Co-infection Patterns Research Articles

Respiratory pathogen analysis in pediatric inpatients unraveled the infection pattern of Mycoplasma pneumoniae post the COVID-19 pandemic.

To counteract the COVID-19 pandemic, nonpharmaceutical interventions (NPIs) were implemented globally, exerting a profound influence on a wide spectrum of infectious diseases, encompassing respiratory tract infections (RTIs). Subsequent to the easing of NPIs, China experienced a significant outbreak of Mycoplasma pneumoniae (MP). Over a decade from 2015 to 2024, our study scrutinized 12 common infectious diseases among pediatric children. Etiologically diagnostic data and clinical outcome metrics of children with RTIs, tested for 13 pathogens, were analyzed to evaluate changes during and after the pandemic compared to pre-pandemic periods, with a notable emphasis on age profile and coinfection patterns of MP. Among 57,471 hospitalized children, 23,178 were diagnosed with infectious diseases. Under NPIs, most respiratory infections declined compared to pre-pandemic levels, rebounding by 69.64% in 2023. While the infection rate of common respiratory pathogens decreased, cases of respiratory syncytial virus increased during the period of extensive NPI implementation. In 2023, pediatric intensive care unit durations for these pathogens increased, suggesting greater severity of illness compared to 2019. MP exhibited the highest infection rate (31.38% average), with a notable outbreak post-pandemic due to severity increase in <3 year olds and rise among older children. NPIs reduced MP coinfections and mitigated their severity, while exerting a significant influence on bacterial coinfections with MP over the span of 5 years, in contrast to their impact on viral pathogens. NPIs effectively curb transmission of respiratory infections by most pathogens, resulting in increased average age of MP infections and altered patterns of coinfection post-pandemic.

A systematic review and guide for using multi-response statistical models in co-infection research.

The simultaneous infection of organisms with two or more co-occurring pathogens, otherwise known as co-infections, concomitant infections or multiple infections, plays a significant role in the dynamics and consequences of infectious diseases in both humans and animals. To understand co-infections, ecologists and epidemiologists rely on models capable of accommodating multiple response variables. However, given the diversity of available approaches, choosing a model that is suitable for drawing meaningful conclusions from observational data is not a straightforward task. To provide clearer guidance for statistical model use in co-infection research, we conducted a systematic review to (i) understand the breadth of study goals and host-pathogen systems being pursued with multi-response models and (ii) determine the degree of crossover of knowledge among disciplines. In total, we identified 69 peer-reviewed primary studies that jointly measured infection patterns with two or more pathogens of humans or animals in natural environments. We found stark divisions in research objectives and methods among different disciplines, suggesting that cross-disciplinary insights into co-infection patterns and processes for different human and animal contexts are currently limited. Citation network analysis also revealed limited knowledge exchange between ecology and epidemiology. These findings collectively highlight the need for greater interdisciplinary collaboration for improving disease management.

Respiratory pathogen dynamics in community fever cases: Jiangsu Province, China (2023–2024)

BackgroundRespiratory infectious diseases have the highest incidence among infectious diseases worldwide. Currently, global monitoring of respiratory pathogens primarily focuses on influenza and coronaviruses. This study included influenza and other common respiratory pathogens to establish a local respiratory pathogen spectrum. We investigated and analyzed the co-infection patterns of these pathogens and explored the impact of lifting non-pharmaceutical interventions (NPIs) on the transmission of influenza and other respiratory pathogens. Additionally, we used a predictive model for infectious diseases, utilizing the commonly used An autoregressive comprehensive moving average model (ARIMA), which can effectively forecast disease incidence.MethodsFrom June 2023 to February 2024, we collected influenza-like illness (ILI) cases weekly from the community in Xuanwu District, Nanjing, and obtained 2046 samples. We established a spectrum of respiratory pathogens in Nanjing and analysed the age distribution and clinical symptom distribution of various pathogens. We compared age, gender, symptom counts, and viral loads between individuals with co-infections and those with single infections. An autoregressive comprehensive moving average model (ARIMA) was constructed to predict the incidence of respiratory infectious diseases.ResultsAmong 2046 samples, the total detection rate of respiratory pathogen nucleic acids was 53.37% (1092/2046), with influenza A virus 479 cases (23.41%), influenza B virus 224 cases (10.95%), and HCoV 95 cases (4.64%) being predominant. Some pathogens were statistically significant in age and number of symptoms. The positive rate of mixed infections was 6.11% (125/2046). There was no significant difference in age or number of symptoms between co-infection and simple infection. After multiple iterative analyses, an ARIMA model (0,1,4), (0,0,0) was established as the optimal model, with an R2 value of 0.930, indicating good predictive performance.ConclusionsThe spectrum of respiratory pathogens in Nanjing, Jiangsu Province, was complex in the past. The primary age groups of different viruses were different, causing various symptoms, and the co-infection of viruses did not correlate with the age and gender of patients. The ARIMA model estimated future incidence, which plateaued in subsequent months.

