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1.
Emerg Infect Dis ; 27(12): 3142-3146, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34808093

RESUMO

Shuni virus is associated with neurologic and febrile illness in animals and humans. To determine potential vectors, we collected mosquitoes in South Africa and detected the virus in species of the genera Mansonia, Culex, Aedes, and Anopheles. These mosquitoes may be associated with Shuni virus outbreaks in Africa and emergence in other regions.

2.
Viruses ; 13(11)2021 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-34834955

RESUMO

Mosquitoes in the Aedes and Culex genera are considered the main vectors of pathogenic flaviviruses worldwide. Entomological surveillance using universal flavivirus sets of primers in mosquitoes can detect not only pathogenic viruses but also insect-specific ones. It is hypothesized that insect-specific flaviviruses, which naturally infect these mosquitoes, may influence their vector competence for zoonotic arboviruses. Here, entomological surveillance was performed between January 2014 and May 2018 in five different provinces in the northeastern parts of South Africa, with the aim of identifying circulating flaviviruses. Mosquitoes were sampled using different carbon dioxide trap types. Overall, 64,603 adult mosquitoes were collected, which were screened by RT-PCR and sequencing. In total, 17 pools were found positive for insect-specific Flaviviruses in the mosquito genera Aedes (12/17, 70.59%) and Anopheles (5/17, 29.41%). No insect-specific viruses were detected in Culex species. Cell-fusing agent viruses were detected in Aedes aegypti and Aedes caballus. A range of anopheline mosquitoes, including Anopheles coustani, An. squamosus and An. maculipalpis, were positive for Culex flavivirus-like and Anopheles flaviviruses. These results confirm the presence of insect-specific flaviviruses in mosquito populations in South Africa, expands their geographical range and indicates potential mosquito species as vector species.

3.
Viruses ; 13(10)2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34696407

RESUMO

Culicoides-borne viruses such as bluetongue, African horse sickness, and Schmallenberg virus cause major economic burdens due to animal outbreaks in Africa and their emergence in Europe and Asia. However, little is known about the role of Culicoides as vectors for zoonotic arboviruses. In this study, we identify both veterinary and zoonotic arboviruses in pools of Culicoides biting midges in South Africa, during 2012-2017. Midges were collected at six surveillance sites in three provinces and screened for Alphavirs, Flavivirus, Orthobunyavirus, and Phlebovirus genera; equine encephalosis virus (EEV); and Rhaboviridae, by reverse transcription polymerase chain reaction. In total, 66/331 (minimum infection rate (MIR) = 0.4) pools tested positive for one or more arbovirus. Orthobunyaviruses, including Shuni virus (MIR = 0.1) and EEV (MIR = 0.2) were more readily detected, while only 2/66 (MIR = 0.1) Middelburg virus and 4/66 unknown Rhabdoviridae viruses (MIR = 0.0) were detected. This study suggests Culicoides as potential vectors of both veterinary and zoonotic arboviruses detected in disease outbreaks in Africa, which may contribute to the emergence of these viruses to new regions.

4.
Artigo em Inglês | MEDLINE | ID: mdl-34528769

RESUMO

BACKGROUND: We aimed to describe the prevalence of human respiratory syncytial virus (HRSV) and evaluate associations between HRSV subgroups and/or genotypes and epidemiologic characteristics and clinical outcomes in patients hospitalized with severe respiratory illness (SRI). METHODS: Between January 2012 and December 2015, we enrolled patients of all ages admitted to two South African hospitals with SRI in prospective hospital-based syndromic surveillance. We collected respiratory specimens and clinical and epidemiological data. Unconditional random effect multivariable logistic regression was used to assess factors associated with HRSV infection. RESULTS: HRSV was detected in 11.2% (772/6908) of enrolled patients of which 47.0% (363/772) were under the age of 6 months. There were no differences in clinical outcomes of HRSV subgroup A-infected patients compared with HRSV subgroup B-infected patients but among patients aged <5 years, children with HRSV subgroup A were more likely be coinfected with Streptococcus pneumoniae (23/208, 11.0% vs. 2/90, 2.0%; adjusted odds ratio 5.7). No significant associations of HRSV A genotypes NA1 and ON1 with specific clinical outcomes were observed. CONCLUSIONS: While HRSV subgroup and genotype dominance shifted between seasons, we showed similar genotype diversity as noted worldwide. We found no association between clinical outcomes and HRSV subgroups or genotypes.

5.
Philos Trans R Soc Lond B Biol Sci ; 376(1837): 20200358, 2021 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-34538140

RESUMO

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.


