No Evidence for Recent Selection at FOXP2 among Diverse Human Populations.

FOXP2, initially identified for its role in human speech, contains two nonsynonymous substitutions derived in the human lineage. Evidence for a recent selective sweep in Homo sapiens, however, is at odds with the presence of these substitutions in archaic hominins. Here, we comprehensively reanalyze FOXP2 in hundreds of globally distributed genomes to test for recent selection. We do not find evidence of recent positive or balancing selection at FOXP2. Instead, the original signal appears to have been due to sample composition. Our tests do identify an intronic region that is enriched for highly conserved sites that are polymorphic among humans, compatible with a loss of function in humans. This region is lowly expressed in relevant tissue types that were tested via RNA-seq in human prefrontal cortex and RT-PCR in immortalized human brain cells. Our results represent a substantial revision to the adaptive history of FOXP2, a gene regarded as vital to human evolution.

Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons.

Direct lineage reprogramming is a promising approach for human disease modeling and regenerative medicine, with poorly understood mechanisms. Here, we reveal a hierarchical mechanism in the direct conversion of fibroblasts into induced neuronal (iN) cells mediated by the transcription factors Ascl1, Brn2, and Myt1l. Ascl1 acts as an "on-target" pioneer factor by immediately occupying most cognate genomic sites in fibroblasts. In contrast, Brn2 and Myt1l do not access fibroblast chromatin productively on their own; instead, Ascl1 recruits Brn2 to Ascl1 sites genome wide. A unique trivalent chromatin signature in the host cells predicts the permissiveness for Ascl1 pioneering activity among different cell types. Finally, we identified Zfp238 as a key Ascl1 target gene that can partially substitute for Ascl1 during iN cell reprogramming. Thus, a precise match between pioneer factors and the chromatin context at key target genes is determinative for transdifferentiation to neurons and likely other cell types.

Differentiation Drives Widespread Rewiring of the Neural Stem Cell Chaperone Network.

Neural stem and progenitor cells (NSPCs) are critical for continued cellular replacement in the adult brain. Lifelong maintenance of a functional NSPC pool necessitates stringent mechanisms to preserve a pristine proteome. We find that the NSPC chaperone network robustly maintains misfolded protein solubility and stress resilience through high levels of the ATP-dependent chaperonin TRiC/CCT. Strikingly, NSPC differentiation rewires the cellular chaperone network, reducing TRiC/CCT levels and inducing those of the ATP-independent small heat shock proteins (sHSPs). This switches the proteostasis strategy in neural progeny cells to promote sequestration of misfolded proteins into protective inclusions. The chaperone network of NSPCs is more effective than that of differentiated cells, leading to improved management of proteotoxic stress and amyloidogenic proteins. However, NSPC proteostasis is impaired by brain aging. The less efficient chaperone network of differentiated neural progeny may contribute to their enhanced susceptibility to neurodegenerative diseases characterized by aberrant protein misfolding and aggregation.

Experimental infection of pigs and ferrets with "pre-pandemic," human-adapted, and swine-adapted variants of the H1N1pdm09 influenza A virus reveals significant differences in viral dynamics and pathological manifestations.

Influenza A viruses are RNA viruses that cause epidemics in humans and are enzootic in the pig population globally. In 2009, pig-to-human transmission of a reassortant H1N1 virus (H1N1pdm09) caused the first influenza pandemic of the 21st century. This study investigated the infection dynamics, pathogenesis, and lesions in pigs and ferrets inoculated with natural isolates of swine-adapted, human-adapted, and "pre-pandemic" H1N1pdm09 viruses. Additionally, the direct-contact and aerosol transmission properties of the three H1N1pdm09 isolates were assessed in ferrets. In pigs, inoculated ferrets, and ferrets infected by direct contact with inoculated ferrets, the pre-pandemic H1N1pdm09 virus induced an intermediary viral load, caused the most severe lesions, and had the highest clinical impact. The swine-adapted H1N1pdm09 virus induced the highest viral load, caused intermediary lesions, and had the least clinical impact in pigs. The human-adapted H1N1pdm09 virus induced the highest viral load, caused the mildest lesions, and had the least clinical impact in ferrets infected by direct contact. The discrepancy between viral load and clinical impact presumably reflects the importance of viral host adaptation. Interestingly, the swine-adapted H1N1pdm09 virus was transmitted by aerosols to two-thirds of the ferrets. Further work is needed to assess the risk of human-to-human aerosol transmission of swine-adapted H1N1pdm09 viruses.

