The Drosophila Dbf4 ortholog Chiffon forms a complex with Gcn5 that is necessary for histone acetylation and viability.

Metazoans contain two homologs of the Gcn5-binding protein Ada2, Ada2a and Ada2b, which nucleate formation of the ATAC and SAGA complexes, respectively. In Drosophila melanogaster, there are two splice isoforms of Ada2b: Ada2b-PA and Ada2b-PB. Here, we show that only the Ada2b-PB isoform is in SAGA; in contrast, Ada2b-PA associates with Gcn5, Ada3, Sgf29 and Chiffon, forming the Chiffon histone acetyltransferase (CHAT) complex. Chiffon is the Drosophila ortholog of Dbf4, which binds and activates the cell cycle kinase Cdc7 to initiate DNA replication. In flies, Chiffon and Cdc7 are required in ovary follicle cells for gene amplification, a specialized form of DNA re-replication. Although chiffon was previously reported to be dispensable for viability, here, we find that Chiffon is required for both histone acetylation and viability in flies. Surprisingly, we show that chiffon is a dicistronic gene that encodes distinct Cdc7- and CHAT-binding polypeptides. Although the Cdc7-binding domain of Chiffon is not required for viability in flies, the CHAT-binding domain is essential for viability, but is not required for gene amplification, arguing against a role in DNA replication.

Serum IP-10 and IL-7 levels are associated with disease severity of coronavirus disease 2019.

We quantified the serum levels of 34 cytokines/chemokines in 30 patients with SARS-CoV-2 infection. Elevated levels of IP-10 and IL-7 were detected in the acute and convalescent stages of the infection and were highly associated with disease severity.

Environmental and Aerosolized Severe Acute Respiratory Syndrome Coronavirus 2 Among Hospitalized Coronavirus Disease 2019 Patients.

During April and May 2020, we studied 20 patients hospitalized with coronavirus disease 2019 (COVID-19), their hospital rooms (fomites and aerosols), and their close contacts for molecular and culture evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Among >400 samples, we found molecular evidence of virus in most sample types, especially the nasopharyngeal (NP), saliva, and fecal samples, but the prevalence of molecular positivity among fomites and aerosols was low. The agreement between NP swab and saliva positivity was high (89.5%; κ = 0.79). Two NP swabs collected from patients on days 1 and 7 post-symptom onset had evidence of infectious virus (2 passages over 14 days in Vero E6 cells). In summary, the low molecular prevalence and lack of viable SARS-CoV-2 virus in fomites and air samples implied low nosocomial risk of SARS-CoV-2 transmission through inanimate objects or aerosols.

Transmission Potential of Asymptomatic and Paucisymptomatic Severe Acute Respiratory Syndrome Coronavirus 2 Infections: A 3-Family Cluster Study in China.

Data concerning the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in asymptomatic and paucisymptomatic patients are lacking. We report a 3-family cluster of infections involving asymptomatic and paucisymptomatic transmission. Eight of 15 (53%) members from 3 families were confirmed with SARS-CoV-2 infection. Of 8 patients, 3 were asymptomatic and 1 was paucisymptomatic. An asymptomatic mother transmitted the virus to her son, and a paucisymptomatic father transmitted the virus to his 3-month-old daughter. SARS-CoV-2 was detected in the environment of 1 household. The complete genomes of SARS-CoV-2 from the patients were > 99.9% identical and were clustered with other SARS-CoV-2 sequences reported from China and other countries.

Detection of Severe Acute Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms.

We investigated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) environmental contamination in 2 rooms of a quarantine hotel after 2 presymptomatic persons who stayed there were laboratory-confirmed as having coronavirus disease. We detected SARS-CoV-2 RNA on 8 (36%) of 22 surfaces, as well as on the pillow cover, sheet, and duvet cover.

Evidence for Cross-species Influenza A Virus Transmission Within Swine Farms, China: A One Health, Prospective Cohort Study.

