Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW’s ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.

Trimethoprim-sulfamethoxazole (SMX-TMP) represents the first-line treatment for non-human immunodeficiency virus (non-HIV) patients with Pneumocystis jirovecii pneumonia (PJP). However, the relationship between SMX peak serum concentrations (Cmax) and clinical outcomes of PJP is not clear yet. This study aim to investigate the impact of initial Cmax of SMX on clinical outcomes non-HIV patients with PJP who were predominantly treated with low-dose SMX-TMP, and to evaluate related adverse drug reactions (ADRs), providing evidence for optimal clinical medication strategies. A retrospective analysis was conducted on 66 non-HIV patients with PJP who received SMX-TMP treatment and had SMX Cmax monitoring results at Hunan University of Medicine General Hospital from January 2022 to December 2024. Patients were divided into high-concentration (SMX Cmax >100 µg/mL) and low-concentration (SMX Cmax ≤100 µg/mL) groups. Statistical analyses were performed to compare clinical improvement rates, 28-day mortality rates, and ADR incidence between the two groups. Factors influencing SMX Cmax, including daily dose and glomerular filtration rate (GFR), were also analyzed. The median SMX Cmax was 108 (78.6–151.0) µg/mL among the 66 patients, with 37 patients (56.66

The prevalence and transmission of avian influenza viruses (AIVs) in the live poultry market (LPM) is a serious public health concern. This study was to investigate the prevalence of different subtypes of avian influenza viruses in environment of LPM, and to analyze the differences and seasonality of the nucleic acid positive rate (NAPR) of A type, H5, H7, and H9 subtypes in feces, sewage, drinking water, breeding cages, and chopping boards. Feces, breeding cages swabs, drinking water, sewage and chopping boards swabs were collected from live poultry market during 2019–2023 from southern and northern China. Real-time PCR was used to screen for virus subtypes. Viruses were isolated, and deep sequencing was performed to obtain whole-genome sequences. Chi-square test was used for statistical analysis of categorical variable, GraphPad Prism software were used to construct graphs. A total of 64,599 environmental samples were collected from live poultry markets in the southern China and northern China between 2019 and 2023. The average NAPR of the A type was significantly higher in the samples collected from the southern China than in those collected from the northern China (P < 0.05). The NAPR of H5, H7, and H9 subtypes carried by the five types of environmental samples in the southern China were significantly different (P < 0.05), and a higher NAPR was detected in chopping boards (10.84

Background:For advanced non-small cell lung cancer (NSCLC) with programmed cell death ligand 1 (PD-L1) expression <1% and no actionable oncogenic alterations, pembrolizumab plus chemotherapy (Pembro-chemo) is widely regarded as the current standard of care. However, emerging therapeutic combinations and preliminary results from ongoing trials challenge its superiority, particularly across different histologic types. Therefore, this study aimed to appraise the effectiveness and safety of first-line treatment for PD-L1 <1% advanced, non-squamous and squamous NSCLC. Methods:PubMed, Ovid Medline, the Cochrane Library, and Embase were searched from database inception to August 15, 2025, to identify phase III randomized controlled trials (RCTs) that explored first-line treatments in treatment-naïve advanced NSCLC, PD-L1 <1%, no epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) alterations; and reported any efficacy outcome were eligible for inclusion. Treatment effectiveness was quantified using overall survival (OS), progression-free survival (PFS) and objective response rate (ORR). Surface under the cumulative ranking value (SUCRA) was used to rank the therapies. Risk of bias for included RCTs was assessed using the Cochrane Risk of Bias 2 tool. Results:Twenty-five phase III RCTs involving 5,815 participants were eligible. Overall, 21 first-line treatments were identified. In terms of OS, pembrolizumab + chemotherapy + canakinumab (Pembro-chemo-canakinumab) (SUCRA =0.90) showed great potential in improving outcomes, although its long-term efficacy still needed to be validated. Nivolumab + ipilimumab (Nivo-ipi) (SUCRA =0.78) closely followed. Both top regimens showed non-significant superiority over Pembro-chemo. Regarding PFS, nivolumab + chemotherapy + bevacizumab (SUCRA =0.88), and serplulimab + chemotherapy (SUCRA =0.87) were the optimal regimens. Specifically for non-squamous patients, Pembro-chemo was optimal for OS (SUCRA =0.90), followed by Nivolumab + chemotherapy + bevacizumab (SUCRA =0.82). Nivolumab + chemotherapy + bevacizumab optimized PFS, with an hazard ratio (HR) of 0.52 [95% confidence interval (CI): 0.30-0.92 vs. Pembro-chemo]. For squamous patients, nivolumab + ipilimumab ± chemotherapy (Nivo-ipi-chemo) led in OS, while serplulimab + chemotherapy in PFS. Conclusions:First-line personalized treatment for PD-L1 <1%, advanced NSCLC should be histology-based, balancing efficacy and toxicity. Pembro-chemo and nivolumab + chemotherapy + bevacizumab combinations are recommended as the optimal first-line options for non-squamous patients, and Nivo-ipi-chemo for squamous patients.

