Prevalence of SARS-CoV-2 virus in saliva, stool, and urine samples of COVID-19 patients in Bihar, India.

Introduction. The coronavirus illness caused by SARS-CoV-2 can cause multiple organ involvement, with varying degrees of severity. Besides inhalation as a route for transmission, feco-oral has also been proposed. Its transmission to sewage systems is a growing public health issue. Objective. To detect SARS-CoV-2 RNA in non-respiratory samples (saliva, urine, and stool) collected from COVID-19 cases, in Bihar. Methods. This cross-sectional observational study was conducted from January 2021 to March 2022 on human non-respiratory samples. A total of 345 samples including saliva (116), stool (97), and urine (132) were collected from 143 COVID-19 cases. Samples were analysed for SARS-CoV-2 by multiplex RT-PCR targeted against E, ORF 1ab, and RdRp genes. Results. In this study, out of 143 cases, a total of 107 (74.8 %) were positive for SARS-CoV-2 RNA in at least one of the non-respiratory samples. Conclusion. There is a high prevalence of SARS-CoV-2 virus in non-respiratory samples.

COVID-19 transmission and control in land public transport: A literature review.

Land public transport is an important link within and between cities, and how to control the transmission of COVID-19 in land public transport is a critical issue in our daily lives. However, there are still many inconsistent opinions and views about the spread of SARS-CoV-2 in land public transport, which limits our ability to implement effective interventions. The purpose of this review is to overview the literature on transmission characteristics and routes of the epidemic in land public transport, as well as to investigate factors affecting its spread and provide feasible measures to mitigate the infection risk of passengers. We obtained 898 papers by searching the Web of Science, Pubmed, and WHO global COVID database by keywords, and finally selected 45 papers that can address the purpose of this review. Land public transport is a high outbreak area for COVID-19 due to characteristics like crowding, inadequate ventilation, long exposure time, and environmental closure. Different from surface touch transmission and drop spray transmission, aerosol inhalation transmission can occur not only in short distances but also in long distances. Insufficient ventilation is the most important factor influencing long-distance aerosol transmission. Other transmission factors (e.g., interpersonal distance, relative orientation, and ambient conditions) should be noticed as well, which have been summarized in this paper. To address various influencing factors, it is essential to suggest practical and efficient preventive measures. Among these, increased ventilation, particularly the fresh air (i.e., natural ventilation), has proven to effectively reduce indoor infection risk. Many preventive measures are also effective, such as enlarging social distance, avoiding face-to-face orientation, setting up physical partitions, disinfection, avoiding talking, and so on. As research on the epidemic has intensified, people have broken down many perceived barriers, but more comprehensive studies on monitoring systems and prevention measures in land public transport are still needed.

Characteristics of newly reported HIV/AIDS cases aged 15 years and older in Shangcheng District from 2006 to 2022 / 预防医学

Objective@#To investigate the characteristics of newly reported HIV/AIDS cases aged 15 years and older in Shangcheng District, Hangzhou City from 2006 to 2022, so as to provide the basis for improving AIDS prevention and control strategies.@*Methods@#Data of newly reported HIV/AIDS cases aged 15 years and older in Shangcheng District from 2006 to 2022 were collected through HIV/AIDS Comprehensive Control System of Chinese Disease Prevention and Control Information System. Population distribution and transmission routes were analyzed, and changing trends in case number were analyzed using average annual percent change (AAPC) and annual percent change (APC).@*Results@#A total of 4 409 HIV/AIDS cases aged 15 years and older were newly reported in Shangcheng District from 2006 to 2022, including 3 932 males (89.18%). There were 3 447 cases (78.18%) under 50 years old and 962 cases (21.82%) being 50 years and older. Sexual contact was a predominant transmission route, with 4 326 cases accounting for 98.12%, including 2 626 cases (59.56%) with homosexual contact and 1 700 cases (38.56%) with heterosexual contact. The number of HIV/AIDS cases showed an overall upward trend from 2006 to 2022 (AAPC=13.038%, P<0.05), with an upward trend from 2006 to 2015 (APC=42.578%, P<0.05) and a downward trend from 2015 to 2022 (APC=-19.713%, P<0.05). The increase in the number of cases aged 50 years and older group was faster than that of cases aged under 50 years (AAPC=22.641% vs. 11.162%, both P<0.05). The increase in the number of cases with homosexual contact transmission was faster than that of cases with heterosexual contact transmission (AAPC=20.417% vs. 7.455%, both P<0.05).@*Conclusions@#The number of newly reported HIV/AIDS cases aged 15 years and older in Shangcheng District performed an overall upward trend from 2006 to 2022. The cases aged 50 years and older and transmitted through homosexual contact increased rapidly, which should be taken seriously.