Background: Our understanding of influenza A virus transmission between humans and pigs is limited. Methods: Beginning in 2015, we used a One Health approach and serial sampling to prospectively study 299 swine workers and 100 controls, their 9000 pigs, and 6 pig farm environments in China for influenza A viruses (IAVs) using molecular, culture, and immunological techniques. Study participants were closely monitored for influenza-like illness (ILI) events. Results: Upon enrollment, swine workers had higher serum neutralizing antibody titers against swine H1N1 and higher nasal wash total immunoglobulin A (IgA) and specific IgA titers against swine H1N1 and H3N2 viruses. Over a period of 12 months, IAVs were detected by quantitative reverse-transcription polymerase chain reaction in 46 of 396 (11.6%) environmental swabs, 235 of 3300 (7.1%) pig oral secretion, 23 of 396 (5.8%) water, 20 of 396 (5.1%) aerosol, and 19 of 396 (4.8%) fecal-slurry specimens. Five of 32 (15.6%) participants with ILI events had nasopharyngeal swab specimens that were positive for IAV, and 17 (53.1%) demonstrated 4-fold rises in neutralization titers against a swine virus. Reassorted Eurasian avian-lineage H1N1, A(H1N1)pdm09-like, and swine-lineage H3N2 viruses were identified in pig farms. The A(H1N1)pdm09-like H1N1 viruses identified in swine were nearly genetically identical to the human H1N1 viruses isolated from the participants with ILI. Conclusions: There was considerable evidence of A(H1N1)pdm09-like, swine-lineage H1N1, and swine-lineage H3N2 viruses circulating, likely reassorting, and likely crossing species within the pig farms. These data suggest that stronger surveillance for novel influenza virus emergence within swine farms is imperative.

Bioaerosol Sampling in Modern Agriculture: A Novel Approach for Emerging Pathogen Surveillance?

BACKGROUND: Modern agricultural practices create environmental conditions conducive to the emergence of novel pathogens. Current surveillance efforts to assess the burden of emerging pathogens in animal production facilities in China are sparse. In Guangdong Province pig farms, we compared bioaerosol surveillance for influenza A virus to surveillance in oral pig secretions and environmental swab specimens. METHODS: During the 2014 summer and fall/winter seasons, we used 3 sampling techniques to study 5 swine farms weekly for influenza A virus. Samples were molecularly tested for influenza A virus, and positive specimens were further characterized with culture. Risk factors for influenza A virus positivity for each sample type were assessed. RESULTS: Seventy-one of 354 samples (20.1%) were positive for influenza A virus RNA by real-time reverse-transcription polymerase chain reaction analysis. Influenza A virus positivity in bioaerosol samples was a statistically significant predictor for influenza A virus positivity in pig oral secretion and environmental swab samples. Temperature of <20°C was a significant predictor of influenza A virus positivity in bioaerosol samples. DISCUSSIONS: Climatic factors and routine animal husbandry practices may increase the risk of human exposure to aerosolized influenza A viruses in swine farms. Data suggest that bioaerosol sampling in pig barns may be a noninvasive and efficient means to conduct surveillance for novel influenza viruses.

A Systematic Review and Meta-Analysis of the Seroprevalence of Influenza A(H9N2) Infection Among Humans.

INTRODUCTION: Given that influenza A(H9N2) is recognized as a pandemic threat, we evaluated the overall burden of influenza A(H9N2) infections among avian-exposed human populations. METHODS: We performed a systematic search of PubMed, AGRICOLA, and CAB Abstracts databases for literature published during 1997-2013. Studies reporting serological evidence of human influenza A(H9N2) infection among avian-exposed populations were included. We used a World Health Organization (WHO)-recommended case definition for serological evidence of infection based on results of hemagglutination inhibition (HI) and microneutralization (MN) assays. We calculated overall seroprevalence through a random effects meta-analysis model. RESULTS: Seroprevalence data reported by the studies ranged from 1% to 43% (median, 9%) by HI, which was not significantly different from the seroprevalence estimated through the WHO-recommended case definition (median, 1.3%; range, 0.5%-42.6%). Reported seroprevalence by MN ranged from 0.6% to 9% (median, 2.7%), which was greater than the seroprevalence estimated through the WHO-recommended case definition (median, 0.3%; range, 0.1%-1.4%). CONCLUSIONS: A small proportion of avian-exposed humans had evidence of influenza A(H9N2) infection. As the virus has a near global distribution in poultry, it seems likely that present surveillance efforts are missing mild or asymptomatic infections among avian-exposed persons. It seems prudent to closely monitor avian-exposed populations for influenza A(H9N2) infection to provide prepandemic warnings.

