Multiple Outbreaks Research Articles

1193. Disinfection of the Sink Drains to Reduce a Source of Serratia marcescens During Infection Outbreaks in a Neonatal Intensive Care Unit

Abstract Background Sink drains are known reservoirs of pathogens and have been associated with multiple nosocomial outbreaks. In this study, the distribution of Serratia marcescens was investigated within the sink environment of a NICU and in colonized or infected newborns. The effect of different types of drain disinfection on bacterial concentration and on the detection of Serratia marcescens in sink drains was also investigated. Methods Sink drains from a NICU were sampled: 20 drains sampled for 6 weeks in the first year and 28 drains sampled for 5 months in the second year. S. marcescens isolated from positive patients were collected. A high-throughput short sequence typing (HiSST) method was developed to identify S. marcescens and compare strains and environmental DNA from sink drains with 56 clinical strains from 5 nosocomial outbreaks. Five interventions were tested: self-disinfecting drains, hot water disinfection, chlorine disinfection, steam disinfection and hot tap water flushing. Bacterial concentration of samples was measured in culture and flow cytometry and the HiSST method was used to identify S. marcescens. Results During the first and second sampling campaigns, 40% and 60% of sink drain samples were positive for S. marcescens with a moderate genotype diversity (1 to 11 different STs). The genotype profile of the 56 clinical strains was heterogeneous (26 STs). Four distinct STs were retrieved in 8 sinks after detection in patients whereas 1 ST was detected in a sink before detection in patient. Some environmental and clinical strains were found in drains for up to a year after the first sampling campaign. Each tested drain intervention reduced culturable bacteria (4-8 log) and viable bacteria (2-3 log), except for chlorine. The self-disinfecting drains, hot water and steam disinfection were able to remove temporarily S. marcescens from the drains. Conclusion The high genotypic diversity of the clinical strains suggests diffuse sources of S. marcescens within the NICU likely to cause nosocomial infection outbreaks. The self-disinfecting drains, hot water and steam disinfection seem to be the best methods to reduce bacterial concentration in drains and eliminate S. marcescens in the short term, thus limiting the risk of pathogens spread from the sink environment to patients. Disclosures All Authors: No reported disclosures.

Investigational Role of Convalescent Plasma in the Management of COVID-19 Disease in Inpatient & Outpatient Settings

Introduction:Historically, both convalescent plasma & hyperimmune globulin have been tried & tested in multiple viral outbreaks in order to confer passive immunity. These products are obtained from previously infected subjects who have fully recovered and are opined to have generated optimal immune response (polyclonal antibodies to the causative pathogen at sufficient titre and biologic activity) to confer passive immunity in the recipient. Neutralizing antibodies are the main active component of such products. In this article practical aspects of obtaining and administering convalescent plasma and evidence-base for its use in the management of COVID-19 disease in inpatient & outpatient settings is presented. Method:A comprehensive search of PubMed & EMBASE from March 2020 to July 2022 was made using 3 search items: COVID-19, convalescent plasma, and hyperimmune globulin. The search items were combined using the Boolean operator. Societal guidelines reviewed at the time of writing this article include: US Food and Drug Administration (FDA), Association for the Advancement of Blood & Biotherapies (AABB), American Society of Hematology (ASH), International Society on Thrombosis and Haemostasis (ISTH), and National Institute for Health and Care Excellence (NICE) in the United Kingdom. Results: Administering COVID-19 convalescent plasma can confer immediate passive immunity that may help shorten the duration of the COVID-19 disease &/or diminish its severity thus preventing life-threatening complications. Besides FDA issued EUA of considering convalescent plasma therapy in immunocompromised individuals with severe COVID disease, other investigational indications for convalescent plasma therapy include a) individuals exposed to SARS-CoV-2 who have not yet become ill (i.e. post-exposure prophylaxis), and b) individuals who are at high-risk of exposure or high-risk of severe disease if exposed (i.e. pre-exposure prophylaxis). Convalescent plasma has recently been successfully tried in the outpatient setting to help reduce disease severity and the incidence of hospitalizations. Conclusion: Convalescent plasma therapy remains an investigational approach to treating severe COVID disease both in inpatient and outpatient settings. Whereas more data is needed to establish its indications, safety, and relative efficacy in novel COVID-19 variant infection cases, its use in immunocompromised individuals with severe COVID disease remains a valid therapeutic consideration.

