Magnetic resonance imaging based on radiomics for differentiating T1-category nasopharyngeal carcinoma from nasopharyngeal lymphoid hyperplasia: a multicenter study.

PURPOSE: To investigate the role of magnetic resonance imaging (MRI) based on radiomics using T2-weighted imaging fat suppression (T2WI-FS) and contrast enhanced T1-weighted imaging (CE-T1WI) sequences in differentiating T1-category nasopharyngeal carcinoma (NPC) from nasopharyngeal lymphoid hyperplasia (NPH). MATERIALS AND METHODS: This study enrolled 614 patients (training dataset: n = 390, internal validation dataset: n = 98, and external validation dataset: n = 126) of T1-category NPC and NPH. Three feature selection methods were used, including analysis of variance, recursive feature elimination, and relief. The logistic regression classifier was performed to construct the radiomics signatures of T2WI-FS, CE-T1WI, and T2WI-FS + CE-T1WI to differentiate T1-category NPC from NPH. The performance of the optimal radiomics signature (T2WI-FS + CE-T1WI) was compared with those of three radiologists in the internal and external validation datasets. RESULTS: Twelve, 15, and 15 radiomics features were selected from T2WI-FS, CE-T1WI, and T2WI-FS + CE-T1WI to develop the three radiomics signatures, respectively. The area under the curve (AUC) values for radiomics signatures of T2WI-FS + CE-T1WI and CE-T1WI were significantly higher than that of T2WI-FS (AUCs = 0.940, 0.935, and 0.905, respectively) for distinguishing T1-category NPC and NPH in the training dataset (Ps all < 0.05). In the internal and external validation datasets, the radiomics signatures based on T2WI-FS + CE-T1WI and CE-T1WI outperformed T2WI-FS with no significant difference (AUCs = 0.938, 0.925, and 0.874 for internal validation dataset and 0.932, 0.918, and 0.882 for external validation dataset; Ps > 0.05). The radiomics signature of T2WI-FS + CE-T1WI significantly performed better than three radiologists in the internal and external validation datasets. CONCLUSION: The MRI-based radiomics signature is meaningful in differentiating T1-category NPC from NPH and potentially helps clinicians select suitable therapy strategies.

Genomic and epidemiological perspectives on the first local sporadic cases of Mpox in China.

From June 7th to 11th, 2023, eight cases of Mpox were identified in Guangzhou, China. This is the first report of multiple local sporadic cases after the imported case in Chongqing, China. Epidemiological investigation revealed that these cases had no history of international travel and no connections with each other. Haplotype network and phylogenetic analyses indicated that the possible origin is likely from Japan, although the direct origin may remain uncertain due to limited genomic sequences and sampling bias in GISAID. The three Guangzhou sequences have accumulated several novel mutations, suggesting the local transmission of Mpox may have been ongoing for some time. Based on the daily cases during the early stage of Mpox outbreak in four other countries, the number of possible infected cases in Guangzhou is inferred to be more than 300, suggesting that swift and efficient control measures must be implemented to mitigate the risk of a potential epidemic.

Persistence of Tembusu Virus in Culex tritaeniorhynchus in Yunnan Province, China.

The Tembusu virus (TMUV), a member of the Flaviviridae family, can be transmitted via mosquitoes and cause poultry disease. In 2020, a strain of TMUV (YN2020-20) was isolated from mosquito samples collected in Yunnan province, China. In vitro experiments showed that TMUV-YN2020-20 produced a significant cytopathic effect (CPE) in BHK, DF-1, and VERO cells, while the CPE in C6/36 cells was not significant. Phylogenetic analysis revealed that the strain belonged to Cluster 3.2 and was closely related to the Yunnan mosquito-derived isolates obtained in 2012 and the Shandong avian-derived isolate obtained in 2014. Notably, TMUV-YN2020-20 developed five novel mutations (E-V358I, NS1-Y/F/I113L, NS4A-T/A89V, NS4B-D/E/N/C22S, and NS5-E638G) at loci that were relatively conserved previously. The results of this study demonstrate the continuous circulation and unique evolution of TMUV in mosquitoes in Yunnan province and suggest that appropriate surveillance should be taken.

Epidemiological and genomic analysis of dengue cases in Guangzhou, China, from 2010 to 2019.