Is the local environment more important than within-host interactions in determining coinfection?

Host populations often vary in the magnitude of coinfection they experience across environmental gradients. Furthermore, coinfection often occurs sequentially, with a second parasite infecting the host after the first has established a primary infection. Because the local environment and interactions between coinfecting parasites can both drive patterns of coinfection, it is important to disentangle the relative contributions of environmental factors and within-host interactions to patterns of coinfection. Here, we develop a conceptual framework and present an empirical case study to disentangle these facets of coinfection. Across multiple lakes, we surveyed populations of five damselfly (host) species and quantified primary parasitism by aquatic, ectoparasitic water mites and secondary parasitism by terrestrial, endoparasitic gregarines. We first asked if coinfection is predicted by abiotic and biotic factors within the local environment, finding that the probability of coinfection decreased for all host species as pH increased. We then asked if primary infection by aquatic water mites mediated the relationship between pH and secondary infection by terrestrial gregarines. Contrary to our expectations, we found no evidence for a water mite-mediated relationship between pH and gregarines. Instead, the intensity of gregarine infection correlated solely with the local environment, with the magnitude and direction of these relationships varying among environmental predictors. Our findings emphasize the role of the local environment in shaping infection dynamics that set the stage for coinfection. Although we did not detect within-host interactions, the approach herein can be applied to other systems to elucidate the nature of interactions between hosts and coinfecting parasites within complex ecological communities.

HPV specificity and multiple infections and association with cervical cytology in Chongqing, China: a cross-sectional study

BackgroundIt is important to assess the relationship between specific HPV genotype or multiple infection and cervical cytology. The protection provided by the HPV vaccine is type-specific, and the epidemiology feature of coinfections needs to be investigated. The aim is to provide baseline information for developing HPV vaccination and management of HPV-positive populations in the region.MethodsA total of 3649 HPV-positive women were collected from 25,572 women who underwent 15 HR-HPV genotypes and ThinPrep cytologic test (TCT) results. Logistic regression was used to determine the correlation between the risk of cytology abnormalities and specific HPV infection. We calculated odds ratios (ORs) to assess coinfection patterns for the common two-type HPV infections. chi-squared test was used to estimate the relationship between single or multiple HPV (divided into species groups) infection and cytology results.ResultsThe results showed there was a positive correlation between HPV16 (OR = 4.742; 95% CI 3.063–7.342) and HPV33 (OR = 4.361; 95% CI 2.307–8.243) infection and HSIL positive. There was a positive correlation between HPV66 (OR = 2.445; 95% CI 1.579–3.787), HPV51 (OR = 1.651; 95% CI 1.086–2.510) and HPV58(OR = 1.661; 95% CI 1.166–2.366) infection and LSIL. Multiple HPV infections with α9 species (OR = 1.995; 95% CI 1.101–3.616) were associated with a higher risk of high-grade intraepithelial lesions (HSIL) compared with single HPV infection. There were positive correlations between HPV66 and HPV56 (α6) (OR = 3.321; 95% CI 2.329–4.735) and HPV39 and HPV68 (α7). (OR = 1.677; 95% CI 1.127–2.495). There were negative correlations between HPV52, 58, 16 and the other HPV gene subtypes.ConclusionHPV33 may be equally managed with HPV16. The management of multiple infections with α9 may be strengthened. The 9-valent vaccine may provide better protection for the population in Chongqing currently. The development of future vaccines against HPV51 and HPV66 may be considered in this region.