Prevalence of orthohantavirus in rodents: A systematic review and meta-analysis

IntroductionOrthohantaviruses are zoonotic diseases transmitted mainly by rodents, particularly mice and rats, associated with multiple outbreaks in different continents. Despite its epidemiological relevance, there is a lack of systematic reviews and meta-analyses. ObjectiveTo determine the combined global prevalence of Orthohantavirus infection in rodents. MethodsA systematic literature review was carried out in six databases (Web of Sciences, Scopus, PubMed, SciELO, Lilacs, Google Scholar) to evaluate the proportion of rodents infected with Orthohantavirus, defined by molecular and immunological techniques. The meta-analysis used a random effects model for the pooled prevalence and 95% confidence intervals (95%CI). Heterogeneity measures, Cochrane's Q, the I2 index and the tau-squared test were estimated. ResultsA total of 35,706 rodents (229 studies) were evaluated for ELISA, in which 3360 were found positive, for seroprevalence of 4.9% (95%CI 4.3–5.4%) (τ2 = 0.001; Q = 4027.708; I2 = 94.339%, p < 0.001). For PCR (N = 8812, 91 studies) it was 3.2% (95%CI 2.5–3.9%) (τ2 = 0.001; Q = 397.483; I2 = 77.358%; p < 0.001). For IFA (N = 555, 7 studies) it was 18.8% (95%CI 9.4–28.2%) (τ2 = 0.011; Q = 51.239; I2 = 88.29%, p < 0.001). At the genus level, the studies evaluated Oligoryzomys (8.98%), Reithrodontomys (8.98%), Peromyscus (8.20%), Rattus (8.20%), and Akodon (6.64%). ConclusionsThe global prevalence of Orthohantavirus is worrisome, with an increase in its report in certain regions, including Latin America. In this context, rodents have a role as reservoirs. The data of the present meta-analysis showed considerable seroprevalences with great variations by years, countries and Orthohantavirus species.

Global Emergence of Resistance to Fluconazole and Voriconazole in Candida parapsilosis in Tertiary Hospitals in Spain During the COVID-19 Pandemic.

Candida parapsilosis is a frequent cause of candidemia worldwide. Its incidence is associated with the use of medical implants, such as central venous catheters or parenteral nutrition. This species has reduced susceptibility to echinocandins, and it is susceptible to polyenes and azoles. Multiple outbreaks caused by fluconazole-nonsusceptible strains have been reported recently. A similar trend has been observed among the C. parapsilosis isolates received in the last 2 years at the Spanish Mycology Reference Laboratory. Yeast were identified by molecular biology, and antifungal susceptibility testing was performed using the European Committee on Antimicrobial Susceptibility Testing protocol. The ERG11 gene was sequenced to identify resistance mechanisms, and strain typing was carried out by microsatellite analysis. We examined the susceptibility profile of 1315 C. parapsilosis isolates available at our reference laboratory between 2000 and 2021, noticing an increase in the number of isolates with acquired resistance to fluconazole, and voriconazole has increased in at least 8 different Spanish hospitals in 2020-2021. From 121 recorded clones, 3 were identified as the most prevalent in Spain (clone 10 in Catalonia and clone 96 in Castilla-Leon and Madrid, whereas clone 67 was found in 2 geographically unrelated regions, Cantabria and the Balearic Islands). Our data suggest that concurrently with the coronavirus disease 2019 pandemic, a selection of fluconazole-resistant C. parapsilosis isolates has occurred in Spain, and the expansion of specific clones has been noted across centers. Further research is needed to determine the factors that underlie the successful expansion of these clones and their potential genetic relatedness.