With a long epidemic history and a large number of dengue cases, Guangzhou is a key city for controlling dengue in China. The demographic information regarding dengue cases, and the genomic characteristics of the envelope gene of dengue viruses, as well as the associations between these factors were investigated from 2010 to 2019, to improve the understanding of the epidemiology of dengue in Guangzhou. Demographic data on 44,385 dengue cases reported to the Notifiable Infectious Disease Report System were analyzed using IBM SPSS Statistics v. 20. Dengue virus isolates from patient sera were sequenced, and phylogenetic trees were constructed using PhyML 3.1. There was no statistical difference in the risk of dengue infection between males and females. Unlike other areas in which dengue is endemic, the infection risk in Guangzhou increased with age. Surveillance identified four serotypes responsible for dengue infections in Guangzhou. Serotype 1 remained prevalent for most of the study period, whereas serotypes 3 and 4 were prevalent in 2012 and 2010, respectively. Different serotypes underwent genotype and sublineage shifts. The epidemiological characteristics and phylogeny of dengue in Guangzhou suggested that although it has circulated in Guangzhou for decades, it has not been endemic in Guangzhou. Meanwhile, shifts in genotypes, rather than in serotypes, might have caused dengue epidemics in Guangzhou.

A Serotype-Specific and Multiplex PCR Method for Whole-Genome Sequencing of Dengue Virus Directly from Clinical Samples.

Dengue virus (DENV) is the most globally prevalent member of the genus Flavivirus in the family Flaviviridae, which can be classified into four serotypes. Historically, molecular epidemiological studies of DENV depended on E gene sequencing. The development of next-generation sequencing (NGS) allowed its application to viral whole-genome sequencing (WGS). In this study, we report the improvement of the existing WGS process for DENV by optimizing the primer design procedure, designing serotype-specific primer panels and reducing the sizes of amplicons. A total of 31 DENV-positive serum samples belonging to 4 serotypes and 9 genotypes of DENV were involved in the validation of the primer panels. The threshold cycle (CT) values of these samples ranged from 23.91 to 35.11. The validation results showed that the length of consensus sequences generated at a coverage depth of 20× or more ranged from 10,370 to 10,672 bp, with 100.00% coverage of the open reading frames and 97.34% to 99.52% coverage of the DENV genome. The amplification efficiency varied across amplicons, genotypes, and serotypes of DENVs. These results indicate that the serotype-specific primer panels allow users to obtain the whole genome of DENV directly from clinical samples, providing a universal, rapid, and effective tool for the integration of genomics with dengue surveillance. IMPORTANCE Dengue virus (DENV) is becoming the most globally prevalent arbovirus. The number of people living under the threat of DENV is increasing year by year. With the development of next-generation sequencing (NGS) technology, whole-genome sequencing (WGS) has been more and more widely used in infectious disease surveillance and molecular epidemiological studies. DENV population sequencing by NGS can increase our understanding of the changing epidemiology and evolution of the DENV genome at the molecular level, which demands universal primer panels and combination with NGS platforms. Multiplex PCR with a short-amplicon approach proved superior for amplifying viral genomes from clinical samples, particularly when the viral RNA was present at low concentrations. Additionally, DENV are known for their genetic diversity within serotype groups and geographical regions, so the primer panels we designed focused on universality, which would be useful in future local DENV outbreaks.

Circulation of genotypes of dengue virus serotype 2 in Guangzhou over a period of 20 years.

BACKGROUND: The dengue epidemic in Guangzhou has imposed a rising burden on society and health infrastructure. Here, we present the genotype data for dengue virus serotype 2 (DENV-2) to improve understanding of this dengue epidemic. METHODS: We sequenced the envelope gene of DENV-2 obtained from patient serum samples and subsequently performed maximum-likelihood phylogenetic analysis using PhyMLv3.1, maximum clade credibility analysis using BEAST v.1.10.4, and selection pressure analysis using Datamonkey 2.0. RESULTS: The prevalent DENV-2 strains identified in Guangzhou region are related to those in Southeast Asian countries. In particular, the Malaysia/Indian subcontinent genotype is prevailing in Guangzhou with no apparent genotype shift having occurred over the past 20 years. However, episodic positive selection was detected at one site. CONCLUSIONS: Local control of the DENV-2 epidemic in Guangzhou requires effective measures to prevent and monitor imported cases. Moreover, the shift between the Malaysia/Indian subcontinent genotype lineages, which originated at different time points, may account for the rise in DENV-2 cases in Guangzhou. Meanwhile, the low rate of dengue haemorrhagic fever in Guangzhou may be explained by the dominance of the less virulent Malaysia/Indian subcontinent genotype.

Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant.

The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.

Assessment of the global circulation and endemicity of dengue.