Biofilm on the pipeline wall is an important transmission route of resistome in drinking water distribution system.

Due to the intensive use of antibiotics, the drinking water distribution system (DWDS) has become one of the hotspots of antibiotic resistance. However, little is known about the role of biofilm in the aspect of spreading resistance in DWDS. In present study, four lab-scale biological annular reactors (BAR) were constructed to investigate the transmission of ARGs exposed to a certain amount of antibiotic (sulfamethoxazole) synergistic disinfectants. It was emphasized that pipe wall biofilm was an important way for ARGs to propagate in the pipeline, and the results were quantified by constructing an operational taxonomic unit (OTU) network map. The network analysis results showed the biofilm contribution to waterborne bacteria was finally estimated to be 51.45% and 34.27% in polyethylen (PE) pipe and ductile iron (DI) pipe, respectively. The proportion of vertical gene transfer (VGT) in biofilm was higher than that in water, and the occurrence of this situation had little relationship with the selection of pipe type. Overall, this study revealed how biofilm promoted the transmission of resistome in bulk water, which can provide insights into assessing biofilm-associated risks and optimizing pipe material selection for biofilm control in DWDS.

Association between socioeconomic deprivation and incidence of infectious intestinal disease by pathogen and linked transmission route: An ecological analysis in the UK.

Infectious intestinal disease (IID) studies conducted at different levels of the surveillance pyramid have found heterogeneity in the association of socioeconomic deprivation with illness. The aim of this study was to analyse the association between socioeconomic deprivation and incidence of IID by certain gastrointestinal pathogens reported to UKHSA. Data were extracted from 2015 to 2018 for Salmonella, Campylobacter, Shigella, Giardia species, and norovirus. Rates were calculated per 100,000 person-years by the index of multiple deprivation quintile, and an ecological analysis was conducted using univariant and multvariable regression models for each pathogen. Incidence of Campylobacter, and Giardia species decreased with increasing deprivation. Conversely, the incidence of norovirus, non-typhoidal Salmonella, Salmonella typhi/paratyphi, Shigella species increased with increasing deprivation. Multivariable analysis results showed that higher deprivation was significantly associated with higher odds of higher number of cases for Shigella flexneri, norovirus and S. typhi/paratyphi. Infections most associated with deprivation were those transmitted by person-to-person spread, and least associated were those transmitted by zoonotic contamination of the environment. Person-to-person transmission can be contained by implementing policies targeting over-crowding and poor hygiene. This approach is likely to be the most effective solution for the reduction of IID.

Comparative analysis of inflight transmission of SARS-CoV-2, influenza, and SARS-CoV-1.

The aim of this study is to evaluate the infection risk of aircraft passengers seated within and beyond two rows of the index case(s) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A(H1N1)pdm09 virus, and SARS-CoV-1. PubMed databases were searched for articles containing information on air travel-related transmission of SARS-CoV-2, influenza A(H1N1)pdm09 virus, and SARS-CoV-1 infections. We performed a meta-analysis of inflight infection data. In the eight flights where the attack rate could be calculated, the inflight SARS-CoV-2 attack rates ranged from 2.6% to 16.1%. The risk ratios of infection for passengers seated within and outside the two rows of the index cases were 5.64 (95% confidence interval (CI):1.94-16.40) in SARS-CoV-2 outbreaks, 4.26 (95% CI:1.08-16.81) in the influenza A(H1N1)pdm09 virus outbreaks, and 1.91 (95% CI:0.80-4.55) in SARS-CoV-1 outbreaks. Furthermore, we found no significant difference between the attack rates of SARS-CoV-2 in flights where the passengers were wearing masks and those where they were not (p = 0.22). The spatial distribution of inflight SARS-CoV-2 outbreaks was more similar to that of the influenza A(H1N1)pdm09 virus outbreaks than to that of SARS-CoV-1. Given the high proportion of asymptomatic or pre-symptomatic infection in SARS-CoV-2 transmission, we hypothesised that the proximity transmission, especially short-range airborne route, might play an important role in the inflight SARS-CoV-2 transmission.