A Bitter Experience That Enlightens the Future: COVID-19 Neurological Affection and Perspectives on the Orexigenic System

The history of coronaviruses revealed that these viruses caused multiple outbreaks in the past, including a previous severe acute respiratory syndrome (SARS) outbreak in 2003. In 2019, a novel SARS virus, SARS-CoV-2, started a drastic pandemic that, up till now, keeps peaking in successive waves owing to the mutational ability of the virus versus the short-term immunity against it. Although the angiotensin-converting enzyme 2 (ACE2) is the gate through which the virus gets access to human cells, yet ACE2 is deemed protective in lung injury yielding vasodilator, anti-fibrotic, and anti-inflammatory peptides. The viral-provoked ACE2 downregulation aggravated a subsequent potentially lethal cytokine storm. Both the tumor necrosis factor-alpha (TNF-α) receptor (TNFR), activated by the proinflammatory cytokine, TNF-α, released during coronavirus disease 2019 (COVID-19), and ACE2 are cleaved by tumor necrosis convertase enzyme (TACE) to render respective soluble decoy mediators. Several risk factors were linked to COVID-19 morbidity and neurological affection, including obesity and diabetes mellitus (DM), attributed toACE2 overexpression in obesity, a low-grade inflammatory state with both obesity and DM, and defective lung reparative machinery, added to low tissue-to-lung ACE2 expression in DM. The ACE2 shedding by SARS-CoV-2 upon its entry into the brain, together with the inflammatory cytokines invading the brain, predispose to such neurological affection. However, ACE2 was not sufficient to justify the occurrence of neurological disorders with COVID-19, owing to its lower brain expression, relative to other tissues. Other mediators should have contributed to such neurological disorders, of which, orexins (OXs) are discussed, owing to multiple functional similarities to ACE2. Eventually, this review highlights such similarities selected according to their possible relevance to COVID-19 symptomatology and pathology. Both ACE2 and OXs confer anti-inflammatory benefits, reduce cerebral endothelial dysfunction, promote neuronal survival and neurogenesis, and add to their therapeutic potentiality in sepsis. Both ACE2 and OXs assist in moderating the stress responses and the stress-activated hypothalamic-pituitary-adrenal axis. Both ACE2 and OXs are affected by obesity and DM. The loss of ACE2 and OXs signaling was suggested in neuro-inflammatory and neurodegenerative diseases. Of interest is the abundance of OXs in the dissemination routes to the brain, namely, the peripheral olfactory and the enteric systems. The presumptive role of OXs as analgesics and antipyretics might add to their favorable profile. Advantageously, the availability of OXs agonists and antagonists makes it applicable to corroborate or abrogate the future utility of targeting the orexigenic system in terms of COVID-19 neurological affection. Elaborative work, exploring in vitro and in vivo models, is recommended to identify or deny such perspective involvement.

Emergence and molecular characterization of the avian infectious bronchitis virus GI-23 in commercial broiler farms from South America.

Avian infectious bronchitis virus (IBV) is the etiological agent of a highly contagious disease in the poultry industry. The spike protein (S1 subunit) is responsible for the molecular diversity of the virus and many genetic types, and lineages are described worldwide. IBV genetic type I-strain 23 (GI-23) has spread across different continents (including Asia, Europe and Africa), causing multiple outbreaks and severe economic losses throughout the poultry industry in the last decade. The present study aimed to report the emergence and molecular characterization of GI-23 in South Brazil, being detected for the first time in South America. Eighty-two broiler flocks presenting clinical suspicion of infectious bronchitis were selected for this study. Tracheal, renal and intestinal samples were collected for IBV detection and genotyping. A total of 57 flocks were positive for IBV by generic RT-qPCR targeting 5' untranslated region and 31 also tested positive for GI-11 by a specific RT-qPCR targeting S1 gene for this lineage. The remaining 26 IBV-positive samples were genotyped by partial and one by complete S1 gene/protein sequencing. Phylogenetic analysis demonstrated that all of them clustered into a specific branch of the GI-23. S1 protein sequence analysis evidenced that all Brazilian GI-23 IBVs had the two characteristic amino acid substitutions A93T and S/H118P/L, but other changes were also observed, such as S37F (n = 21; 81%), G117S (n = 17, 65%), P122S (n = 16; 61%) and W71R (n = 9; 35%). This study brings new insights into the epidemiology of the IBV GI-23 in the world, highlighting its emergence and molecular characteristics in Brazil, South America.