Equine influenza A(H3N8) virus isolated from Bactrian camel, Mongolia.

Because little is known about the ecology of influenza viruses in camels, 460 nasal swab specimens were collected from healthy (no overt illness) Bactrian camels in Mongolia during 2012. One specimen was positive for influenza A virus (A/camel/Mongolia/335/2012[H3N8]), which is phylogenetically related to equine influenza A(H3N8) viruses and probably represents natural horse-to-camel transmission.

Challenges and opportunities of strain diversity in gut microbiome research.

Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.

Assessing the nonlinear association of environmental factors with antibiotic resistance genes (ARGs) in the Yangtze River Mouth, China.

The emergence of antibacterial resistance (ABR) is an urgent and complex public health challenge worldwide. Antibiotic resistant genes (ARGs) are considered as a new pollutant by the WHO because of their wide distribution and emerging prevalence. The role of environmental factors in developing ARGs in bacterial populations is still poorly understood. Therefore, the relationship between environmental factors and bacteria should be explored to combat ABR and propose more tailored solutions in a specific region. Here, we collected and analyzed surface water samples from Yangtze Delta, China during 2021, and assessed the nonlinear association of environmental factors with ARGs through a sigmoid model. A high abundance of ARGs was detected. Amoxicillin, phosphorus (P), chromium (Cr), manganese (Mn), calcium (Ca), and strontium (Sr) were found to be strongly associated with ARGs and identified as potential key contributors to ARG detection. Our findings suggest that the suppression of ARGs may be achieved by decreasing the concentration of phosphorus in surface water. Additionally, Group 2A light metals (e.g., magnesium and calcium) may be candidates for the development of eco-friendly reagents for controlling antibiotic resistance in the future.

Seeking the mission-minded.

A rural hospital attracts clinicians who want to care for the underserved at home and abroad.

Metagenomic analysis of endemic viruses in oral secretions from Chinese pigs.

BACKGROUND: Pigs are unique reservoirs for virus ecology. Despite the increased use of improved biosecurity measures, pig viruses readily circulate in Chinese swine farms. OBJECTIVES: The main objective of this study was to examine archived swine oral secretion samples with a panel of pan-species viral assays such that we might better describe the viral ecology of swine endemic viruses in Chinese farms. METHODOLOGY: Two hundred (n = 200) swine oral secretion samples, collected during 2015 and 2016 from healthy pigs on six swine farms in two provinces in China, were screened with molecular pan-species assays for coronaviruses (CoVs), adenoviruses (AdVs), enteroviruses (EVs), and paramyxoviruses (PMV). Samples were also screened for porcine circovirus (PCV) 3, porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV). RESULTS: Among 200 swine oral secretion samples, 152 (76.0%) were found to have at least one viral detection. Thirty-four samples (17%) were positive for more than one virus, including 24 (70.5%) with dual detection and 10 (29.5%) with triple detection. Seventy-eight (39.0%) samples were positive for porcine AdVs, 22 (11.0%) were positive for porcine CoVs, 21 (10.5%) were positive for IAVs, 13 (6.5%) were positive for PCV, 7 (3.5%) were positive for PMV, six (3.0%) were positive for PRRSV and five (2.5%) were positive for porcine EV. CONCLUSION: Our findings underscore the high prevalence of numerous viruses among production pigs in China and highlight the need for routine, periodic surveillance for novel virus emergence with the goal of protecting pigs.

Environmental bioaerosol surveillance as an early warning system for pathogen detection in North Carolina swine farms: A pilot study.