Dengue is a significant public health issue, affecting hundreds of millions of people worldwide. As it is spreading from tropical and subtropical zones, some regions previously recognised as non-endemic are at risk of becoming endemic. However, the global circulation of dengue is not fully understood and quantitative measurements of endemicity levels are lacking, posing an obstacle in the precise control of dengue spread. In this study, a sequence-based pipeline was designed based on random sampling to study the transmission of dengue. The limited intercontinental transmission was identified, while regional circulation of dengue was quantified in terms of importation, local circulation and exportation. Additionally, hypo- and hyper-endemic regions were identified using a new metric, with the former characterised by low local circulation and increased importation, whereas the latter by high local circulation and reduced importation. In this study, the global circulation pattern of dengue was examined and a sequence-based endemicity measurement was proposed, which will be helpful for future surveillance and targeted control of dengue.

Genomic Elucidation of a COVID-19 Resurgence and Local Transmission of SARS-CoV-2 in Guangzhou, China.

While China experienced a peak and decline in coronavirus disease 2019 (COVID-19) cases at the start of 2020, regional outbreaks continuously emerged in subsequent months. Resurgences of COVID-19 have also been observed in many other countries. In Guangzhou, China, a small outbreak, involving less than 100 residents, emerged in March and April 2020, and comprehensive and near-real-time genomic surveillance of SARS-CoV-2 was conducted. When the numbers of confirmed cases among overseas travelers increased, public health measures were enhanced by shifting from self-quarantine to central quarantine and SARS-CoV-2 testing for all overseas travelers. In an analysis of 109 imported cases, we found diverse viral variants distributed in the global viral phylogeny, which were frequently shared within households but not among passengers on the same flight. In contrast to the viral diversity of imported cases, local transmission was predominately attributed to two specific variants imported from Africa, including local cases that reported no direct or indirect contact with imported cases. The introduction events of the virus were identified or deduced before the enhanced measures were taken. These results show the interventions were effective in containing the spread of SARS-CoV-2, and they rule out the possibility of cryptic transmission of viral variants from the first wave in January and February 2020. Our study provides evidence and emphasizes the importance of controls for overseas travelers in the context of the pandemic and exemplifies how viral genomic data can facilitate COVID-19 surveillance and inform public health mitigation strategies.

Decreased dengue cases attributable to the effect of COVID-19 in Guangzhou in 2020.

The dengue fever epidemic in Guangzhou may have been affected by the Coronavirus Disease 2019 (COVID-19) pandemic. The number of dengue cases dropped drastically in 2020, and there have been only 2 local cases, suggesting that dengue has not become endemic in Guangzhou.

The Rise in Norovirus-Related Acute Gastroenteritis During the Fight Against the COVID-19 Pandemic in Southern China.

Background: There has been a significant decline in the morbidity of almost all infectious diseases during the COVID-19 pandemic. However, while the incidence of norovirus-related acute gastroenteritis declined in Guangzhou, China during the initial period of the pandemic, incidence increased significantly once the new school year began in September 2020. Methods: Norovirus-related acute gastroenteritis clusters and outbreaks were assessed in Guangzhou from 2015 to 2020. Medians and interquartile ranges were compared between groups using the Mann-Whitney U-test, and attack rates were calculated. Results: While 78,579 cases of infectious diarrhea were reported from 2015 to 2019, with an average of 15,716 cases per year, only 12,065 cases of infectious diarrhea were reported in 2020. The numbers of sporadic cases and outbreaks reported from January to August 2020 were lower than the average numbers reported during the same time period each year from 2015 to 2019 but began to increase in September 2020. The number of cases in each reported cluster ranged from 10 to 70 in 2020, with a total of 1,280 cases and an average attack rate of 5.85%. The median number of reported cases, the cumulative number of cases, and the attack rate were higher than the average number reported each year from 2015 to 2019. The intervention time in 2020 was also higher than the average intervention time reported during 2015-2019. The main norovirus genotypes circulating in Guangzhou during 2015-2020 included genogroup 2 type 2 (GII.2) (n = 79, 26.69%), GII.17 (n = 36, 12.16%), GII.3 (n = 27, 9.12%), GII.6 (n = 8, 2.7%), GII.4 Sydney_2012 (n = 7, 2.36%), and GII.4 (n = 6, 2.03%). Conclusions: Our findings illustrate the importance of maintaining epidemiological surveillance for viral gastroenteritis during the COVID-19 pandemic. Local disease prevention and control institutions need to devote sufficient human resources to control norovirus clusters.

Community evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission through air.