Post-Covid Era: Predictive Aspect of Psychological Condition Due to Sudden Pandemic

Covid-19 has impacted the lives of people in various aspects positive as well as negative. It has an&#x0D; impact on different areas of life, including the economy, industries, global markets, agriculture,&#x0D; human health, etc. The virus caused disruptions to daily life and restrictions on activities in many communities during its multiple outbreaks. Hope for a potential end to the pandemic emerged with the stepping up of vaccination campaigns. However, the continual appearance of mutant strains and vaccine hesitancy has been problems both nationally and internationally. People's normal activities, routines, and livelihoods have been disrupted by self-isolation and quarantine, potentially leading to an increase in loneliness, anxiety, depression, insomnia, excessive alcohol and drug use, and self-harm or suicidal activity. The psychological aspects of the post-covid-19 era are the effect of covid-19 on CNS, and physiological and psychological diseases caused due to covid-19. The article explains Post Trauma Stress Disorder as a psychological scar, Social evils arising due to covid-19, and predictive reasons for the increase in mental illness&#x0D; Keywords- Covid-19, Pandemic, Mental Health, Post Trauma Stress Disorder, Depression, Anxiety

Prevalence and concentration of Campylobacter in faeces of dairy cows: A systematic review and meta-analysis.

The consumption of raw milk from dairy cows has caused multiple food-borne outbreaks of campylobacteriosis in the European Union (EU) since 2011. Cross-contamination of raw milk through faeces is an important vehicle for transmission of Campylobacter to consumers. This systematic review and meta-analysis, aimed to summarize data on the prevalence and concentration of Campylobacter in faeces of dairy cows. Suitable scientific articles published up to July 2021 were identified through a systematic literature search and subjected to screening and quality assessment. Fifty-three out of 1338 identified studies were eligible for data extraction and 44 were further eligible for meta-analysis. The pooled prevalence was calculated in two different meta-analytic models: a simple model based on one average prevalence estimate per study and a multilevel meta-analytic model that included all prevalence outcomes reported in each study (including different subgroups of e.g. health status and age of dairy cows). The results of the two models were significantly different with a pooled prevalence estimate of 29%, 95% CI [23–36%] and 51%, 95% CI [44–57%], respectively. The effect of sub-groups on prevalence were analyzed with a multilevel mixed-effect model which showed a significant effect of the faecal collection methods and Campylobacter species on the prevalence. A meta-analysis on concentration data could not be performed due to the limited availability of data. This systematic review highlights important data gaps and limitations in current studies and variation of prevalence outcomes between available studies. The included studies used a variety of methods for sampling, data collection and analysis of Campylobacter that added uncertainty to the pooled prevalence estimates. Nevertheless, the performed meta-analysis improved our understanding of Campylobacter prevalence in faeces of dairy cows and is considered a valuable basis for the further development of quantitative microbiological risk assessment models for Campylobacter in (raw) milk and food products thereof.

Newcastle Disease Genotype VII Prevalence in Poultry and Wild Birds in Egypt.

Newcastle Disease Virus (NDV) genotype VII is a highly pathogenic Orthoavulavirus that has caused multiple outbreaks among poultry in Egypt since 2011. This study aimed to observe the prevalence and genetic diversity of NDV prevailing in domestic and wild birds in Egyptian governorates. A total of 37 oropharyngeal swabs from wild birds and 101 swabs from domestic bird flocks including chickens, ducks, turkeys, and pelicans, were collected from different geographic regions within 13 governorates during 2019–2020. Virus isolation and propagation via embryonated eggs revealed 91 swab samples produced allantoic fluid containing haemagglutination activity, suggestive of virus presence. The use of RT-PCR targeted to the F gene successfully detected NDV in 85 samples. The geographical prevalence of NDV was isolated in 12 governorates in domestic birds, migratory, and non-migratory wild birds. Following whole genome sequencing, we assembled six NDV genome sequences (70–99% of genome coverage), including five full F gene sequences. All NDV strains carried high virulence, with phylogenetic analysis revealing that the strains belonged to class II within genotype VII.1.1. The genetically similar yet geographically distinct virulent NDV isolates in poultry and a wild bird may allude to an external role contributing to the dissemination of NDV in poultry populations across Egypt. One such contribution may be the migratory behaviour of wild birds; however further investigation must be implemented to support the findings of this study. Additionally, continued genomic surveillance in both wild birds and poultry would be necessary for monitoring NDV dissemination and genetic diversification across Egypt, with the aim of controlling the disease and protecting poultry production.