Disease outbreaks can readily threaten swine production operations sometimes resulting in large economic losses. Pathogen surveillance in swine farms can be an effective approach for the early identification of new disease threats and the mitigation of transmission before broad dissemination among a herd occurs. Non-invasive environmental bioaerosol sampling could be an effective and affordable approach for conducting routine surveillance in farms, providing an additional tool for farmers to protect their animals and themselves from new disease threats. In this pilot study, we implemented a non-invasive, prospective bioaerosol sampling strategy in a swine farm located in the United States to detect economically important swine pathogens. Farm personnel collected air samples from two swine barns for 23 weeks between July and December 2017. Samples were then tested within 24 hr of collection by molecular techniques for a number of economically important swine pathogens. Of the 86 bioaerosol samples collected, 4 (4.7%) were positive for influenza A, 1 (1.2%) was positive for influenza D, 13 (15.1%) were positive for PCV2, and 13 (15.1%) were positive for PCV3. Overall, this pilot study showed that our bioaerosol surveillance strategy was feasible and able to generate data that could be quickly disseminated back to the farm stakeholders (within 24 hr). We were also able to identify PCV2, PCV3 and influenza A virus in air samples as clinical disease became apparent in the pigs, strongly suggesting that bioaerosol sampling can be used as an effective non-invasive surveillance approach for the detection of multiple pathogens in this and likely other animal production environments.

Genetic diversity of Anaplasma and Ehrlichia bacteria found in Dermacentor and Ixodes ticks in Mongolia.

Anaplasma and Ehrlichia are tick-borne bacterial pathogens that cause human granulocytic anaplasmosis, human monocytic ehrlichiosis, and are severe threats to livestock economies like Mongolia. In this study, ticks were collected, identified, and pooled (n = 299) from three distinct environments across central Mongolia. Each pool was initially tested for Anaplasma/Ehrlichia using a 16S rRNA PCR assay that detects both genera, and specific PCR testing was done to identify those positive samples. Maximum likelihood estimation (MLE) of infection rates of ticks collected from the environment in Selenge aimag (province) found infection rates of Ixodes persulcatus ticks to be 2.0% (95% CI: 0.7, 4.3%) for A. phagocytophilum and 0.8% (95% CI: 0.1, 2.5%) for both nonspecific Ehrlichia and Anaplasma. Ehrlichia muris was only detected in I. persulcatus ticks collected from the Selenge aimag, where the MLE was 1.2% (95% CI: 0.1, 2.5%). The calculated MLE infection rate of Anaplasma spp. in questing Dermacentor nuttalli ticks ranged from 1.9% (95% CI: 1.1, 9.1%) in the Tov aimag to 2.3% (95% CI: 1.3, 10.8%) in the Selenge aimag. However, when examining MLE in ticks removed from livestock, estimates increase substantially, ranging from 7.8% (95% CI: 4.2, 13.3%) in Dornogovi to 22.5% (95% CI: 14.3, 34.3%) in Selenge, suggesting that livestock play a key role in disease maintenance. Considering the collective economic losses that can result from these pathogens and the potential for illness in nomadic herdsmen, these results highlight the need for enhanced TBD surveillance and prevention measures within Mongolia.

Discrepancies between self-reported tick bites and evidence of tick-borne disease exposure among nomadic Mongolian herders.

Twenty-six per cent of Mongolians live pastoral lifestyles, increasing their likelihood of exposure to ticks and placing them at a higher risk for contracting tick-borne diseases (TBDs). Anaplasma spp. and Rickettsia spp. have been identified in ticks, livestock and humans in Mongolia, but no known qualitative research has been conducted investigating the association between nomadic herder characteristics, tick bite history and exposure to TBDs. To better understand the association between self-reported tick bites and symptoms versus actual exposure to TBDs, this study paired serological data with 335 surveys administered to Mongolian herders, ages 12-69, from 2014 to 2015. Logistic regression results identified no significant associations between reported tick bites or symptoms with serological evidence of Anaplasma spp. and Rickettsia spp. controlling for age, gender and aimag. Among the 335 respondents who were seropositive to either Anaplasma spp. or Rickettsia spp., 32.9% self-reported experiencing abnormal symptoms such as redness, inflammation, headache, arthritis or fever after being bitten. Alternatively, 17.3% (58/335) of individuals reported experiencing symptoms following a tick bite in instances where serological results indicated no exposure to Anaplasma spp. or Rickettsia spp. Results also identified inconsistencies in reporting and seroprevalence among different age groups, with children having the highest reporting and treatment seeking rates but low levels of exposure in comparison with other groups. While survey results showed that individuals were aware of peak tick seasons and tick species that inhabit specific areas, 58% of heads of households (49/84) were unaware that ticks can cause disease in livestock or dogs. This study suggests that herders are an at-risk population in Mongolia with gaps in awareness of TBD risk. Increased surveillance paired with focused outreach to prevent TBDs targeted to the herder population is encouraged.