Assuntos
Reservatórios de Doenças/virologia , Saúde Global , Pandemias/prevenção & controle , Zoonoses/prevenção & controle , Zoonoses/virologia , Animais , Animais Selvagens , COVID-19/prevenção & controle , COVID-19/veterinária , Ecologia , Humanos , Laboratórios , Aprendizado de Máquina , Fatores de Risco , SARS-CoV-2 , Vírus , Zoonoses/epidemiologia
6.
PLoS One ; 16(8): e0255941, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34383824

RESUMO

BACKGROUND: Severe acute respiratory illness (SARI) is an important cause of mortality in young children, especially in children living with HIV infection. Disparities in SARI death in children aged <5 years exist in urban and rural areas. OBJECTIVE: To compare the factors associated with in-hospital death among children aged <5 years hospitalized with SARI in an urban vs. a rural setting in South Africa from 2009-2013. METHODS: Data were collected from hospitalized children with SARI in one urban and two rural sentinel surveillance hospitals. Nasopharyngeal aspirates were tested for ten respiratory viruses and blood for pneumococcal DNA using polymerase chain reaction. We used multivariable logistic regression to identify patient and clinical characteristics associated with in-hospital death. RESULTS: From 2009 through 2013, 5,297 children aged <5 years with SARI-associated hospital admission were enrolled; 3,811 (72%) in the urban and 1,486 (28%) in the rural hospitals. In-hospital case-fatality proportion (CFP) was higher in the rural hospitals (6.9%) than the urban hospital (1.3%, p<0.001), and among HIV-infected than the HIV-uninfected children (9.6% vs. 1.6%, p<0.001). In the urban hospital, HIV infection (odds ratio (OR):11.4, 95% confidence interval (CI):5.4-24.1) and presence of any other underlying illness (OR: 3.0, 95% CI: 1.0-9.2) were the only factors independently associated with death. In the rural hospitals, HIV infection (OR: 4.1, 95% CI: 2.3-7.1) and age <1 year (OR: 3.7, 95% CI: 1.9-7.2) were independently associated with death, whereas duration of hospitalization ≥5 days (OR: 0.5, 95% CI: 0.3-0.8) and any respiratory virus detection (OR: 0.4, 95% CI: 0.3-0.8) were negatively associated with death. CONCLUSION: We found that the case-fatality proportion was substantially higher among children admitted to rural hospitals and HIV infected children with SARI in South Africa. While efforts to prevent and treat HIV infections in children may reduce SARI deaths, further efforts to address health care inequality in rural populations are needed.

7.
BMC Infect Dis ; 21(1): 539, 2021 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-34098893

RESUMO

BACKGROUND: In sub-Saharan Africa, acute respiratory infections (ARI), acute gastrointestinal infections (GI) and acute febrile disease of unknown cause (AFDUC) have a large disease burden, especially among children, while respective aetiologies often remain unresolved. The need for robust infectious disease surveillance to detect emerging pathogens along with common human pathogens has been highlighted by the ongoing novel coronavirus disease 2019 (COVID-19) pandemic. The African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA) is a sentinel surveillance study on the aetiology and clinical characteristics of ARI, GI and AFDUC in sub-Saharan Africa. METHODS: ANDEMIA includes 12 urban and rural health care facilities in four African countries (Côte d'Ivoire, Burkina Faso, Democratic Republic of the Congo and Republic of South Africa). It was piloted in 2018 in Côte d'Ivoire and the initial phase will run from 2019 to 2021. Case definitions for ARI, GI and AFDUC were established, as well as syndrome-specific sampling algorithms including the collection of blood, naso- and oropharyngeal swabs and stool. Samples are tested using comprehensive diagnostic protocols, ranging from classic bacteriology and antimicrobial resistance screening to multiplex real-time polymerase chain reaction (PCR) systems and High Throughput Sequencing. In March 2020, PCR testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and analysis of full genomic information was included in the study. Standardised questionnaires collect relevant clinical, demographic, socio-economic and behavioural data for epidemiologic analyses. Controls are enrolled over a 12-month period for a nested case-control study. Data will be assessed descriptively and aetiologies will be evaluated using a latent class analysis among cases. Among cases and controls, an integrated analytic approach using logistic regression and Bayesian estimation will be employed to improve the assessment of aetiology and associated risk factors. DISCUSSION: ANDEMIA aims to expand our understanding of ARI, GI and AFDUC aetiologies in sub-Saharan Africa using a comprehensive laboratory diagnostics strategy. It will foster early detection of emerging threats and continued monitoring of important common pathogens. The network collaboration will be strengthened and site diagnostic capacities will be reinforced to improve quality management and patient care.