Frequency of Detection of Respiratory Pathogens in Clinically Healthy Show Horses Following a Multi-County Outbreak of Equine Herpesvirus-1 Myeloencephalopathy in California.

Actively shedding healthy horses have been indicated as a possible source of respiratory pathogen outbreak, transmission, and spread. Using nasal swabs from clinically healthy sport horses submitted for qPCR testing after an outbreak of equine herpesvirus-1 (EHV-1) myeloencephalopathy (EHM) in the spring of 2022, this study aimed to identify the rate of clinically healthy horses shedding common and less characterized respiratory pathogens within the sport horse population to better understand their role in outbreaks. Swabs were collected during a required quarantine and testing period, according to the United States Equestrian Federation (USEF), and showed return-to-competition requirements. Common respiratory pathogens, such as equine influenza virus (EIV), EHV-4, and equine rhinitis B virus (ERBV), were found at low but stable frequencies within previously reported ranges, whereas EHV-1 and Streptococcus equi subspecies equi (S. equi) were found at or above previously reported frequencies. Less characterized respiratory pathogens, such as EHV-2, EHV-5, and S. equi subspecies zooepidemicus (S. zooepidemicus), were found within previously reported ranges. Common respiratory pathogens, especially EHV-1 following the multiple EHM outbreaks, were found to be circulating in clinically healthy sport horse populations, reflecting their silent transmission. The strategy of quarantine and EHV-1 qPCR testing of clinically healthy horses was successful at eliminating additional EHM outbreaks and facilitating safe return to competition with no reported respiratory disease outbreaks following the subsequent shows in California.

Ornithobacterium rhinotracheale Isolated from Turkeys over a 20-Year Period Harbor Similar Antimicrobial Susceptibility Profiles and Multidrug Resistance.

Infections with Ornithobacterium rhinotracheale are causing respiratory diseases that require antibiotic treatment in poultry worldwide. In the field, this agent is known to often be resistant to many antimicrobials, complicating therapeutic interventions. Therefore, there is a clear need to monitor trends in resistance development. In the present study, antibiotic resistance profiles of 64 O. rhinotracheale strains isolated from diseased turkeys from 2002 to 2021 were investigated against 19 antimicrobial substances by the microdilution method. Susceptibility toward chloramphenicol, carbapenem, and sulfamethozaxole combination was found for all strains. Most isolates were also susceptible to penicillins (98%-100%), with the exception of oxacillin, cephalosporins (84%-100%), tetracycline (89%), and tylosin (88%). In the case of quinolones, 89% of isolates showed intermediate resistance to enrofloxacin, whereas 90% showed full resistance to nalidixic acid. Full resistance to the tested aminoglycosides and colistin was revealed for all strains. Eighteen different AMR profiles were elucidated; more than half of the isolates (53%) shared the same AMR profile. Similar susceptibility profiles of O. rhinotracheale isolates were found on the different farms, proving some stability over the years. All isolates were classified as multidrug resistant. Multiple outbreaks within a flock or in successive flocks within a farm comprised 46 O. rhinotracheale isolates. Here, occasional changes in susceptibility for some antimicrobial substances were observed. In general, most of the changes occurred in quinolones, followed by tetracycline switching mainly from intermediate resistance to full resistance and vice versa. The present surveillance provides actual data on effective antibiotic treatments in case of disease outbreaks and contributes to the One Health concept acknowledging the important link between animal and human health.