Prevalence of Co-infection of Culture-Proven Bacterial Pathogens in Microbiologically Confirmed Pulmonary Tuberculosis Patients From a Tertiary Care Center.

Tuberculosis (TB) is a chronic condition that weakens the immune system, causes structural changes in the lungs, and can lead to infections by other bacterial pathogens. Very few studies have been done to understand the magnitude of co-infection with other bacterial pathogens, so this study was conducted to understand the co-infection pattern and burden. A total of 174 microbiologically confirmed pulmonary TB patients' samples, identified by cartridge-based nucleic acid amplification test, were further tested for other bacterial pathogens by culture over a period of five months from May 2023 to September 2023. The isolates' identification and drug susceptibility were performed using the VITEK 2 system (bioMérieux, Marcy-l'Étoile, France). Of the 174 pulmonary samples tested, 19 samples grew a significant amount of other bacterial pathogens, making the prevalence 10.91% (19/174). Among the pulmonary samples tested, 54.59% were sputum, 38.5% were bronchoalveolar lavage, and 6.89% were endotracheal aspirate. Additionally, 70.11% of the patients tested were in the age group of 19-60 years. Of the patients who had co-infection, 94.73% (18/19) were male. The most common bacterial infection was caused by Pseudomonas aeruginosa, which was identified in 36.84% of the co-infection cases (7/19). This was followed by Acinetobacter baumannii in 31.57% (6/19), Klebsiella pneumoniae in 26.31% (5/19), and Stenotrophomonas maltophilia in 5.28% (1/19). Acinetobacter baumannii and Klebsiella pneumoniae showed high drug resistance, ranging from 60% to 100% against various groups of drugs tested. None of the patient samples with co-infection showed rifampicin resistance. Among all the samples with co-infection, the majority (42.10%, or 8/19) had a high load of Mycobacterium tuberculosis complex detected by CBNAAT Ultra (Cepheid, Sunnyvale, California). Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae are unusual pathogens causing infection in community patients and are known to cause illness in hospitalized patients. These organisms' resistance was also similar to the resistance shown by hospital-acquired infections. Thisindicates that bacterial co-infection in pulmonary TB patients will be similar to the pattern of hospital-acquired infections. The high prevalence of bacterial co-infections (10.91%) in patients with pulmonary TB poses a significant challenge as these bacterial pathogens are not susceptible to anti-tubercular drugs. Therefore, comprehensive screening for other bacterial infections in all pulmonary TB patients is crucial for effective treatment and outcomes.

The Prevalence of Sexually Transmitted Infections among Male Patients at a Dermato-Venereology Outpatient Clinic in Gdańsk, Poland: Findings from a Single-Center Study.

Background: Sexually transmitted infections (STIs) are a significant public health concern worldwide, yet data on their prevalence and epidemiology, particularly in Central and Eastern Europe, remain scarce. This study aimed to assess the prevalence, anatomical localization, symptomatic/asymptomatic course, and co-infection patterns of STIs among men. Methods: This retrospective study analyzed data collected between May 2021 and July 2023, including sociodemographic, sexual behavior, and clinical data from 139 male participants. Molecular polymerase chain reaction (PCR) tests were conducted for Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Mycoplasma genitalium, and Trichomonas vaginalis. Results: Of the participants, 36% tested positive for at least one STI, with the urethra being the most common site of infection. NG and CT were the most prevalent infections. The majority of infections were asymptomatic, highlighting the importance of comprehensive screening, especially in high-risk populations like men who have sex with men (MSM). Conclusions: This study emphasizes the need for targeted screening strategies, particularly for extragenital STIs, and underscores the role of MSM in STI epidemiology. The findings highlight the importance of routine screening, even for asymptomatic individuals, to effectively control STI spread. Future research should validate and expand upon these findings to enhance STI prevention and management efforts.

SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts.