Which smokers enroll in a hospital based smoking cessation trial? Survey of smoking related behaviors, quit attempts, and motivation to quit.

BACKGROUND: Understanding smoking behaviors in hospital patients who smoke may improve inpatient cessation treatments. This study aimed to describe smoking-related behaviors, past-quit attempts, and self-reported difficulties experienced in quitting among those who enrolled in a smoking cessation trial of varenicline. METHODS: Baseline data were obtained from adult hospitalized smokers (average ≥ 10 cigarettes/day in 4-weeks prior to hospitalization) who enrolled in a randomized, placebo-controlled trial of varenicline ± nicotine lozenges at five Australian public hospitals. A logistic regression model tested the association between participant characteristics and quitting in the previous 12 months. RESULTS: Participants' (n = 320; 57% male, 52.5 ± 12.1 years old) motivation and confidence in quitting were high. A total of 120 participants (37.5%) had attempted quitting in the previous 12-months. Prior hospitalization (P = .008) and employment status (P = .015) were significantly associated with past quit attempts. No statistically significant differences were noted in the reason for hospitalization or the level of nicotine dependence between participants who attempted quitting in the previous 12 months and their counterparts. Smoking cessation pharmacotherapy was used by 55% of those attempting to quit; nicotine replacement therapy (65.2%) and varenicline (16.7%) most common. Stress or anxiety, urges to smoke and a lack of motivation were the difficulties experienced in past quit attempts. CONCLUSIONS: Those who had a prior hospitalization and were unemployed had significantly greater odds of reporting past quit attempts. Further research is needed to investigate the degree of adherence among inpatient smokers with the smoke-free hospital policies and the frequency of NRT provision and uptake on admission.

Offering mailed nicotine replacement therapy and Quitline support before elective surgery: a randomised controlled trial.

OBJECTIVE: To assess whether offering free mailed nicotine replacement therapy (NRT) and telephone counselling to smokers on elective surgery waiting lists increases quitting before surgery. DESIGN, SETTING: Randomised, controlled trial at Frankston Hospital, a public tertiary referral hospital in Melbourne. PARTICIPANTS: Adult smokers added to elective surgery waiting lists for operations at least ten days in the future, 1 April 2019 - 3 April 2020. INTERVENTION: In addition to normal care, intervention participants received a brochure on the risks of low frequency smoking, an offer of Quitline call-back registration, and an offer of mailed NRT according to reported daily smoking: 1-9 cigarettes/day, 2 mg lozenges; 10-15/day, 7-14 mg patches [three weeks] and 2 mg lozenges; > 15/day, 7-21 mg patches [five weeks] and 2 mg lozenges. MAIN OUTCOME MEASURES: Primary outcome: quitting at least 24 hours before surgery, verified by exhaled carbon monoxide testing. SECONDARY OUTCOMES: quitting at least four weeks before surgery, adverse events, and (for those who had quit before surgery) abstinence three months after surgery. RESULTS: Of 748 eligible participants (control, 363; intervention, 385), 516 (69%) had undergone elective surgery when the trial was terminated early (for COVID-19-related reasons) (intervention group, 274; control group, 242). 122 of the 385 intervention participants (32%) had accepted the offer of cessation support. The proportions of intervention participants who quit at least 24 hours before surgery (18% v 9%; odds ratio [OR], 1.97; 95% CI, 1.22-3.15) or at least four weeks before surgery (9% v 4%; OR, 2.20; 95% CI, 1.08-4.50) were larger than for the control group. Three months after surgery, 27 of 58 intervention (47%) and 12 of 25 control participants (48%) who quit before surgery reported not smoking in the preceding seven days. No major adverse events were reported. CONCLUSION: Uptake of free mailed NRT and Quitline support by smokers on elective surgery waiting lists was good, and offering additional support was associated with higher proportions of smokers quitting before surgery. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry, ACTRN12619000032156 (prospective).