Inference in Gaussian state-space models with mixed effects for multiple epidemic dynamics

The estimation from available data of parameters governing epidemics is a major challenge. In addition to usual issues (data often incomplete and noisy), epidemics of the same nature may be observed in several places or over different periods. The resulting possible inter-epidemic variability is rarely explicitly considered. Here, we propose to tackle multiple epidemics through a unique model incorporating a stochastic representation for each epidemic and to jointly estimate its parameters from noisy and partial observations. By building on a previous work for prevalence data, a Gaussian state-space model is extended to a model with mixed effects on the parameters describing simultaneously several epidemics and their observation process. An appropriate inference method is developed, by coupling the SAEM algorithm with Kalman-type filtering. Moreover, we consider here incidence data, which requires to develop a new version of the filtering algorithm. Its performances are investigated on SIR simulated epidemics for prevalence and incidence data. Our method outperforms an inference method separately processing each dataset. An application to SEIR influenza outbreaks in France over several years using incidence data is also carried out. Parameter estimations highlight a non-negligible variability between influenza seasons, both in transmission and case reporting. The main contribution of our study is to rigorously and explicitly account for the inter-epidemic variability between multiple outbreaks, both from the viewpoint of modeling and inference with a parsimonious statistical model.

Frequency of Common Neurological Manifestations among Patients Presenting with Human Immunodeficiency Virus Positivity

Background: Unsafe injection practices and injection drug use have been linked to multiple HIV outbreaks in Pakistan since 2003.HIV/AIDS has a wide range of clinical manifestations, and it affects a variety of organ systems. It is neuro-invasive, neurotropic and neurovirulent, and can directly induce nervous system diseases due to its preference for the nervous system.Objective: To determine the frequency of common neurological symptoms in patients who have tested positive for the human immunodeficiency virus.Material and Methods: This descriptive cross-sectional study was conducted on 131 patients for 6 months in the Department of Medicine, Lady Reading Hospital, Peshawar (9/7/2019 to 8/1/2020). Routine examinations, CSF cultures, monofilament tests, detailed histories, and ICD-9 criteria inspection were performed on all patients to detect the existence of common neurological symptoms such as TBM, cryptococcal meningitis, peripheral neuropathy, headache, seizures, and dementia. A pre-designed proforma was used to record the data. The data was analyzed us SPSS version 20. Results: The current study showed that 66% of the patients were men and 34% were women with a mean age of 36±10.51 years. Mean duration of the disease was 1±7.33 years. TBM (45%), cryptococcal meningitis (15%), peripheral neuropathy (16%), headache (26%), seizures (28%), and dementia were the most common neurological symptoms (5%).Conclusion: TBM (45%), cryptococcal meningitis (15%), peripheral neuropathy (16%), headache (26%), seizures (28%), and dementia (5%) were the most prevalent neurological symptoms in patients with human immunodeficiency virus positive, according to our findings.Key Words: Neurological manifestations, HIV /AIDS infection.

Monkeypox virus in 2022 outbreak: what do we need to know?

Monkeypox disease is a zoonotic disease that is caused by the monkeypox virus (MPXV). The MPXV belongs to the Poxviridae family as same as variola virus which cause smallpox disease. MPXV caused multiple outbreaks in endemic and non-endemic countries since the first human case discovered in 1970 in Democratic Republic of Congo. Although there have been multiple outbreaks, the largest outbreak occurred in 2022 which gained MPXV alot of attention from the world. This review aims to provide the currently founding evidence of clinical symptoms, treatment, and prevention of monkeypox disease. This review highlights the genetic changed of MPXV in 2022 outbreak. In previous endemic, MPXV had been classified into 2 clade, clade I and clade II. However, MPXV found in 2022 outbreak had been reported to be new strain named clade III which many mutations related to human-to-human transmission potential. Most of the cases from the 2022 outbreak were among young men particularly men who has sex with men different from previous endemic which most cases were children. There is currently no treatment specifically made for MPXV, however, because MPXV is genetically similar to smallpox, the treatments used for smallpox can be used to treat monkeypox disease.