Multi-strain infection is a common yet under-investigated phenomenon of many pathogens. Currently, biologists analyzing SNP information sometimes have to discard mixed infection samples as many downstream analyses require monogenomic inputs. Such a protocol impedes our understanding of the underlying genetic diversity, co-infection patterns, and genomic relatedness of pathogens. A scalable tool to learn and resolve the SNP-haplotypes from polygenomic data is an urgent need in molecular epidemiology. We develop a slice sampling Markov Chain Monte Carlo algorithm, named SNP-Slice, to learn not only the SNP-haplotypes of all strains in the populations but also which strains infect which hosts. Our method reconstructs SNP-haplotypes and individual heterozygosities accurately without reference panels and outperforms the state-of-the-art methods at estimating the multiplicity of infections and allele frequencies. Thus, SNP-Slice introduces a novel approach to address polygenomic data and opens a new avenue for resolving complex infection patterns in molecular surveillance. We illustrate the performance of SNP-Slice on empirical malaria and HIV datasets and provide recommendations for using our method on empirical datasets. The implementation of the SNP-Slice algorithm, as well as scripts to analyze SNP-Slice outputs, are available at https://github.com/nianqiaoju/snp-slice.

Global prevalence of Borrelia burgdorferi and Anaplasma phagocytophilum coinfection in Ixodes tick populations: protocol for a systematic review and meta-analysis

IntroductionIxodes ticks are pivotal in transmitting diseases like Lyme disease and human granulocytic anaplasmosis, caused by Borrelia burgdorferi and Anaplasma phagocytophilum, respectively. These pathogens not only affect humans through single...

Coinfection frequency in water flea populations is a mere reflection of parasite diversity

In nature, parasite species often coinfect the same host. Yet, it is not clear what drives the natural dynamics of coinfection prevalence. The prevalence of coinfections might be affected by interactions among coinfecting species, or simply derive from parasite diversity. Identifying the relative impact of these parameters is crucial for understanding patterns of coinfections. We studied the occurrence and likelihood of coinfections in natural populations of water fleas (Daphnia magna). Coinfection prevalence was within the bounds expected by chance and parasite diversity had a strong positive effect on the likelihood of coinfections. Additionally, coinfection prevalence increased over the season and became as common as a single infection. Our results demonstrate how patterns of coinfection, and particularly their temporal variation, are affected by overlapping epidemics of different parasites. We suggest that monitoring parasite diversity can help predict where and when coinfection prevalence will be high, potentially leading to increased health risks to their hosts.

Infection and co-infection patterns of common upper respiratory tract viruses in patients with flu-like symptoms attending a fever clinic of a tertiary care hospital during the COVID-19 pandemic

Infection and co-infection patterns of common upper respiratory tract viruses in patients with flu-like symptoms attending a fever clinic of a tertiary care hospital during the COVID-19 pandemic

Ranavirus and helminth parasite co-infection in invasive American bullfrogs in the Atlantic forest, Brazil

Emerging infectious diseases threaten amphibian species across the globe. In Brazil, the American bullfrog (Aquarana catesbeiana) is a highly invasive species that can potentially transmit parasites and pathogens to native amphibians. This is the first assessment of co-infection of Ranavirus and helminth macroparasites in invasive populations of bullfrogs in South America. We collected, measured, and euthanized 65 specimens of A. catesbeiana sampled from 9 sites across three states of Brazil in the Atlantic Forest biome. We collected and identified helminth macroparasites and sampled host liver tissue to test for the presence and load of Ranavirus with quantitative PCR. We documented patterns of prevalence, parasite load, and co-infection with generalized linear mixed models, generalized logistic regressions, and randomization tests. Most individual bullfrogs did not exhibit clinical signs of infection, but the overall Ranavirus prevalence was 27% (95% confidence interval, [CI 17–38]). Bullfrogs were infected with helminth macroparasites from 5 taxa. Co-infection of helminth macroparasites and Ranavirus was also common (21% CI [12–31]). Bullfrog size was positively correlated with total macroparasite abundance and richness, and the best-fitting model included a significant interaction between bullfrog size and Ranavirus infection status. We observed a negative correlation between Ranavirus viral load and nematode abundance (slope = −0.22, P = 0.03). Invasive bullfrogs (A. catesbeiana) in Brazil were frequently infected with both Ranavirus and helminth macroparasites, so adult bullfrogs could serve as reservoir hosts for both pathogens and parasites. However, many macroparasites collected were encysted and not developing. Coinfection patterns suggest a potential interaction between Ranavirus and macroparasites because helminth abundance increased with bullfrog size but was lower in Ranavirus infected individuals. Future studies of bullfrogs in the Atlantic Forest should investigate their potential role in pathogen and parasite transmission to native anurans.