FOXO3 directly regulates an autophagy network to functionally regulate proteostasis in adult neural stem cells.

Maintenance of a healthy proteome is essential for cellular homeostasis and loss of proteostasis is associated with tissue dysfunction and neurodegenerative disease. The mechanisms that support proteostasis in healthy cells and how they become defective during aging or in disease states are not fully understood. Here, we investigate the transcriptional programs that are essential for neural stem and progenitor cell (NSPC) function and uncover a program of autophagy genes under the control of the transcription factor FOXO3. Using genomic approaches, we observe that FOXO3 directly binds a network of target genes in adult NSPCs that are involved in autophagy, and find that FOXO3 functionally regulates induction of autophagy in these cells. Interestingly, in the absence of FOXO activity, aggregates accumulate in NSPCs, and this effect is reversed by TOR (target of rapamycin) inhibition. Surprisingly, enhancing FOXO3 causes nucleation of protein aggregates, but does not increase their degradation. The work presented here identifies a genomic network under the direct control of a key transcriptional regulator of aging that is critical for maintaining a healthy mammalian stem cell pool to support lifelong neurogenesis.

The Association of Broadband Internet Access and Telemedicine Utilization in rural Western Tennessee: an observational study.

BACKGROUND: Broadband access has been highlighted as a national policy priority to improve access to care in rural communities. OBJECTIVE: To determine whether broadband internet availability was associated with telemedicine adoption among a rural patient population in western Tennessee. METHODS: Observational study using electronic medical record data from March 13th, 2019 to March 13th, 2021. Multivariable logistic regression incorporating individual-level characteristics with broadband availability, income, educational attainment, and primary care physician supply at the zip code level, and rural status as determined at the county level. SETTING: Single health system in western Tennessee. PARTICIPANTS: Adult patients with one or more in-person or remote encounter in a health system in western Tennessee and residing in western Tennessee between March 13th, 2019 and March 13th, 2021 (N = 54,688). OUTCOME MEASURES: Completion of one or more video encounters in the year following March 13th, 2020 (N = 3199; 7%). Our primary characteristic of interest was the proportion of residents in each zip code with access to the internet meeting the Federal Communications Commission definition of broadband access, adjusting for age, gender, race, income, educational attainment, insurance type, rural status, and primary care provider supply. RESULTS: Patients in a rural western Tennessee health system were predominantly white (79%), residing in rural zip codes (73%) with median household incomes ($52,085) less than state and national averages. Patients residing in a zip code where there is 80 to 100% broadband access compared to 0 to 20% were more likely in the year following March 13th, 2020 to have completed both telemedicine and in-person visits ([OR; 95% CI] 1.57; 1.29, 1.94), completed only telemedicine visits (2.26; 1.71, 2.97), less likely to have only completed in-person visits (0.81; 0.74, 0.89), but no more or less likely to have accessed no care (1.07; 0.97, 1.18). DISCUSSION: The availability of broadband internet was shown to be one of many factors associated with the utilization of telemedicine for a rural, working-class community after March 13th, 2020. CONCLUSIONS: Access to broadband internet is a determinant of access to telemedicine for patients in rural communities and should be a priority for policymakers interested in improving health and access to care for rural patients.

Hospital entrance smoking is reduced by broadcasting recorded antitobacco messages from Australian primary school children over entrance public address system.

