LGBTQ+ community) and (2)improving access by allowing for at-home self-collection. The objective of this study was to elucidate analytical and pre-analytical variables associated with at-home SC STI testing with the intention of improving inclusion and access to sexual healthcare. Methods Paired PC/SC rectal (n = 164) and throat (n = 159) swabs were compared for CT/NG detection; reproducibly equivocal results (n = 3) were considered positive. Limit of detection (LoD) for CT/NG was performed by serial dilution to determine a concentration at the point of failure below which detection becomes unreliable (n = 20). Concentrations of 2–10× the LoD were used in subsequent experiments. Interference testing was performed to determine if hand contaminants (1% v/v) would impact assay performance (n = 5/contaminant). To evaluate shipping stability, samples were challenged using winter or summer simulation with temperature cycling designed to mimic extreme seasonal fluctuations. Additional experiments were performed on urine samples to evaluate the impact of underfilling/overfilling or removing the transport medium from the sample tube. CT/NG detection was performed using the Hologic Aptima Combo 2 Nucleic Acid Amplification Assay. Results Relative to provider collected samples, rectal swabs demonstrated a positive agreement of 95.5% for CT (n = 22 (13.4%) positive PC) and 100% for NG (n = 9 (5.5%) positive PC) with an overall agreement of 97.5% for CT and 98.1% for NG. Throat samples demonstrated a positive agreement of 100% for both CT and NG (CT: n = 2 (1.3%) positive PC; NG: n = 11 (6.9%) positive PC) with an overall agreement of 100% for CT and 96.8% for NG. Although there was one false negative rectal SC relative to PC, almost all swab/organism combinations had positive results by SC that were negative by PC: 3+ SC for rectal CT; 3+ SC for rectal NG; 5+ SC for throat NG. LoDs were 0.03–0.06 IFU/mL for CT and 0.06–0.5 CFU/mL for GC using urine or vaginal swabs. Hand contaminants did not interfere with CT/NG detection, and samples demonstrated ≥ 95% agreement after winter and summer shipping stability challenges. Urine results were unaffected by underfilling (≥0.5 mL urine), overfilling (≤4.5 mL urine), or removal of transport medium (≥0.5 mL buffer volume). Conclusions Self-collection of extra-genital swabs for CT/NG detection may offer better sensitivity than physician collected samples without compromising the analytical prowess of the assay. Home collected STI specimens are a viable option for improving access to STI screening and offer a non-stigmatizing approach to sexual health.

The Diagnostic Performance of Various Clinical Specimens for the Detection of COVID-19: A Meta-Analysis of RT-PCR Studies.

The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a systematic literature review process. A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to November 2022. A snowball search on Google, Google Scholar, Research Gate, and MedRxiv, as well as bibliographic research, was performed to identify any other relevant articles. Observational studies that assessed the clinical usefulness of the RT-PCR technique in different human samples for the detection or screening of COVID-19 among patients or patient samples were considered for this review. The primary outcomes considered were sensitivity and specificity, while parameters such as positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient were considered secondary outcomes. A total of 85 studies out of 10,213 non-duplicate records were included for the systematic review, of which 69 articles were considered for the meta-analysis. The meta-analysis indicated better pooled sensitivity with the nasopharyngeal swab (NPS) than saliva (91.06% vs. 76.70%) and was comparable with the combined NPS/oropharyngeal swab (OPS; 92%). Nevertheless, specificity was observed to be better with saliva (98.27%) than the combined NPS/OPS (98.08%) and NPS (95.57%). The other parameters were comparable among different samples. The respiratory samples and throat samples showed a promising result relative to other specimens. The sensitivity and specificity of samples such as nasopharyngeal swabs, saliva, combined nasopharyngeal/oropharyngeal, respiratory, sputum, broncho aspirate, throat swab, gargle, serum, and the mixed sample were found to be 91.06%, 76.70%, 92.00%, 99.44%, 86%, 96%, 94.4%, 95.3%, 73.63%, and above 98; and 95.57%, 98.27%, 98.08%, 100%, 37%, 100%, 100%, 97.6%, and above 97, respectively. NPS was observed to have relatively better sensitivity, but not specificity when compared with other clinical specimens. Head-to-head comparisons between the different samples and the time of sample collection are warranted to strengthen this evidence.

MOSAIC: A cohort study of human mpox virus disease

Background: Human mpox is a viral disease caused by an Orthopoxvirus, human mpox virus (hMPXV), typically causing fever and a rash. Mpox has historically been endemic to parts of Central and West Africa, with small numbers of imported cases reported elsewhere, but starting May 2022 an unprecedented global outbreak caused by clade IIb hMPXV was reported outside traditionally endemic countries. This prompted the initiation of MOSAIC, a cohort study implemented in Europe and Asia that aims to describe clinical and virologic outcomes of PCR-confirmed hMPXV disease, including those who receive antiviral therapy. The study is ongoing. Methods: MOSAIC recruits participants of any age with laboratory-confirmed mpox disease who provide informed consent. Participants enrol in the cohort for a total of six months. Blood, lesion and throat samples are collected at several timepoints from the day of diagnosis or the first day of treatment (Day 1) until Day 28 for PCR detection of hMPXV. Clinical data are collected by clinicians and participants (via a self-completion questionnaire) for six months to characterize the signs and symptoms associated with the illness, as well as short- and more long-term outcomes. Discussion: The design and prompt implementation of clinical research response is key in addressing emerging outbreaks. MOSAIC began enrolment within two months of the start of the international mpox epidemic. While the number of cases is now low, the study remains open for inclusion. ICTRP registration: EU CT number: 2022-501132-42-00 (22/06/2022)