Unique genomic sequences in a novel Mycobacterium avium subsp. hominissuis lineage enable fine scale transmission route tracing during pig movement.

Mycobacterium avium subsp. hominissuis (MAH) is one of the most prevalent mycobacteria causing non-tuberculous mycobacterial disease in humans and animals. Of note, MAH is a major cause of mycobacterial granulomatous mesenteric lymphadenitis outbreaks in pig populations. To determine the precise source of infection of MAH in a pig farm and to clarify the epidemiological relationship among pig, human and environmental MAH lineages, we collected 50 MAH isolates from pigs reared in Japan and determined draft genome sequences of 30 isolates. A variable number of tandem repeat analysis revealed that most pig MAH isolates in Japan were closely related to North American, European and Russian human isolates but not to those from East Asian human and their residential environments. Historical recombination analysis revealed that most pig isolates could be classified into SC2/4 and SC3, which contain MAH isolated from pig, European human and environmental isolates. Half of the isolates in SC2/4 had many recombination events with MAH lineages isolated from humans in East Asia. To our surprise, four isolates belonged to a new lineage (SC5) in the global MAH population. Members of SC5 had few footprints of inter-lineage recombination in the genome, and carried 80 unique genes, most of which were located on lineage specific-genomic islands. Using unique genetic features, we were able to trace the putative transmission route via their host pigs. Together, we clarify the possibility of species-specificity of MAH in addition to local adaptation. Our results highlight two transmission routes of MAH, one exposure on pig farms from the environment and the other via pig movement. Moreover, our study also warns that the evolution of MAH in pigs is influenced by MAH from patients and their residential environments, even if the MAH are genetically distinct.

Factors Associated With Helicobacter Pylori Infection Among School-Aged Children From a High Prevalence Area in Vietnam.

Objectives: The study aimed to identify prevalence of H. pylori infection and associated risk factors among pupils of Ho Chi Minh city (HCMC). Methods: A total of 1,476 pupils aged 6-15 years were enrolled in this cross-sectional study using multiple-stage sampling method. Infection status was assessed using stool antigen-test. A questionnaire was used to obtain socio-demographic, behavioral, and environmental factors. Logistic regression was performed to assess possible factors related to the infection. Results: Of the 1,409 children included in the analysis, 49.2% were male and 95.8% were of Kinh ethnicity. About 43.5% of parents completed college or university. The overall prevalence of H. pylori was 87.7%. Infrequency of handwashing with soap after toilet, the use of only water to clean after toilet, crowded living areas, larger family size, and younger age were independently contributing to an increased prevalence of H. pylori. Conclusion: H. pylori infection is highly prevalent in HCMC, and is associated with poor hygienic practices, crowded living areas, larger family size, and younger age. These findings highlight the importance of fecal-oral route and the attribution of crowded living conditions to the spreading of H. pylori in HCMC. Therefore, preventive programs should be set up with a focus on education of hygiene practices, and oriented to those living in crowded conditions.

Transmission of Hepatitis E Virus.

Transmission of hepatitis E virus (HEV) occurs predominantly by the fecal-oral route. Large epidemics of hepatitis E in the developing countries of Asia and Africa are waterborne and spread through contaminated drinking water. The reservoir of HEV in developed countries is believed to be in animals with zoonotic transmission to humans, possibly through direct contact or the consumption of undercooked contaminated meat. And HEV transmission through blood transfusion, organ transplantation, and vertical transmission has been reported.

No Substantial Histopathologic Changes in Mops condylurus Bats Naturally Infected with Bombali Virus, Kenya.

We found similar mild perivascular inflammation in lungs of Bombali virus-positive and -negative Mops condylurus bats in Kenya, indicating the virus is well-tolerated. Our findings indicate M. condylurus bats may be a reservoir host for Bombali virus. Increased surveillance of these bats will be important to reduce potential virus spread.