ISSUE ADDRESSED: Smoking near hospital entrances occurs frequently despite smoke-free policies, resulting in multiple issues including second-hand smoke exposure (SHS) to vulnerable populations. Primary school children were engaged through their health curriculum to produce antismoking audio recordings for broadcast over a hospital entrance loudspeaker system to determine if this reduced smoking. METHOD: Students produced original recordings against hospital grounds smoking during class workshops, from which a collection (n = 16) was selected. Episodes of entrance smoking and total entrance traffic were recorded using security camera infrastructure over a 5-week period. A computer-controlled entrance loudspeaker played a message which was followed by silence until a new (different) message was played. Intensity of messaging was moderate in week 3 (every 5 minutes), increasing to high in week 4 (3 minutely) and compared to no messages (weeks 1-2 preintervention) and week 5 (postintervention). RESULTS: Smokers presented 316 times, smoking 523 cigarettes over 155 hours of observation (patients 70.6%, visitors 29.4%). SHS exposure was high given 172 others used the entrance/hour. Smoking was highest in the preintervention period (weeks 1-2), median five cigarettes/hr [IQR,3-7 (min = 0, max = 12)], falling to four cigarettes/hr during 5-minutely broadcasts [IQR,2-5 (min = 1, max = 14)] (P = .06), but zero cigarettes/hr during 3-minutely broadcasts [IQR,0-1(min = 0, max = 7)] (P < .0001). Postintervention (no broadcasts), smoking increased from zero to 1 cigarette/hr [IQR,0-3 (min = 0, max = 5)]; (P = .052). Nonsmoker movements did not change significantly between each period. CONCLUSION: Intensive (3 minutely) broadcasting of short antismoking messages significantly reduced hospital entrance smoking. SO WHAT?: Health services can positively interact with the health curriculum of primary schools against tobacco use while developing low-cost strategies to effectively deter entrance smoking.

Society for Perioperative Assessment and Quality Improvement (SPAQI) Consensus Statement on Perioperative Smoking Cessation.

Smokers are at increased risk for surgical complications. Despite the known benefits of smoking cessation, many perioperative health care providers do not routinely provide smoking cessation interventions. The variation in delivery of perioperative smoking cessation interventions may be due to limited high-level evidence for whether smoking cessation interventions used in the general population are effective and feasible in the surgical population, as well as the challenges and barriers to implementation of interventions. Yet smoking is a potentially modifiable risk factor for improving short- and long-term patient outcomes. The purpose of the Society for Perioperative Assessment and Quality Improvement (SPAQI) Consensus Statement on Perioperative Smoking Cessation is to present recommendations based on current scientific evidence in surgical patients. These statements address questions regarding the timing and intensity of interventions, roles of perioperative health care providers, and behavioral and pharmacological interventions. Barriers and strategies to overcome challenges surrounding implementation of interventions and future areas of research are identified. These statements are based on the current state of knowledge and its interpretation by a multidisciplinary group of experts at the time of publication.

FoxO3 regulates neuronal reprogramming of cells from postnatal and aging mice.

We and others have shown that embryonic and neonatal fibroblasts can be directly converted into induced neuronal (iN) cells with mature functional properties. Reprogramming of fibroblasts from adult and aged mice, however, has not yet been explored in detail. The ability to generate fully functional iN cells from aged organisms will be particularly important for in vitro modeling of diseases of old age. Here, we demonstrate production of functional iN cells from fibroblasts that were derived from mice close to the end of their lifespan. iN cells from aged mice had apparently normal active and passive neuronal membrane properties and formed abundant synaptic connections. The reprogramming efficiency gradually decreased with fibroblasts derived from embryonic and neonatal mice, but remained similar for fibroblasts from postnatal mice of all ages. Strikingly, overexpression of a transcription factor, forkhead box O3 (FoxO3), which is implicated in aging, blocked iN cell conversion of embryonic fibroblasts, whereas knockout or knockdown of FoxO3 increased the reprogramming efficiency of adult-derived but not of embryonic fibroblasts and also enhanced functional maturation of resulting iN cells. Hence, FoxO3 has a central role in the neuronal reprogramming susceptibility of cells, and the importance of FoxO3 appears to change during development.