Coinfection and nonrandom recombination drive the evolution of swine enteric coronaviruses

ABSTRACT Coinfection with multiple viruses is a common phenomenon in clinical settings and is a crucial driver of viral evolution. Although numerous studies have demonstrated viral recombination arising from coinfections of different strains of a specific species, the role of coinfections of different species or genera during viral evolution is rarely investigated. Here, we analyzed coinfections of and recombination events between four different swine enteric coronaviruses that infect the jejunum and ileum in pigs, including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), and a deltacoronavirus, porcine deltacoronavirus (PDCoV). Various coinfection patterns were observed in 4,468 fecal and intestinal tissue samples collected from pigs in a 4-year survey. PEDV/PDCoV was the most frequent coinfection. However, recombination analyses have only detected events involving PEDV/TGEV and SADS-CoV/TGEV, indicating that inter-species recombination among coronaviruses is most likely to occur within the same genus. We also analyzed recombination events within the newly identified genus Deltacoronavirus and found that sparrows have played a unique host role in the recombination history of the deltacoronaviruses. The emerging virus PDCoV, which can infect humans, has a different recombination history. In summary, our study demonstrates that swine enteric coronaviruses are a valuable model for investigating the relationship between viral coinfection and recombination, which provide new insights into both inter- and intraspecies recombination events among swine enteric coronaviruses, and extend our understanding of the relationship between coronavirus coinfection and recombination.

Effects of residential acaricide treatments on patterns of pathogen coinfection in blacklegged ticks.

Medically important ixodid ticks often carry multiple pathogens, with individual ticks frequently coinfected and capable of transmitting multiple infections to hosts, including humans. Acquisition of multiple zoonotic pathogens by immature blacklegged ticks (Ixodes scapularis) is facilitated when they feed on small mammals, which are the most competent reservoir hosts for Anaplasma phagocytophilum (which causes anaplasmosis in humans), Babesia microti (babesiosis) and Borrelia burgdorferi (Lyme disease). Here, we used data from a large-scale, long-term experiment to ask whether patterns of single and multiple infections in questing nymphal I. scapularis ticks from residential neighbourhoods differed from those predicted by independent assortment of pathogens, and whether patterns of coinfection were affected by residential application of commercial acaricidal products. Quantitative polymerase chain reaction was used for pathogen detection in multiplex reactions. In control neighbourhoods and those treated with a fungus-based biopesticide deployed against host-seeking ticks (Met52), ticks having only single infections of either B. microti or B. burgdorferi were significantly less common than expected, whereas coinfections with these 2 pathogens were significantly more common. However, use of tick control system bait boxes, which kill ticks attempting to feed on small mammals, eliminated the bias towards coinfection. Although aimed at reducing the abundance of host-seeking ticks, control methods directed at ticks attached to small mammals may influence human exposure to coinfected ticks and the probability of exposure to multiple tick-borne infections.

A case series of co-infection in Mycobacterium tuberculosis and other pathogens: insights from nanopore sequencing