The causative agent of coronavirus disease 2019 (COVID-19), known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread accumulatively to 240 countries and continues to evolve. To gain a comprehensive understanding of the epidemiological characteristics of imported variants in China and their correlation with global circulating variants, genomic surveillance data from 11 139 imported COVID-19 cases submitted by Chinese provincial CDC laboratories between 2021 and 2022 were analyzed. Consensus sequences underwent rigorous quality checks, followed by amino acid mutations analysis using Nextclade. Sequences with satisfactory quality control status were classified according to the Pango nomenclature. The results showed that the dominant variants in imported cases reflected the global epidemic trend. An increase in the number of imported SARS-CoV-2 lineages monitored in China in the second half of 2022, and the circulating Omicron subvariants changed from the ancestral lineages of BA.5 and BA.2 into the lineages containing key amino acid mutations of spike protein. There was significant variation in the detection of Omicron subvariants among continents (chi(2) = 321.968, p < 0.001) in the second half of 2022, with four lineages (BA.2.3.7, BA.2.2, BA.5.2.7, and XBB.1.2) identified through imported surveillance mainly prevalent respectively in Taiwan, China, Hong Kong SAR, China, Russian Federation, and Singapore. These findings revealed the alterations in circulating imported variants from 2021 to 2022 in China, reflecting the higher diversity of lineages in the second half of 2022, and revealed the predominant lineages of countries or regions that are in close contacts to China, providing new insights into the global prevalence of SARS-CoV-2.

This study delineates the enhancement of a Reverse Transcription Polymerase Chain Reaction (RT-PCR) method for the amplification of the complete genome of the influenza A virus during heterosubtypic co-infection, relying on the amplification of intact gene segments. The precision of the method was assessed using all amplicons, which underwent both capillary electrophoresis and DNA sequencing. Five samples featuring co-infection of Influenza A viruses with H1N1 and H3N2 subtypes were evaluated. The improved strategy successfully amplified all eight segments of H3N2 strains in four samples, and the entire genome of H1N1 strains in three samples.

Introduction:In the first half of 2023, a global shift was observed towards the predominance of XBB variants. China faced a significant epidemic between late 2022 and early 2023 due to Omicron subvariants BA.5.2 and BF.7. This study aims to depict the evolving variant distribution among provincial-level administrative divisions (PLADs) in China and explore the factors driving the predominance of XBB replacement.Methods:Sequences from local and imported coronavirus disease 2019 (COVID-19) cases recorded between January 1 and June 30, 2023, were included. The study analyzed the changing distribution of viral variants and assessed how the prior dominance of specific variants, XBB subvariants, and imported cases influenced the prevalence of the XBB replacement variant.Results:A total of 56,486 sequences were obtained from local cases, and 8,669 sequences were from imported cases. Starting in April, there was a shift in the prevalence of XBB from imported to local cases, with varying dominance among PLADs. In PLADs previously high in BF.7, the rise of XBB was delayed. A positive correlation was found between XBB proportions in imported cases from January to March and local cases in April. The distribution pattern of XBB subvariants differed between local and imported cases within the same PLAD. No significant differences were noted in the replacement rates of XBB subvariants.Conclusions:The timing of XBB dominance differed among various PLADs in China in the first half of 2023, correlating closely with the prevalence of XBB variants among imported cases.

Objectives Pro-protein convertase subtilisin/kexin 9 (PCSK9) decreases the clearance of the pathogenic lipids, supporting the potential role of PCSK9 in the prognosis of sepsis. Methods In this prospective cohort study, patients with sepsis were consecutively recruited from 1 to 2020 to 30 September 2021 at the First People’s Hospital of Huaihua, China. All the eligible patients were categorized into low-PCSK9 and high-PCSK9 groups, based on their PCSK9 levels at admission. Time-dependent receiver operating characteristic curves and Cox proportional hazards regression were used to evaluate the association between PCSK9 level and 28-day mortality of sepsis. Results Of the 203 enrolled patients, 56 (27.59%) died during the 28-day follow-up. The PCSK9 level was positively related to the C-reactive protein level. The cut-off point of PCSK9 levels for 28-day mortality risk was 370 ng/ml. Through comparison between high-PCSK9 (> 370 ng/ml) with low-PCSK9 (≤ 370 ng/ml) groups, the adjusted HR for mortality was 2.56 (95% CI: 1.25–5.23, p = 0.01). Conclusions The 28-day mortality of sepsis increased significantly as the baseline circulating PCSK9 level exceeded 370 ng/ml, indicating circulating PCSK9 levels may be a potential biomarker to predict the prognosis of sepsis.