Healthcare-associated hepatitis B and C transmission to patients in the EU/EEA and UK: a systematic review of reported outbreaks between 2006 and 2021.

Healthcare-associated transmission was the second most common hepatitis B (HBV) and hepatitis C (HCV) transmission route according to 2006-2012 European surveillance data, but data quality and completeness issues hinder comprehensive characterisation of this important issue. We carried out a systematic review of published literature on healthcare-associated transmission of HBV or HCV in European Union (EU) and European Economic Area (EEA) countries and the United Kingdom to complement surveillance data and identify higher-risk settings. We searched the PubMed and Embase databases and grey literature over the period January 2006 to September 2021, for publications reporting transmission events after 2000 in the EU/EEA and UK related to a healthcare setting or procedure. We collected data on the country, number of patients, setting type and route of transmission. In 65 publications from 16 countries, 43 HBV and 48 HCV events were identified resulting in 442 newly infected patients. Most events were reported from Italy (7 HBV and 12 HCV), Germany (8 HBV and 5 HCV) and the United Kingdom (8 HBV and 5 HCV). The number of patients infected from a single source within an event ranged from 1 to 53. Five large outbreaks of over 20 cases were identified, including two in Poland and one each in Belgium, Hungary and Slovakia. The majority of transmission events occurred through blood transfusions or in dialysis units. However, there were a number of outbreaks in seemingly low risk settings such as CT/MRI scanning units. A failure to adequately follow infection prevention control (IPC) precautions was reported in 30% of included studies. Healthcare-associated transmission of hepatitis B and C continues to occur in a range of community and hospital settings across EU/EEA countries and often results in large outbreaks, although the true extent of the situation cannot be fully determined due to under-reporting. Strict IPC precautions should be implemented across all healthcare settings and regularly audited, and surveillance systems strengthened and standardised to allow for comprehensive and consistent reporting of nosocomial transmission of hepatitis across the EU.

Genotypes and transmission routes of noroviruses causing sporadic acute gastroenteritis among adults and children, Japan, 2015-2019.

Noroviruses (NoVs) are major causes of acute viral gastroenteritis at all ages worldwide. The molecular epidemiology of sporadic cases remains poorly understood, especially in adults. Additionally, no studies have analyzed the transmission route in sporadic acute gastroenteritis. In this study, we investigated cases of very mild sporadic NoV acute gastroenteritis in adults (medical staff) who do not visit the outpatient clinic and child outpatients. We also evaluated genotype differences between adults and children and possible transmission routes in adults during 5 years. The number of NoV positives were 58 in adults and 124 in children. In adults, the NoV positivity rate in this study was higher (64.4%) than that in previous reports of outpatients (10%) and inpatients (5%) in the United State. This finding suggested that the NoV positivity rate might be high in adults with very mild acute gastroenteritis. In adults, human-to-human transmission rates from children and food-borne transmission (raw oysters) were 21.6% (11/51) and 19.6% (10/51), respectively. Among adults, GII.2, GII.4, and GII.17 were the predominant genotypes, with rates of 32.7%, 30.9%, and 21.8%, respectively. Among children, GII.4 and GII.2 were the predominant genotypes, with rates of 45.5% and 40.6%, respectively. GII.17 was only detected in 0.8% (1/123) of children. Trends in NoV genotypes are expected to differ depending on the patient's age. Investigating sporadic cases including the patient's background (age and transmission route) may be helpful to monitor the trend of NoV strains, forecast prevalent NoV GII genotypes, and develop NoV vaccines.

An Updated Review on SARS-CoV-2 Infection in Animals.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has lasted for two years and caused millions of infections and deaths in humans. Although the origin of SARS-CoV-2 infection in humans remains unknown, infection in animals has been frequently reported in varieties of animals all over the world. Both experimental and natural infections of SARS-CoV-2 in different animal species provide useful information on viral host range and pathogenicity. As the pandemic continues to evolve, SARS-CoV-2 infection in animals will be expanding. In this review, we summarized SARS-CoV-2 testing and infection in animals as well as SARS-CoV-2 strains and transmission in animals. Current data showed that at least 18 different animal species tested positive for SARS-CoV-2. These 18 animal species belong to pet, captive, farmed, and wild animals. Fifteen of the eighteen animal species were known to be positive for the Delta variant and ten animal species were infected with two different types of variants. Human-to-animal, animal-to-animal, and animal-to-human transmission events were suggested in different outbreaks involved in animal infection with SARS-CoV-2. Continued testing, immunization, and surveillance are warranted.