FOXO transcription factors: key regulators of cellular quality control.

FOXO transcription factors are conserved regulators of longevity downstream of insulin signaling. These transcription factors integrate signals emanating from nutrient deprivation and stress stimuli to coordinate programs of genes involved in cellular metabolism and resistance to oxidative stress. Here, we discuss emerging evidence for a pivotal role of FOXO factors in promoting the expression of genes involved in autophagy and the ubiquitin-proteasome system--two cell clearance processes that are essential for maintaining organelle and protein homeostasis (proteostasis). The ability of FOXO to maintain cellular quality control appears to be critical in processes and pathologies where damaged proteins and organelles accumulate, including aging and neurodegenerative diseases.

Feasibility of reconstructed ancestral H5N1 influenza viruses for cross-clade protective vaccine development.

Since the reemergence of highly pathogenic H5N1 influenza viruses in humans in 2003, these viruses have spread throughout avian species in Asia, Europe, and Africa. Their sustained circulation has resulted in the evolution of phylogenetically diverse lineages. Viruses from these lineages show considerable antigenic variation, which has confounded vaccine planning efforts. We reconstructed ancestral protein sequences at several nodes of the hemagglutinin (HA) and neuraminidase (NA) gene phylogenies that represent ancestors to diverse H5N1 virus clades. By using the same methods that have been used to generate currently licensed inactivated H5N1 vaccines, we were able to produce a panel of replication competent influenza viruses containing synthesized HA and NA genes representing the reconstructed ancestral proteins. We identified two of these viruses that showed promising in vitro cross-reactivity with clade 1, 2.1, 2.2, 2.3.4, and 4 viruses. To confirm that vaccine antigens derived from these viruses were able to elicit functional antibodies following immunization, we created whole-virus vaccines and compared their protective efficacy versus that of antigens from positive control, naturally occurring, and broadly reactive H5N1 viruses. The ancestral viruses' vaccines provided robust protection against morbidity and mortality in ferrets challenged with H5N1 strains from clades 1, 2.1, and 2.2 in a manner similar to those based on the control strains. These findings provide proof of principle that viable, computationally derived vaccine seed viruses can be constructed within the context of currently licensed vaccine platforms. Such technologies should be explored to enhance the cross reactivity and availability of H5N1 influenza vaccines.

Varenicline and Nicotine Replacement Therapy for Smokers Admitted to Hospitals: A Randomized Clinical Trial.