BackgroundTuberculosis (TB) continues to be a major global health burden, and co-infection with other pathogens further complicates the diagnosis and treatment of this infectious disease. The present retrospective study aimed to evaluate the clinical utility of nanopore sequencing in identifying co-infection caused by Mycobacterium tuberculosis (M.tb) and other pathogens.MethodsPatients with M.tb co-infection from December 2021 to March 2023 at the Jiangxi Provincial Chest Hospital were retrospectively studied. Data were collected including demographics, symptoms, imaging findings, pathogen diagnosis tests, and treatment history. Pathogen tests involved culture, AFB smear, Xpert MTB/RIF, and nanopore sequencing.ResultsThe enrolled patients included 20 M.tb cases and three nontuberculous mycobacteria (NTM) cases co-infected with other pathogens. Common clinical symptoms included cough (47.83%), expectoration (34.78%), and asthma (17.39%). Radiological examinations showed typical features of pulmonary tuberculosis, including nodules (73.91%), cord-like shadows (34.78%), cavities (34.78%), and destroyed lung manifestations (17.39%). Nanopore sequencing identified M.tb in a significant majority of the cases (86.96%), outperforming traditional culture tests (39.13%), acid-fast bacilli (AFB) tests (27.27%), and Xpert MTB/RIF (53.84%) tests. Notably, nanopore sequencing revealed that M.tb was frequently co-infected with Candida albicans, Klebsiella pneumoniae, and Mycobacterium abscessus. Three specific cases of co-infection with distinct diagnosis and treatment characteristics were presented in detail. They illustrated the complexity of TB co-infection management and the potential of nanopore sequencing for accurate diagnosis and informing the tailored therapeutic approaches.ConclusionNanopore sequencing-based metagenomics method can help clinicians to identify TB co-infection patterns and formulate a rational drug regimen in time.

Prevalence and genotype distribution of HPV infections among women in Chengdu,China

BackgroundHuman papilloma virus (HPV) infection among female is the cause of cervical cancer and genital warts. In China, the HPV vaccination rate and the target population screening rate among females are low, and the aims of this study on the genotype distribution and prevalence of HPV infection were to provide more targeted strategies for the prevention and treatment of cervical cancer and HPV-related diseases.MethodsPolymerase chain reaction-reverse dot blot (PCR-RDB) was adopted for HPV genotyping test, the prevalence and 23 genotypes distribution of HPV infections among 181,705 women in Chengdu from 2013 to 2020 were analysed.ResultsThe overall prevalence rate of HPV infection among 181,705 cases was 23.28%, the prevalence of HR-HPV at the age group < 20 years, 60–69 years and ≥ 70 years were higher than the overall prevalence.The prevalence of HPV showed a bimodal U-shaped curve with age; the first and second peak common occurred among females < 20 years old (42.97%) and 60–69 years old (37.56%), respectively.The top five genotypes of HPV infection among females in Chengdu were HPV52/16/58/81/53. Single infection (73.26%) was the main HPV infection pattern, followed by double infection (19.17%) and multiple infection (7.57%), the infection rate of HPV showed a gradual declined as the patterns of HPV coinfections increased, low-risk and high-risk coinfection was higher in low-risk HPV infection (43.68%) and lower in high-risk HPV infection (13.59%). The prevalence of genotypes − 6 and − 81 infection was the second highest at the age group of 20 and 40–59, respectively, while the prevalence of HPV16 was the highest at the age group of ≥ 70 among 23 genotypes among the 181,705 women.ConclusionsThe prevalence of HPV infections among women in Chengdu is higher than domestic certain developed citys, among the five vaccines available, nonavalent vaccine is more suitable for Chengdu females. For young females prioritizing vaccination is essential in the current context.Double screening for HPV DNA is important in middle-aged women (30–49 years), and screening should not be lacking in older women (> 65 years). Additionally,for patients with genital warts, it is necessary to screen for high-risk HPV infection and provide appropriate management and treatment. Given the limitations of this study, future HPV research should aim to achieve full coverage of the target population, and our studies should also include cellular or pathological data of HPV-positive cases, vaccination rates, and various lifestyle details.

Cattle tick-borne pathogens sharing the same vectors in Benin and Burkina Faso: variations in prevalence and coinfection patterns

Understanding interactions between pathogens at the level of the individual host and the population in West Africa, may have noteworthy implications for predictions of diseases emergence and disease control programmes. Hence, the current study was aimed at investigating the interactions between Anaplasma marginale, Babesia bigemina and B. bovis in West African cattle. Twelve sentinel steers in each of the eight selected herds were randomly chosen to perform a one-year-long survey designed to monthly collect blood sample and to diagnose possible infections of the steers. This allowed identifying A. marginale as the most prevalent pathogen across the three surveyed regions (range: 0.60-1), followed by B. bigemina (0.24-0.85) and B. bovis (0.10-0.64); the same ranking order of the tick-borne pathogens was observed when considering the apparent duration of cattle infection. Regarding interaction patterns, mainly avoidance was revealed between A. marginale and B. bigemina and between B. bigemina and B. bovis. Such negative interaction seemed to be beneficial to the West African cattle surveyed, helping them to escape from babesiosis caused by B. bovis. Altogether, studied Boophilus tick-borne pathogens negatively interact within cattle in Benin and Burkina Faso. This pattern raises new questions regarding the underlying mechanisms and potential consequences.