Epidemiological Evidence for Fecal-Oral Transmission of Murine Kobuvirus.

Background: Murine Kobuvirus (MuKV) is a novel picornavirus of the genus Kobuvirus, and was first identified in the feces of murine rodents in the USA in 2011. There is limited information on the transmission route of MuKV. Thus, we conducted a study to investigate virus detection rates in fecal, serum, throat, and lung tissue samples from murine rodents. Results: A total of 413 fecal samples, 385 lung samples, 269 throat swab samples, and 183 serum samples were collected from 413 murine rodents (Rattus norvegicus, Rattus tanezumi, and Rattus rattus) captured in urban Shenzhen. Kobuviruses were detected via RT-PCR. Only fecal samples were positive, with prevalence rates of 34.9% in Rattus norvegicus and 29.4% in Rattus tanezumi. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions indicated that all of the MuKV sequences obtained belonged to Aichivirus A, and were genetically closely related to other MuKVs reported in China, Hungary, and the USA. Twenty-eight full-length MuKV sequences were acquired. Phylogenetic analysis of two sequences randomly selected from the two species (SZ59 and SZ171) indicated that they shared very high nucleotide and amino acid identity with one another (94.0 and 99.3%, respectively), and comparison with human Kobuvirus revealed amino acid identity values of ~80%. Additionally, a sewage-derived sequence shared high similarity with the rat-derived sequences identified in this study, with respective nucleotide and amino acid identity values from 86.5 and 90.7% to 87.2 and 91.1%. Conclusion: The results of the current study provide evidence that murine Kobuvirus is transmitted via the fecal-oral route.

Exploration of a new hepatitis a surveillance system in Beijing, China: based on molecular epidemiology.

BACKGROUND: The incidence of hepatitis A virus (HAV) infection is low in Beijing, China, but the risk of outbreaks still exists. It is difficult to identify possible sources of infection among sporadic cases based on a routine surveillance system. Therefore, a more effective surveillance system needs to be established. METHODS: The epidemiological data of hepatitis A were obtained from a routine surveillance system. Patients with HAV confirmed at the local hospitals were asked to complete a questionnaire that included additional case information and possible sources of infection. Serum and fecal specimens were also collected for testing HAV RNA by polymerase chain reaction. In addition, the 321-nucleotide segment of the VP1/2A junction region was sequenced to determine the HAV genotype. RESULTS: In 2019, 110 HAV cases were reported in Beijing, with an incidence rate of 0.51/100,000. 61(55.5%) of these patients were male. The greatest proportion of these patients were aged from 30 to 60 years. The rate was lower in suburban and rural areas compared to urban areas. Contaminated food consumption, particularly seafood consumption, was the primary potential source of infection. Among the 16 specimens of confirmed HAV cases that could be sequenced, 93.8% were HAV IA, and 6.3% were HAV IB. In addition, the samples collected from all HAV sequences in this investigation showed 89.4-100% nucleotide homology. Two groups (each with three sporadic cases) showed 100% nucleotide homology. The three sporadic cases in one group had the same possible source of infection: contaminated salad with raw vegetables and seafood. In the other group, the three sporadic cases did not have an epidemiological connection. CONCLUSIONS: In a low HAV prevalent area, such as in Beijing, incorporating molecular epidemiology into the routine surveillance system could help inform possible clusters of outbreaks and provide support for earlier control of HAV transmission. Nevertheless, increased sampling from detected cases and improved specimen quality are needed to implement such a system.

Can imported cold food cause COVID-19 recurrent outbreaks? A review.

The coronavirus disease 2019 (COVID-19) pandemic is still spreading all over the world. Although China quickly brought the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) under control in 2020, sporadic outbreaks have recurred from time to time. Outbreaks since June 2020 have suggested that the imported cold food supply chain is a major cause for the recurrence and spread of COVID-19. Here we review recurrent outbreaks in China from June 2020 to March 2021, and we analyse the main causes for recurrence and transmission by the supply of imported cold food from port to fork. Contaminated cold food or food packaging material can transmit the virus through 'person-to-thing-to-person', by contrast with the classical 'person-to-person' pathway. We decribe safety precautions for the food system, operating environment and people along the cold chain logistics. Surface disinfection and nucleic acid inspection are needed in each stage of the logistics of imported cold food supply.