Importance: Varenicline is the most effective sole pharmacotherapy for smoking cessation. If used in combination with nicotine replacement therapy (NRT), cessation rates may be further improved, but the efficacy and safety of the combination need to be evaluated. Objective: To examine whether hospitalized smokers treated with varenicline and NRT lozenges achieve higher prolonged smoking abstinence rates compared with those treated with varenicline alone. Design, Setting, and Participants: A double-blind, placebo-controlled randomized clinical trial was conducted in adult medical or surgical inpatients of 5 Australian public hospitals with a history of smoking 10 cigarettes or more per day, interested in quitting, and available for 12-month follow-up between May 1, 2019, and May 1, 2021 (final 12-month data collection in May 2022). Data analysis was performed from June 1 to August 30, 2023. Interventions: A 12-week varenicline regimen was initiated during hospitalization at standard doses in all participants. Participants were randomized to additionally use NRT (2 mg) or placebo lozenges if there was an urge to smoke. Behavioral support (Quitline) was offered to all participants. Main Outcomes and Measures: The primary outcome was biochemically verified sustained abstinence at 6 months. Secondary outcomes included self-reported prolonged abstinence, 7-day point prevalence abstinence (3, 6, and 12 months), and medicine-related adverse events. Results: A total of 320 participants (mean [SD] age, 52.5 [12.1] years; 183 [57.2%] male) were randomized. The conduct of biochemical verification was affected by COVID-19 restrictions; consequently, the biochemically verified abstinence in the intervention vs control arms (18 [11.4%] vs 16 [10.1%]; odds ratio [OR], 1.14; 95% CI, 0.56-2.33) did not support the combination therapy. The secondary outcomes in the intervention vs control arms of 7-day point prevalence abstinence at 6 months (54 [34.2%] vs 37 [23.4%]; OR, 1.71; 95% CI, 1.04-2.80), prolonged abstinence at 12 months (47 [29.9%] vs 30 [19.1%]; OR, 1.77; 95% CI, 1.05-3.00), and 7-day point prevalence abstinence at 12-months (48 [30.6%] vs 31 [19.7%]; OR, 1.79; 95% CI, 1.07-2.99) significantly improved with the combination therapy. The self-reported 6-month prolonged abstinence (61 [38.6%] vs 47 [29.7%]; OR, 1.49; 95% CI, 0.93-2.39) favored the combination therapy but was not statistically significant. Medicine-related adverse events were similar in the 2 groups (102 [74.5%] in the intervention group vs 86 [68.3%] in the control group). Conclusions and Relevance: In this randomized clinical trial of the combination of varenicline and NRT lozenges in hospitalized adult daily smokers, the combination treatment improved self-reported abstinence compared with varenicline alone, without compromising safety, but it did not improve biochemically validated abstinence. Trial Registration: anzctr.org.au Identifier: ACTRN12618001792213.

Single-cell transcriptomics of peripheral blood in the aging mouse.

Compositional and transcriptional changes in the hematopoietic system have been used as biomarkers of immunosenescence and aging. Here, we use single-cell RNA-sequencing to study the aging peripheral blood in mice and characterize the changes in cell-type composition and transcriptional profiles associated with age. We identified 17 clusters from a total of 14,588 single cells. We detected a general upregulation of antigen processing and presentation and chemokine signaling pathways and a downregulation of genes involved in ribosome pathways with age. In old peripheral blood, we also observed an increased percentage of cells expressing senescence markers (Cdkn1a, and Cdkn2a). In addition, we detected a cluster of activated T cells exclusively found in old blood, with lower expression of Cd28 and higher expression of Bcl2 and Cdkn2a, suggesting that the cells are senescent and resistant to apoptosis.

Does offering small financial incentives to smokers at the time of being wait-listed for surgery increase smoking cessation by the day of surgery? A randomised feasibility trial.

OBJECTIVE: This study aims to assess whether offering small financial incentives to smokers on elective surgery wait-lists is feasible and increases quitting before surgery. DESIGN: Randomised controlled trial, prospective, double-blinded. SETTING: Single-centre, Australian metropolitan public hospital. PARTICIPANTS: 620 adult smokers (≥10 cigarettes per day) were randomised on being wait-listed for elective surgery and 404 underwent operations (28 January 2021-31 July 2022) at the hospital (65.2%) by trial's end. INTERVENTION: Intervention participants were offered at wait-listing an $A70 supermarket voucher for verified abstinence on the day of surgery, provided they registered an intention to quit before surgery. Registrants intending to quit were also referred to Quitline. Neither intervention was offered to control participants (usual care). Smokers wait-listed from 17 May 2021 were offered an increased incentive of $A140. MAIN OUTCOME MEASURES: Primary outcome, quitting at least 24 hours before surgery, verified by exhaled carbon monoxide testing. Feasibility outcomes were the proportion taking up offers, ease of patient contact and disputes about quit status. RESULTS: Of 620 randomised participants (control 312, intervention 308), 404 had surgery at the hospital during the trial (control 214, intervention 190), which was lower than expected (for COVID-19 reasons). Offering $A70 resulted in 21.9% registering to quit, increasing to 32.6% with $A140. Telephone calls were the most effective means to gain registrations. The proportion of intervention group patients verified quit at least 24 hours before surgery was similar to controls (9.5% vs 8.9%, OR 1.1, 95% CI 0.5 to 2.2). Quitline contact was higher in the intervention group (13.2% vs 2.3%, OR 6.3, 95% CI 2.3 to 21.6). Disputes over test results did not occur, but 17.4% of intervention participants claiming quit failed verification. CONCLUSION: A single offer of financial rewards for perioperative cessation was feasible, without achieving clinically important quit differences. TRIAL REGISTRATION NUMBER: ACTRN12620000130965.