Surveillance of Vermont wildlife in 2021–2022 reveals no detected SARS-CoV-2 viral RNA

Previous studies have documented natural infections of SARS-CoV-2 in various domestic and wild animals. More recently, studies have been published noting the susceptibility of members of the Cervidae family, and infections in both wild and captive cervid populations. In this study, we investigated the presence of SARS-CoV-2 in mammalian wildlife within the state of Vermont. 739 nasal or throat samples were collected from wildlife throughout the state during the 2021 and 2022 harvest season. Data was collected from red and gray foxes (Vulpes vulples and Urocyon cineroargentus, respectively), fishers (Martes pennati), river otters (Lutra canadensis), coyotes (Canis lantrans), bobcats (Lynx rufus rufus), black bears (Ursus americanus), and white-tailed deer (Odocoileus virginianus). Samples were tested for the presence of SARS-CoV-2 via quantitative RT-qPCR using the CDC N1/N2 primer set and/or the WHO-E gene primer set. Surprisingly, we initially detected a number of N1 and/or N2 positive samples with high cycle threshold values, though after conducting environmental swabbing of the laboratory and verifying with a second independent primer set (WHO-E) and PCR without reverse transcriptase, we showed that these were false positives due to plasmid contamination from a construct expressing the N gene in the general laboratory environment. Our final results indicate that no sampled wildlife were positive for SARS-CoV-2 RNA, and highlight the importance of physically separate locations for the processing of samples for surveillance and experiments that require the use of plasmid DNA containing the target RNA sequence. These negative findings are surprising, given that most published North America studies have found SARS-CoV-2 within their deer populations. The absence of SARS-CoV-2 RNA in populations sampled here may provide insights in to the various environmental and anthropogenic factors that reduce spillover and spread in North American’s wildlife populations.

Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan, a tropical island of China

The risk of emerging infectious diseases (EID) is increasing globally. More than 60% of EIDs worldwide are caused by animal-borne pathogens. This study aimed to characterize the virome, analyze the phylogenetic evolution, and determine the diversity of rodent-borne viruses in Hainan Province, China. We collected 682 anal and throat samples from rodents, combined them into 28 pools according to their species and location, and processed them for next-generation sequencing and bioinformatics analysis. The diverse viral contigs closely related to mammals were assigned to 22 viral families. Molecular clues of the important rodent-borne viruses were further identified by polymerase chain reaction for phylogenetic analysis and annotation of genetic characteristics such as arenavirus, coronavirus, astrovirus, pestivirus, parvovirus, and papillomavirus. We identified pestivirus and bocavirus in Leopoldoms edwardsi from Huangjinjiaoling, and bocavirus in Rattus andamanensis from the national nature reserves of Bangxi with low amino acid identity to known pathogens are proposed as the novel species, and their rodent hosts have not been previously reported to carry these viruses. These results expand our knowledge of viral classification and host range and suggest that there are highly diverse, undiscovered viruses that have evolved independently in their unique wildlife hosts in inaccessible areas.

To investigate the anti-bacterial activity of crude extracts of Mintha pipertia and Allium sativum against throat infection causing bacteria streptococci collected from various diagnostic laboratories and hospitals of Mingora swat

Streptococcus (S) pyogenes one of the major Gram-positive pathogens responsible for upper respiratory tract and nosocomial infections. This is a Gram Positive, aerobic, no motile, and non-spore-forming ubiquitous bacteria. The present study was conducted to evaluate the in vitro antibacterial activity of ethanol and aqueous extract of peppermint and garlic against 29 isolates of S. pyogenes recovered from the throat sample of patientsin Swat KPK-Pakistan. These isolates were purified to identify the target bacterial isolates by gram staining and biochemical tests. The Agar dilution and well method was applied for the antibacterial activity of garlic and peppermint extracts. All of the subject isolates were exposed to different concentrations of peppermint. MIC of aqua extract of peppermint was 250µL/mL and ethanol extract was 100µL/mL. The zone size was 29mm and 36mm respectively. So the ethanol extract of peppermint was found to be more effective as compared to the aqueous extract. On the other hand, Garlic has shown equal effectiveness of water and ethanol extraction with MIC value of all is 50µL/mL and zone of inhibition was 38mm. Ciprofloxacin antibiotic disk was used as reference standard.

Absence of association between persistent skin lesion and virological replication in severe disseminated monkeypox infection in solid organ transplant recipient

The Monkeypox (mpox) virus outbreak has been controlled worldwide. We report the case of a combined pancreas-kidney transplant recipient who presented a severe and prolonged cutaneous infection with onset of 3 successive rashes while receiving tecovirimat therapy. During follow-up, skin lesions, blood and throat samples were collected. Viral culture and mpox PCR were performed. No positive viral culture was obtained from blood and throat. The lowest mpox CT-values were obtained early after onset of skin lesions and were more likely to be associated with positive viral cultures. Furthermore, we observed persistent skin lesions up to 3 months. On these persistent lesions, mpox PCR positives were obtained but were not associated with positive viral culture after 23 days. In this immunocompromised host, who was receiving tecovirimat, in accordance with existing recommendations a 21-day isolation period appeared to be adapted. That said, isolation should not be systematically extended if complete healing of skin lesions has not been achieved.