BACKGROUND: Nine COVID-19 (Corona Virus Disease, 2019) cases were observed in one community in Guangzhou. All the cases lived in three vertically aligned units of one building sharing the same piping system, which provided one unique opportunity to examine the transmission mode of SARS-CoV-2. METHODS: We interviewed the cases on the history of travelling and close contact with the index patients. Respiratory samples from all the cases were collected for viral phylogenetic analyses. A simulation experiment in the building and a parallel control experiment in a similar building were then conducted to investigate the possibility of transmission through air. RESULTS: Index patients living in Apartment 15-b had a travelling history in Wuhan, and four cases who lived in Apartment 25-b and 27-b were subsequently diagnosed. Phylogenetic analyses showed that virus of all the patients were from the same strain of the virus. No close contacts between the index cases and other families indicated that the transmission might not occur through droplet and close contacts. Airflow detection and simulation experiment revealed that flushing the toilets could increase the speed of airflow in the pipes and transmitted the airflow from Apartment 15-b to 25-b and 27-b. Reduced exhaust flow rates in the infected building might have contributed to the outbreak. CONCLUSIONS: The outbreak of COVID-19 in this community could be largely explained by the transmission through air, and future efforts to prevent the infection should take the possibility of transmission through air into consideration. A disconnected drain pipe and exhaust pipe for toilet should be considered in the architectural design to help prevent possible virus spreading through the air.

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China.

Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 infection and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China's most populous province, during early 2020 resulted in 1,388 reported RNA-positive cases from 1.6 million tests. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China, we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. Combined epidemiological and phylogenetic analyses indicate multiple independent introductions to Guangdong, although phylogenetic clustering is uncertain because of low virus genetic variation early in the pandemic. Our results illustrate how the timing, size, and duration of putative local transmission chains were constrained by national travel restrictions and by the province's large-scale intensive surveillance and intervention measures. Despite these successes, COVID-19 surveillance in Guangdong is still required, because the number of cases imported from other countries has increased.

COVID-19 Outbreak Associated with Air Conditioning in Restaurant, Guangzhou, China, 2020.

During January 26-February 10, 2020, an outbreak of 2019 novel coronavirus disease in an air-conditioned restaurant in Guangzhou, China, involved 3 family clusters. The airflow direction was consistent with droplet transmission. To prevent the spread of the virus in restaurants, we recommend increasing the distance between tables and improving ventilation.

Dengue Underestimation in Guangzhou, China: Evidence of Seroprevalence in Communities With No Reported Cases Before a Large Outbreak in 2014.

OBJECTIVE: Dengue has become a serious public health problem in southern China particularly with a record-breaking outbreak in 2014. Serological evidence from areas with no known dengue cases reported prior to 2014 could provide information on possible unrecognized circulation of dengue virus (DENV) before this outbreak. METHOD: Between March and May 2015, we performed a cross-sectional serosurvey using a stratified random sampling method among individuals aged 1-84 years-old in 7 communities in Guangzhou with no reported dengue cases before 2014. Sera of subjects were initially screened with the indirect DENV IgG enzyme-linked immunosorbent assay, and positive samples were further tested by the indirect immunofluorescence assay to identify specific serotypes. RESULTS: A total of 850 subjects had complete information available. The overall seroprevalence against DENV was 6.59% (56 of 850; 95% CI, 4.92%-8.26%). The seroprevalence increased with age in general (3.86%, 4.58%, 8.72%, 7.22%, and 10.69% among participants in ≤14, 15-29, 30-44, 45-59 and ≥60 years age group, respectively). Living in rural or peri-urban communities and longer years of residence therein were risk factors for higher seroprevalence, whereas wearing long sleeves and pants when outdoors was associated with lower seroprevalence. Of the total subjects, 55.36% (31 of 56) sera were successfully identified with specific serotypes, with 12.90% (4 of 31) being coinfected with 2 serotypes. CONCLUSIONS: Dengue transmission in the study communities had occurred prior to the 2014 massive outbreak, possibly for many years, but went undiagnosed and unreported. A proportion of the study population experienced secondary infection as different serotypes of DENV increased the risk for severe diseases. Active surveillance and education of both healthcare providers and the general population should be conducted in areas at risk for dengue emergence in order to better reduce disease burden.

Evolutionary and phylodynamic analyses of Dengue virus serotype I in Guangdong Province, China, between 1985 and 2015.