Due to growing activities of avian influenza, more attention should be paid to avian influenza virus infections. Global summaries or national reports lack data on epidemiological patterns of avian influenza. A descriptive epidemiological analysis of avian influenza outbreaks from 2018 to 2022 was conducted, particularly fowl infections, human infections, and sequence alterations. The number of fowl infection outbreaks in the first half of 2022 was the highest level in the five-year period. Countries or regions could reliably be classified into three clusters according to fowl infection activity scores, with 60.0% of countries or regions in C1 in Europe. Additionally, two host infection patterns of countries were noted, led by the Taiwan (China) region and Germany. Human infections also increased, with 88.1% of cases being in China with an increasing risk of cases in northern China. Sequences that were furin cleavage motif present spread from Asia to Europe and North America over the five-year period. Continuous changes in the global activities of avian influenza highlight the need for sustained global surveillance, including strengthening monitoring capacity for vulnerable population and dynamically detecting new cases or genetic variations of the avian influenza virus under the One Health framework.

Recent evidence has revealed that circulating coagulation factor prekallikrein (PK), an important part of the kallikrein-kinin system, regulates cholesterol metabolism, but the association between serum PK and lipid levels is unclear. This cross-sectional study included 256 subjects (aged from 1 month to 90 years) who underwent physical examinations at the First People’s Hospital of Huaihua, China. After overnight fasting, serum was collected for PK and lipid testing. Spearman correlation analysis and multivariable logistic regression analysis were used to analyze the association of PK level with lipid levels and the likelihood risk of hyperlipidemia. The possible threshold value of PK was calculated according to the receiver operating characteristic (ROC) curve. The median serum PK level was 280.9 µg/mL (IQR 168.0, 377.0), and this level changed with age but not sex. The serum PK level was positively correlated with the serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. A nonlinear relationship was observed between serum PK and high-density lipoprotein cholesterol (HDL-C) levels. The serum PK level was positively correlated with HDL-C when its level was lower than 240 µg/mL and negatively correlated with HDL-C when its level was higher than 240 µg/mL. The regression analysis demonstrated that an elevated serum PK level was significantly associated with the likelihood risk of hypercholesterolemia and hypertriglyceridemia. The ROC curve showed that the possible threshold values of serum PK for hypercholesterolemia and hypertriglyceridemia occurrences were 344.9 µg/mL and 305.7 µg/mL, respectively. Elevated serum PK levels were significantly associated with the likelihood of hypercholesterolemia and hypertriglyceridemia, and the possible threshold values of PK levels were 344.9 µg/mL and 305.70 µg/mL, respectively, suggesting that higher PK levels may be a risk factor for cardiovascular diseases.

On December 9, 2021, 2 international passengers arrived in Tianjin Binhai International Airport from Warsaw, Poland via airplane and tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), using nucleic acid tests. The first case (Patient A) was a flight crew member, a 35-year-old male, who had returned to Warsaw with the same flight on December 10, 2021. The second case (Patient B) was a 17-year-old female student, who has been transferred to Haihe Hospital for isolation. Both cases are Polish nationality that had recently lived in Warsaw, Poland. According to the investigation, neither patient had disease symptoms nor medication history. Patient B received the Pfizer/BNT162b2 vaccine on September 27, 2021. Patient A was vaccinated on May 25, 2021, but no further vaccine information was collected as Patient A had left China. No other infections from this flight have been detected.