CellBiAge: Improved single-cell age classification using data binarization.

Aging is a major risk factor for many diseases. Accurate methods for predicting age in specific cell types are essential to understand the heterogeneity of aging and to assess rejuvenation strategies. However, classifying organismal age at single-cell resolution using transcriptomics is challenging due to sparsity and noise. Here, we developed CellBiAge, a robust and easy-to-implement machine learning pipeline, to classify the age of single cells in the mouse brain using single-cell transcriptomics. We show that binarization of gene expression values for the top highly variable genes significantly improved test performance across different models, techniques, sexes, and brain regions, with potential age-related genes identified for model prediction. Additionally, we demonstrate CellBiAge's ability to capture exercise-induced rejuvenation in neural stem cells. This study provides a broadly applicable approach for robust classification of organismal age of single cells in the mouse brain, which may aid in understanding the aging process and evaluating rejuvenation methods.

Epidemiology and molecular characterization of avian influenza A viruses H5N1 and H3N8 subtypes in poultry farms and live bird markets in Bangladesh.

Avian influenza virus (AIV) remains a global threat, with waterfowl serving as the primary reservoir from which viruses spread to other hosts. Highly pathogenic avian influenza (HPAI) H5 viruses continue to be a devastating threat to the poultry industry and an incipient threat to humans. A cross-sectional study was conducted in seven districts of Bangladesh to estimate the prevalence and subtypes (H3, H5, and H9) of AIV in poultry and identify underlying risk factors and phylogenetic analysis of AIVs subtypes H5N1 and H3N8. Cloacal and oropharyngeal swab samples were collected from 500 birds in live bird markets (LBMs) and poultry farms. Each bird was sampled by cloacal and oropharyngeal swabbing, and swabs were pooled for further analysis. Pooled samples were analyzed for the influenza A virus (IAV) matrix (M) gene, followed by H5 and H9 molecular subtyping using real-time reverse transcription-polymerase chain reaction (rRT-PCR). Non-H5 and Non-H9 influenza A virus positive samples were sequenced to identify possible subtypes. Selected H5 positive samples were subjected to hemagglutinin (HA) and neuraminidase (NA) gene sequencing. Multivariable logistic regression was used for risk factor analysis. We found that IAV M gene prevalence was 40.20% (95% CI 35.98-44.57), with 52.38%, 46.96%, and 31.11% detected in chicken, waterfowl, and turkey, respectively. Prevalence of H5, H3, and H9 reached 22%, 3.4%, and 6.9%, respectively. Waterfowl had a higher risk of having AIV (AOR: 4.75), and H5 (AOR: 5.71) compared to chicken; more virus was detected in the winter season than in the summer season (AOR: 4.93); dead birds had a higher risk of AIVs and H5 detection than healthy birds, and the odds of H5 detection increased in LBM. All six H5N1 viruses sequenced were clade 2.3.2.1a-R1 viruses circulating since 2015 in poultry and wild birds in Bangladesh. The 12 H3N8 viruses in our study formed two genetic groups that had more similarity to influenza viruses from wild birds in Mongolia and China than to previous H3N8 viruses from Bangladesh. The findings of this study may be used to modify guidelines on AIV control and prevention to account for the identified risk factors that impact their spread.