Risk-aware temporal cascade reconstruction to detect asymptomatic cases.

This paper studies the problem of detecting asymptomatic cases in a temporal contact network in which multiple outbreaks have occurred. We show that the key to detecting asymptomatic cases well is taking into account both individual risk and the likelihood of disease-flow along edges. We consider both aspects by formulating the asymptomatic case detection problem as a directed prize-collecting Steiner tree (Directed PCST) problem. We present an approximation-preserving reduction from this problem to the directed Steiner tree problem and obtain scalable algorithms for the Directed PCST problem on instances with more than 1.5M edges obtained from both synthetic and fine-grained hospital data. On synthetic data, we demonstrate that our detection methods significantly outperform various baselines (with a gain of 3.6 times ). We apply our method to the infectious disease prediction task by using an additional feature set that captures exposure to detected asymptomatic cases and show that our method outperforms all baselines. We further use our method to detect infection sources (“patient zero”) of outbreaks that outperform baselines. We also demonstrate that the solutions returned by our approach are clinically meaningful by presenting case studies.

Spatiotemporal dynamics of HIV-1 CRF63_02A6 sub-epidemic.

HIV-1 epidemic in Russia is one of the fastest growing in the world reaching 1.14 million people living with HIV-1 (PLWH) in 2021. Since mid-1990s, the HIV-1 epidemic in Russia has started to grow substantially due to the multiple HIV-1 outbreaks among persons who inject drugs (PWID) leading to expansion of the HIV-1 sub-subtype A6 (former Soviet Union (FSU) subtype A). In 2006, a local HIV-1 sub-epidemic caused by the distribution of novel genetic lineage CRF63_02A6 was identified in Siberia. In this study, we used a comprehensive dataset of CRF63_02A6 pol gene sequences to investigate the spatiotemporal dynamic of the HIV-1 CRF63_02A6 sub-epidemic. This study includes all the available CRF63_02A6 HIV-1 pol gene sequences from Los Alamos National Laboratory (LANL) HIV Sequence Database. The HIV-1 subtypes of those sequences were conferred using phylogenetic analysis, and two automated HIV-1 subtyping tools Stanford HIVdb Program and COMET. Ancestral state reconstruction and origin date were estimated using Nextstrain. Evolutionary rate and phylodynamic analysis were estimated using BEAST v 1.10.4. CRF63_02A6 was assigned for 872 pol gene sequences using phylogenetic analysis approach. Predominant number (n = 832; 95.4%) of those sequences were from Russia; the remaining 40 (4.6%) sequences were from countries of Central Asia. Out of 872 CRF63_02A6 sequences, the corresponding genetic variant was assigned for 75.7 and 79.8% of sequences by Stanford and COMET subtyping tools, respectively. Dated phylogenetic analysis of the CRF63_02A6 sequences showed that the virus most likely originated in Novosibirsk, Russia, in 2005. Over the last two decades CRF63_02A6 has been widely distributed across Russia and has been sporadically detected in countries of Central Asia. Introduction of new genetic variant into mature sub-subtype A6 and CRF02_AGFSU epidemics could promote the increase of viral genetic diversity and emergence of new recombinant forms. Further HIV-1 studies are needed due to a continuing rapid virus distribution. Also, the implementation of HIV-1 prevention programs is required to reduce HIV-1 transmission. This study also highlights the discrepancies in HIV-1 subtyping approaches. The reference lists of HIV-1 sequences implemented in widely used HIV-1 automated subtyping tools need to be updated to provide reliable results.

The Impact of Sustainable Development of Cold Chain Logistics on China’s COVID-19 Pandemic

Currently, there are multiple COVID-19 outbreaks in China’s imported cold chain product logistics. Cold chain logistics (CCL) have become an important source and weak link of China’s epidemic risk. This article discusses the differential effect of CCL on COVID-19 epidemic risk in different regions of China from an econometric analysis perspective. By comparing the development level of China and foreign countries, it can be observed that the sustainability of CCL may be a key factor affecting the risks of the epidemic. This article confirms the inverse correlation between the level of sustainability of CCL and the risk of epidemics from both mechanism analysis and empirical tests. Developing sustainability is not only beneficial to the development of the CCL industry itself but also an effective way to mitigate the risk of epidemics.