Prevalence of Respiratory Polyomaviruses Among Pediatric Patients With Respiratory Symptoms in Singapore.

Background: Although WU polyomavirus (WU) and KI polyomavirus (KI) have been demonstrated to infect the human respiratory tract, it remains unclear if WU or KI cause human disease. We sought to further investigate the relationship between WU and KI infection and respiratory disease in a pediatric population with respiratory symptoms in Singapore. Methods: We conducted a cross-sectional study of pediatric patients with respiratory symptoms in a Singaporean pediatrics hospital. Upon consent, residual respiratory samples from pediatric inpatients, previously screened for common respiratory viruses, were collected and further screened for WU and KI using qPCR. The amplicons of positive samples were sequenced for confirmation. The severity of a patient's illness was assessed by chart review post-discharge looking for clinical markers of respiratory status such as presenting symptoms, diagnoses, and interventions. Results: From December 2016 to April 2017, 201 patients with residual respiratory samples were enrolled in the study. The average age of all participants recruited was 45 months. WU and KI were detected in 13% (26/201) and 3% (6/201) of patients, respectively. Conducting bivariate and multivariate modeling, patients with WU or KI positivity were not at increased risk of SARI, need for additional oxygen, intravenous fluids, and did not receive additional oral antibiotics or bronchodilators during admission. In contrast, patients with RSV detections were at increased risk of requiring supplemental oxygen during hospital admission. Conclusion: While limited in sample size, our pilot study data do not support the hypothesis that molecular evidence of WU or KI was associated with increased morbidity among a sample of general, pediatric patients with respiratory illness in Singapore.

Evidence for transovarial transmission of tick-borne rickettsiae circulating in Northern Mongolia.

Transstadial transmission of tick-borne rickettsiae has been well documented. Few studies, however, have evaluated the role of transovarial transmission of tick-borne rickettsiae, particularly in nature within the host-vector ecosystem. This cross-sectional study aimed to understand the role of transovarial transmission of tick-borne rickettsiae among feeding ticks at different life stages. Tick eggs laid by engorged wild-caught adult female ticks were pooled and tested for Rickettsia spp. and Anaplasma/Ehrlichia spp. using molecular techniques, while adult fed ticks were tested individually. Additionally, larval and nymphal ticks were collected in the wild from small mammals, pooled and tested for Rickettsia spp. and Anaplasma/Ehrlichia spp. There were 38 fed adult and 618 larvae/nymphs (60 pools total) Dermacentor spp. ticks collected from livestock and rodents. All individual adult ticks and tick pools were positive for Rickettsia spp. While none of the larvae/nymphs were positive for Anaplasma/Ehrlichia spp., two adult fed ticks were positive. Rickettsia spp. DNA was detected in 91% (30/33) of the pooled eggs tested, and one pool of eggs tested positive for Anaplasma/Ehrlichia spp. Sequencing data revealed Rickettsia spp. shared ≥99% identity with R. raoultii ompA. Anaplasma/Ehrlichia spp. shared ≥89% identity with A. ovis 16S ribosomal RNA. This study identified potential transovarial transmission of Rickettsia spp. and Anaplasma spp. among D. nuttalli ticks. Additional studies are needed to further assess the proportion of transovarial transmission occurring in nature to better understand the burden and disease ecology of tick-borne rickettsiae in Mongolia.

Adenovirus Type 21 Outbreak Among Lung Transplant Patients at a Large Tertiary Care Hospital.

Here we summarize an April 2016, 7-patient cluster of human adenovirus (HAdV) infections in a cardiothoracic surgery intensive care unit. We show that the patients were infected with a single HAdV21b type. Rapid HAdV typing diagnostics and effective antiviral interventions are needed for immunocompromised patients suffering from HAdV infections.