To determine the evolutionary and phylodynamic history of DENV-1 in Guangdong, the strains detected between 1985 and 2015 were determined with phylogenetic and Bayesian analyses of the E gene. Three DENV-1 genotypes (I, V, and VI) were circulating in Guangdong, and genotype I was detected most frequently. The evolutionary rate of DENV-1 was estimated to be 1.03 × 10-3 nucleotide substitutions/site/year. The most recent ancestor of the viruses existed approximately 141 years ago. The observed epidemiological dynamics correlated with similar fluctuations in diversity, and the epidemiological dynamics of DENV-1 transmission reflect dramatic changes in the viral population sizes. Two recombination events were identified in those strains. The selection pressures were estimated and revealed an abundance of negatively selected sites but few positively selected sites. These data improve our understanding of the evolution and molecular epidemiology of DENV-1 and provide insights that will facilitate the surveillance and control of DENV-1.

Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014.

Nasopharyngeal swabs were collected from patients through the influenza surveillance network of the CDC of Guangdong. All specimens between 2009 and 2014 were checked for influenza virus using MDCK cells and further subtyped. Of those collected, 542 H1N1pdm09, 230 A(H3N2)and 448 B viruses selected at random were subjected to fluorescence-based NAI assays. Viral RNA was extracted from resistant isolates, and their NA genes were amplified by RT-PCR. Alignment of nucleotides and amino acids was performed. We performed structural modelling and simulations of mutants using Modeller 9.x and AutoDock and analyzed conformations and binding affinities. All tested seasonal type B and H3N2 viruses from 2009 to 2014 remained sensitive to oseltamivir. However, there were five strains (out of 198 tested isolates acquired between June and September 2013) that were resistant to oseltamivir. Another three resistant strains were identified among isolates from March to April 2014. We found that 2013/2014 oseltamivir-resistant strains and 2012/2013/2014 oseltamivir-sensitive strains had all or some of the following mutations: N44S, N200S,V241I, I321V,N369K, N386 K and K432E. MutationsV241I, N369K, N386K and K432E, alone or in conjunction with H275Y, had a significant impact on the binding pattern and affinity of oseltamivir for neuraminidase, rendering neuraminidase less susceptible.

[Effect of supply of fresh poultry products on reducing environment contamination of avian influenza virus in markets].

OBJECTIVE: To evaluate the effect of supply of fresh poultry products on reducing environment contamination of avian influenza virus (AIV) in markets in Guangzhou. METHODS: A total of 40 markets, including 20 selling alive poultry and 20 selling fresh poultry products, were selected randomly in Guangzhou to conduct environment surveillance in 80 poultry stalls every 4 months from July 2014 to April 2015. Four smear samples were collected from different sites of each poultry stall to detect nucleic acid of AIV. The positive samples were further detected for AIV subtype H5, H7 and H9 nucleic acids. RESULTS: Among 40 alive poultry stalls, 95.0% (38/40) kept alive poultry overnight, 25.0% (10/40) were disinfected daily, 95.0% (38/40) were cleaned up weekly, 95.0% (38/40) were closed for one day every month. Among 40 fresh poultry product stalls, 20.0% (8/40) were disinfected daily, 90.0% (36/40) were cleaned up weekly, and 96.0% (38/40) ever sold dressed poultry from alive poultry markets. The positive rate of AIV in alive poultry markets was 40.4% (252/623), higher than that in fresh poultry product markets (32.3%, 197/610), the difference was significant (χ(2)=8.85, P=0.003), and the positive rate of subtype H9 virus in alive poultry markets was 28.6% (178/623), higher than that in fresh poultry product markets (16.2%, 99/610), the difference was significant (χ(2)=26.95, P<0.001). In fresh poultry product markets, the positive rate of AIV in stalls selling dressed poultry was 37.3% (180/482), higher than that in stalls selling no dressed poultry (13.3%, 17/128), the difference was significant (χ(2)=26.78, P<0.001), and the positive rate of subtype H9 virus in stalls selling dressed poultry was 19.1% (92/482), higher than that in stalls selling no dressed poultry (5.5%, 7/128), the difference was significant (χ(2)=13.80, P<0.001). Both the positive rate of AIV and the positive rate of subtype H9 virus were highest in the second round surveillance (October 2014). The differences in AIV and its subtype H5, H7 and H9 virus positive rates of environmental samples from four different sites were not significant, respectively. In the same sample site, the positive rate of subtype H9 virus in alive poultry markets was higher than that in fresh poultry product markets the difference was significant (P<0.05). CONCLUSIONS: The supply of fresh poultry products could effectively reduce the level of environment contamination of AIV in markets. Dressed poultry supplement caused the risk of AIV spread in fresh poultry product markets.