Enacted Ebola Stigma and Health-related Quality of Life in Post Ebola Epidemic: A Psychosocial Mediation Framework Through Social Support, Self-Efficacy, and Coping.

On-site experiences and reports have shown that the multiple outbreaks of Ebola virus disease (EVD) in the Democratic Republic of the Congo (DRC) resulted in pervasive experience of stigma against many people who have recovered from EVD as well as their families and close relatives. Three evidence-based protective factors which are supposed to mitigate the impact of enacted Ebola stigma on health-related quality of life (HRQoL) of individuals in this epidemic context were identified. We expected that positive religious coping, perceived social support, and general self-efficacy would mediate the relationship between enacted Ebola stigma and HRQoL. These hypotheses were tested through multiple mediation model using the structural equation modeling among a large sample of adult populations (N = 1614; 50% women) in the province of Equateur in the DRC, in the aftermath of the 9th Ebola outbreak. The mediation model yielded adequate fit statistics and the results provided strong evidence that higher levels of enacted Ebola stigma were associated with lower HRQoL. They confirmed the synergetic mediating effects of positive religious coping, perceived social support from family (but not from others sources) and general self-efficacy. Futher exploratory findings revealed that the perceived social support from family buffered the impact of enacted Ebola stigma on HRQoL. If replicated by a longitudinal study, our findings lay a solid foundation for empirical-based community mental health interventions for reducing enacted Ebola stigma and promoting HRQoL during epidemics, especially in the DRC.

Emerging challenges to realizing global polio eradication and their solutions

Background: The Global Polio Eradication Initiative (GPEI) promised to eradicate polio by 2000, yet the disease remains endemic in 2 countries. The current threat of resurgence in countries with low vaccine coverage and circulating vaccinederived poliovirus (cVDPV) outbreaks due to oral polio vaccine warrants a strategy review. Aims: To review the performance of the GPEI from a context based in Pakistan, identifying threats to success and suggesting strategy modifications to help achieve eradication. Methods: This was a desk review of the effectiveness of GPEI that was launched in 1988 to eradicate polio by 2000. Subsequent failure to eradicate led to multiple iterations in strategy and planning documents. These documents were reviewed alongside relevant literature to explore the reasons for failure and emergence of cVDPV. Results: GPEI has been effective in reducing the global polio disease burden by &gt; 99%, but it remains endemic in Pakistan and Afghanistan. cVDPV has caused multiple outbreaks since 2000, and caused 7 times more cases than wild poliovirus (WPV) globally in 2020. The Polio Eradication and Endgame Strategic Plan 2013–2018 aimed to eradicate WPV and cVDPV simultaneously. In 2019, Pakistan saw an upsurge in WPV amid an outbreak of cVDPV infection that continued throughout 2020. Wild polio eradication was not realized and the country was unable to transition to inactivated polio vaccine as predicted in the strategic plan. Conclusion: Over 20 countries now report cVDPV outbreaks and many others are at risk. A country-specific modified strategy is required to eradicate WPV and cVDPV simultaneously, more so in endemic countries.

Epidemic evolution: Source, lock-down and removal modifications to the SIR model

The original purpose of this article was to modify the original SIR equations to allow for a direct source of infection (without which the original equations would have no solutions unless one starts with an already infected population) and also to see to what extent one could obtain multiple outbreaks of an infectious disease. In the course of developing the basic ideas several other factors arose to take prominent roles. Perhaps one of the more salient factors is the point that choosing an arbitrary time to change conditions from say a lock-down for the population to a less stringent social behavior, such as allowing partial or complete opening of businesses and schools, etc. should be based on knowledge of the disease and its evolution. Such decisions are usually made by politicians who have less than full information concerning the consequences of their actions. Several examples are given to illustrate these points.