Epidemiological trend of notifiable infectious diseases in Yangpu District of Shanghai during 1950‒2020 / 上海预防医学

ObjectiveTo analyze the characteristics and trends of notifiable infectious diseases in Yangpu District of Shanghai， from 1950 to 2020， and to provide scientific basis for the formulation of control measures. MethodsDescriptive epidemiological method was used to collect and analyze the epidemiological data of notifiable infectious diseases. ResultsA total of 1 186 675 cases from 38 types of infectious diseases were reported. The annual morbidity of Class A and Class B infectious diseases fluctuated between 138.22/105 and 7 861.45/105， showing a decreasing trend. Among the 3 785 cases of death， the top five were measles， viral hepatitis， dysentery， tuberculosis and epidemic cerebrospinal meningitis. The high incidence diseases were intestinal infectious diseases， and the respiratory infectious diseases fluctuated in a wide range. Furthermore， blood-borne infectious diseases and sexual -transmitted diseases had continued to increase in recent years. As the result of normative vaccination， the incidence of associated infectious disease showed a downward trend. ConclusionThe incidence of infectious diseases in Yangpu District was on the drop from 1950 to 2020. Prevention and control work should focus on respiratory infectious diseases， blood-borne infectious diseases and sexual -transmitted diseases in the future. Furthermore， it is important to guarantee normative vaccination， especially， for prevention and control of infectious diseases.

An overview of Zika virus genotypes and their infectivity

ABSTRACT Zika virus (ZIKV) is an enveloped, single-stranded RNA arbovirus belonging to the genus Flavivirus. It was first isolated from a sentinel monkey in Uganda in 1947. More recently, ZIKV has undergone rapid geographic expansion and has been responsible for outbreaks in Southeast Asia, the Pacific Islands, and America. In this review, we have highlighted the influence of viral genetic variants on ZIKV pathogenesis. Two major ZIKV genotypes (African and Asian) have been identified. The Asian genotype is subdivided into Southwest Asia, Pacific Island, and American strains, and is responsible for most outbreaks. Non-synonymous mutations in ZIKV proteins C, prM, E, NS1, NS2A, NS2B, NS3, and NS4B were found to have a higher prevalence and association with virulent strains of the Asian genotype. Consequently, the Asian genotype appears to have acquired higher cellular permissiveness, tissue persistence, and viral tropism in human neural cells. Therefore, mutations in specific coding regions of the Asian genotype may enhance ZIKV infectivity. Considering that mutations in the genomes of emerging viruses may lead to new virulent variants in humans, there is a potential for the re-emergence of new ZIKV cases in the future.

Dynamics of Neospora caninum-Associated Abortions in a Dairy Sheep Flock and Results of a Test-and-Cull Control Programme.

Neospora caninum is an apicomplexan parasite that can cause abortions and perinatal mortality in sheep. Although ovine neosporosis has been described worldwide, there is a lack of information about the relationship between N. caninum serostatus and the reproductive performance. In this study, we described the infection dynamics in a dairy sheep flock with an abortion rate up to 25% and a N. caninum seroprevalence of 32%. Abortions were recorded in 36% and 9% of seropositive and seronegative sheep, respectively. Seropositive sheep were more likely to abort twice (OR = 4.44) or three or more times (OR = 10.13) than seronegative sheep. Endogenous transplacental transmission was the main route of transmission since 86% of seropositive sheep had seropositive offspring. Within dams that had any abortion, seropositive sheep were more likely than seronegative ones to have female descendants that aborted (OR = 8.12). The slight increase in seropositivity with the age, the low percentage of animals with postnatal seroconversion or with low avidity antibodies, and the seropositivity of one flock dog, indicated that horizontal transmission might have some relevance in this flock. A control programme based on selective culling of seropositive sheep and replacement with seronegative animals was effective in reducing the abortion rate to 7.2%.