Detection and genetic diversity of subgroup K avian leukosis virus in local chicken breeds in Jiangxi from 2021 to 2023.

Avian leukosis virus subgroup K (ALV-K) is a new subgroup of avian leukosis virus (ALV) that was first identified in Chinese native chickens in recent years. To further understand the molecular epidemiology and evolutionary diversity of ALV-K, this study investigated the molecular epidemiology of 73,664 chicken plasma samples collected from Jiangxi native chicken flocks. The results showed that ALV-J was the most predominant ALV subtype in Jiangxi native chickens, with a high positivity rate of 4.34%. From 2021 to 2023, there was a gradual upward trend in the proportion of positive numbers of ALV-K among ALV-positive samples, and there was a trend of outbreaks. ALV-J and ALV-K were the main co-infection patterns. Genetic evolutionary analysis based on ALV-K gp85 gene showed that the isolated ALV-K in this study were distributed in various branches of the evolutionary tree with genetic diversity. The homology results showed that the amino acid homology of the isolated ALV-K gp85 gene ranged from 33.9 to 88.1% with the reference strains of subtypes A, B, C, D, E, and J, and from 91.9 to 100% with the other ALV-K reference strains. Multiple mutations were present in the ALV-K gp85, and especially significant mutations were found in the highly variable region hr2. The results of ALV-K replication efficiency showed that the replication efficiency of ALV-K was significantly lower than that of ALV-J. These results enriched the genome sequence data of ALV-K in Chinese geoducks, and laid the foundation for further research on the pathogenesis and prevention of ALV-K.

Pathogen community composition and co-infection patterns in a wild community of rodents

Pathogen community composition and co-infection patterns in a wild community of rodents

High-risk HPV prevalence and vaccination coverage among Indigenous women in the Colombian Amazon: Implications for cervical cancer prevention. Cross-sectional study.

Cervical cancer, primarily caused by Human Papillomavirus (HPV) transmission through sexual contact, necessitates comprehensive strategies to combat its impact on women's health. Yet, certain underserved populations, such as low socioeconomic and ethnic minority groups, encounter barriers in accessing timely interventions and early diagnosis. This cross-sectional study was conducted with the aim of assessing HPV prevalence, genotype distribution, and co-infections among 280 adult women residing in a Colombian Indigenous Reserve within the Amazon region. The research adhered to a community-centric approach that respected cultural norms, native languages, and Indigenous authorities' permission. The study revealed an overall HPV infection prevalence of 31.1% (n = 87, 95% CI 25.7-36.8), with 22.5% (n = 63, 95% CI 17.7-27.8) of women infected by at least one high-risk HPV genotype and 15.0% (n = 42, 95% CI 11-19.7) infected by at least one LR genotype. These results align with the findings of other Colombian studies. Notable high-frequency genotypes included 16, 52, 66, 56, and 68, with the most common combinations being [66-52] and [66-58]. The study also assessed the prevalence of HPV vaccination, revealing a rate of 22.9%, lower than the national average. In vaccinated women, the prevalence of genotypes 16 and 18 was significantly reduced, as anticipated. Importantly, it was observed that 57.1% of all high-risk HPV infections could have been prevented with the use of the nonavalent vaccine. These findings underscore the critical need to enhance adherence to early cervical cancer detection and monitor positive cases to evaluate high-risk HPV persistence. Efforts should be directed toward continuing vaccination coverage against high-risk HPV 16 and 18 with the quadrivalent vaccine, while also striving to make the nonavalent vaccine accessible for inclusion in large-scale public health programs. Additionally, the study did not identify a specific pattern of co-infection. The study emphasizes the significance of adopting a locally tailored epidemiological approach to guide and promote cervical cancer prevention efforts in Indigenous communities.