Background: Many studies have explored the epidemiological characteristics of influenza. However, most previous studies were conducted in a specific region without a national picture which is important to develop targeted strategies and measures on influenza control and prevention. Objectives: To explore the association between ambient temperature and incidence of influenza, to estimate the attributable risk from temperature in 30 Chinese cities with different climatic characteristics for a national picture, and to identify the vulnerable populations for national preventative policy development. Methods: Daily meteorological and influenza incidence data from the 30 Chinese cities over the period 2016-19 were collected. We estimated the city-specific association between daily mean temperature and influenza incidence using a distributed lag non-linear model and evaluated the pooled effects using multivariate meta-analysis. The attributable fractions compared with reference temperature were calculated. Stratified analyses were performed by region, sex and age. Results: Overall, an N-shape relationship between temperature and influenza incidence was found in China. The cumulative relative risk of the peak risk temperature (5.1 degrees C) was 2.13 (95%CI: 1.41, 3.22). And 60% (95%eCI: 54.3%, 64.3%) of influenza incidence was attributed to ambient temperature during the days with sensitive temperatures (1.6 degrees C-14.4 degrees C). The ranges of sensitive temperatures and the attributable disease burden due to temperatures varied for different populations and regions. The residents in South China and the children aged <= 5 and 6-17 years had higher fractions attributable to sensitive temperatures. Conclusions: Tailored preventions targeting on most vulnerable populations and regions should be developed to reduce influenza burden from sensitive temperatures.

On April 23, 2022, an international flight KQ880 from Nairobi, Kenya arrived at Guangzhou Baiyun International Airport, Guangzhou City, Guangdong Province. All passengers were transferred to the quarantine hotel for routine 14-day medical observation and regular tested of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid. One of the patients, a 27-year-old Chinese male, reported positive SARS-CoV-2 nucleic acid on April 27, 2022. The patient had a history of full coronavirus disease 2019 (COVID-19) vaccination and denied exposure to other COVID-19 cases in the past 14 days. After diagnosis, he was transferred to Guangzhou Eighth People’s Hospital for treatment. On April 30, 2022, a nasal swab sample from the patient was sequenced using the Illumina MiniSeq platform (Illumina, San Diego, CA, USA), and genotyping results showed that the patient was infected with Omicron subvariant BA.2.12.1. A total of 33 amino acid mutation sites (T19I, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452Q, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, S704L, N764K, D796Y, Q954H, N969K and L24del, P25del, P26del) were detected on the spike gene, two of which (L452Q and S704L) were key sites defining the signature of sublineage BA.2.12.1 (1-2) (Figure 1). The sequence has been submitted to the National Genomics Data Center (under the accession number WGS025539). On May 4, 2022, the World Health Organization reminded to closely monitor BA.2.12.1 subvariants (2). Compared to other Omicron variants, BA.2.12.1 subvariants shows stronger immune escape, even after having been vaccinated with booster dose (3). Several studies have shown that the transmissibility of BA.2.12.1 is about 23% to 27% faster than that of BA.2. Omicron BA 2.12.1 subvariants spread very fast, which led to the resurgence of the epidemic in many parts of the United States, and cases have been reported in at least 17 countries (4). Public health officials are focusing on this subvariant and trying to learn more. Author Affiliations

Introduction:After the epidemic in Wuhan City was brought under control in 2020, local outbreaks of coronavirus disease 2019 (COVID-19) in the mainland of China were mainly due to imported COVID-19 cases. The ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to generate new variants. Some have been designated as variants of concern (VOCs) by the World Health Organization (WHO). To better assess the role of imported SARS-CoV-2 surveillance and the prevalence of VOCs in 2021, the genomic surveillance data of SARS-CoV-2 from imported COVID-19 cases of 2021 in the mainland of China were analyzed.Methods:The analyses included the number of sequence submissions, time of sequence deposition, and time of detection of the VOCs in order to determine the timeliness and sensitivity of the surveillance. The proportions of VOCs were analyzed and compared with data from the Global Initiative of Sharing All Influenza Data (GISAID).Results:A total of 3,355 sequences of imported cases were submitted from 29 provincial-level administrative divisions, with differences in the number of sequence submissions and median time of sequence deposition. A total of 2,388 sequences with more than 90% genomic coverage were used for lineage analysis. The epidemic trend from Alpha to Delta to Omicron in imported cases was consistent with that in the GISAID. In addition, VOCs from imported cases were usually identified after WHO designation and before causing local outbreaks.Conclusions:The global distribution of SARS-CoV-2 VOCs changed rapidly in 2021. Robust genomic surveillance of the imported SARS-CoV-2 in the mainland of China is of great significance.

Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is the dominant circulating strain worldwide. To assess the importation of SARS-CoV-2 variants in the mainland of China during the Omicron epidemic, the genomic surveillance data of SARS-CoV-2 from imported coronavirus disease 2019 (COVID-19) cases in the mainland of China during the first half of 2022 were analyzed.Methods: Sequences submitted from January to July 2022, with a collection date before June 30, 2022, were incorporated. The proportions of SARS-CoV-2 variants as well as the relationships between the origin and destination of each Omicron imported case were analyzed.Results: 4,946 sequences of imported cases were submitted from 27 provincial-level administrative divisions (PLADs), and the median submission interval was within 1 month after collection. In 3,851 Omicron sequences with good quality, 1 recombinant (XU) and 4 subvariants under monitoring (BA.4, BA.5, BA.2.12.1, and BA.2.13) were recorded, and 3 of them (BA.4, BA.5, and BA.2.12.1) caused local transmissions in the mainland of China later than that recorded in the surveillance. Omicron subvariants dominated in the first half of 2022 and shifted from BA.1 to BA.2 then to BA.4 and BA.5. The percentage of BA.2 in the imported SARS-CoV-2 surveillance data was far higher than that in the Global Initiative on Sharing All Influenza Data (GISAID). The imported cases from Hong Kong Special Administrative Region, China, accounted for 32.30% of Omicron cases sampled, and 98.71% of them were BA.2.Conclusions: The Omicron variant showed the intra-Omicron evolution in the first half of 2022, and all of the Omicron subvariants were introduced into the mainland of China multiple times from multiple different locations.

On April 29, 2022, a flight arrived at Baiyun International Airport, Guangzhou City, Guangdong Province, from Amsterdam Schiphol Airport, Netherlands. After the first test of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid at the airport, all passengers were admitted to a quarantine hotel for a routine 14-day medical observation. On April 30, one of the passengers (a 20-year-old Chinese female) was reported positive for coronavirus disease 2019 (COVID-19), and then a nasopharyngeal swab sample was immediately retested on May 1 and reported positive. The patient was fully vaccinated against COVID-19 and completed 14 days of quarantine before flying to China. She denied any history of exposure to COVID-19 cases. After diagnosis, the patient was sent to Foshan Fourth People’s Hospital for treatment. On May 4, 2022, the viral genomic sequence of the patient was obtained using the Illumina MiniSeq platform (Illumina, San Diego, CA, USA), and genotyping results showed that the genome belonged to the Omicron/variant of concern (VOC) sublineage BA.4, with a total of 30 amino acid mutations (V3G, T19I, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K) and 5 deletions (L24del, P25del, P26del, H69del, V70del) in the Spike protein gene. The phylogenetic tree indicates that the sequenced BA.4 has high similarity to the genome detected in Denmark on May 4, 2022 (GISAID: EPI_ISL_12648960) (Figure 1). The sequence has been deposited in the National Genomics Data Center (under the accession number WGS025540). On May 4, 2022, the World Health Organization reminded to closely monitor Omicron BA.4 subvariants (1). BA.4 is driving the upsurge in South Africa and has rapidly replaced BA.2, with over 50% of sequenced cases since the first week of April 2022 (2). Compared to BA.2, the BA.4 subvariants also showed stronger immune escape to the plasma of 3-dose vaccinees, even vaccinated BA.1 convalescent plasma (3-4). Cases of BA.4 infection have been reported in at least 20 countries, mainly from South Africa (62.39%) (5-6). Researchers are focusing on this subvariant and trying to learn more.

The Omicron variants spread rapidly worldwide after being initially detected in South Africa in November 2021. It showed increased transmissibility and immune evasion with far more amino acid mutations in the spike (S) protein than the previously circulating variants of concern (VOCs). Notably, on 15 July 2022, we monitored the first VOC / Omicron subvariant BA.2.75 in China from an imported case. Moreover, nowadays, this subvariant still is predominant in India. It has nine additional mutations in the S protein compared to BA.2, three of which (W152R, G446S, and R493Q reversion) might contribute to higher transmissibility and immune escape. This subvariant could cause wider spread and pose a threat to the global situation. Our timely reporting and continuous genomic analysis are essential to fully elucidate the characteristics of the subvariant BA.2.75 in the future.

Da-Yan Wang,1 Shun-Xiang Qi,1 Xi-Yan Li, Jun-Feng Guo, Min-Ju Tan, Guang-Yue Han, Yan-Fang Liu, Yu Lan, Lei Yang, Wei-Juan Huang, Yan-Hui Cheng, Xiang Zhao, Tian Bai, Zhao Wang, He-Jiang Wei, Ning Xiao, and Yue-Long Shu Authors affiliations: National Institute for Viral Disease Control and Prevention, China CDC, Beijing, People’s Republic of China (D.-Y. Wang, X.-Y. Li, J.-F. Guo, M.-J. Tan, Y. Lan, L. Yang, W.-J. Huang, Y.-H. Cheng, X. Zhao, T. Bai, Z. Wang, N. Xiao, H.-J. Wei, Y.-L. Shu); and Hebei Center for Disease Control and Prevention, Hebei Province, People’s Republic of China (S.-X. Qi, G.-Y. Han, Y.-F. Liu)