Assuntos
Doenças Transmissíveis/diagnóstico , Doenças Transmissíveis/epidemiologia , Programas de Rastreamento , Vigilância de Evento Sentinela , Teorema de Bayes , Burkina Faso , Estudos de Casos e Controles , Costa do Marfim , República Democrática do Congo , Febre/epidemiologia , Febre/microbiologia , Gastroenteropatias/epidemiologia , Gastroenteropatias/microbiologia , Humanos , Reação em Cadeia da Polimerase em Tempo Real , Infecções Respiratórias/epidemiologia , África do Sul
8.
Parasit Vectors ; 14(1): 339, 2021 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-34174956

RESUMO

BACKGROUND: There is a paucity of recent data and knowledge on mosquito diversity and potential vectors of arboviruses in South Africa, with most of the available data dating back to the 1950s-1970s. Aedes and Culex species are the major vectors of some of the principal arboviruses which have emerged and re-emerged in the past few decades. METHODS: In this study we used entomological surveillance in selected areas in the north-eastern parts of South Africa from 2014 to 2018 to assess mosquito diversity, with special emphasis on the Aedes species. The impact of trap types and environmental conditions was also investigated. Identification of the blood meal sources of engorged females collected during the study period was carried out, and DNA barcodes were generated for selected species. RESULTS: Overall, 18.5% of the total Culicidae mosquitoes collected belonged to the genus Aedes, with 14 species recognised or suspected vectors of arboviruses. Species belonging to the Neomelaniconion subgenus were commonly collected in the Bushveld savanna at conservation areas, especially Aedes mcintoshi and Aedes circumluteolus. Aedes aegypti was present in all sites, albeit in low numbers. Temperature was a limiting factor for the Aedes population, and they were almost exclusively collected at temperatures between 18 °C and 27 °C. The cytochrome oxidase subunit I (COI) barcode fragment was amplified for 21 Aedes species, and for nine of these species it was the first sequence information uploaded on GenBank. CONCLUSION: This study provides a better understanding of the diversity and relative abundance of Aedes species in the north-east of South Africa. The information provided here will contribute to future arboviral research and implementation of efficient vector control and prevention strategies.


Assuntos
Aedes/fisiologia , Comportamento Alimentar , Aedes/classificação , Aedes/genética , Animais , Ecossistema , Complexo IV da Cadeia de Transporte de Elétrons/genética , Feminino , Proteínas de Insetos/genética , Mosquitos Vetores/classificação , Mosquitos Vetores/genética , Mosquitos Vetores/fisiologia , África do Sul , Temperatura
9.
Viruses ; 13(5)2021 05 19.
Artigo em Inglês | MEDLINE | ID: mdl-34069356

RESUMO

The Orthobunyavirus genus, family Peribunyaviridae, contains several important emerging and re-emerging arboviruses of veterinary and medical importance. These viruses may cause mild febrile illness, to severe encephalitis, fetal deformity, abortion, hemorrhagic fever and death in humans and/or animals. Shuni virus (SHUV) is a zoonotic arbovirus thought to be transmitted by hematophagous arthropods. It was previously reported in a child in Nigeria in 1966 and horses in Southern Africa in the 1970s and again in 2009, and in humans with neurological signs in 2017. Here we investigated the epidemiology and phylogenetic relationship of SHUV strains detected in horses presenting with febrile and neurological signs in South Africa. In total, 24/1820 (1.3%) horses submitted to the zoonotic arbovirus surveillance program tested positive by real-time reverse transcription (RTPCR) between 2009 and 2019. Cases were detected in all provinces with most occurring in Gauteng (9/24, 37.5%). Neurological signs occurred in 21/24 (87.5%) with a fatality rate of 45.8%. Partial sequencing of the nucleocapsid gene clustered the identified strains with SHUV strains previously identified in South Africa (SA). Full genome sequencing of a neurological case detected in 2016 showed 97.8% similarity to the SHUV SA strain (SAE18/09) and 97.5% with the Nigerian strain and 97.1% to the 2014 Israeli strain. Our findings suggest that SHUV is circulating annually in SA and despite it being relatively rare, it causes severe neurological disease and death in horses.


Assuntos
Infecções por Bunyaviridae/veterinária , Doenças dos Cavalos/epidemiologia , Doenças dos Cavalos/virologia , Orthobunyavirus , África Austral/epidemiologia , Animais , Feminino , Genoma Viral , Genômica/métodos , Geografia Médica , Doenças dos Cavalos/diagnóstico , Cavalos , Masculino , Orthobunyavirus/classificação , Orthobunyavirus/genética , Filogenia , Estações do Ano , Sequenciamento Completo do Genoma
10.
Acta Trop ; 219: 105913, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33831346

RESUMO

Biting midges in the genus Culicoides (Diptera; Ceratopogonidae) are vectors of pathogens that can cause diseases of major economic importance in humans and animals. Identifying host ranges of these biting midges might aid in understanding the complex epidemiology of such diseases, often involving reservoir hosts and multiple species. In this study, we aim to identify bloodmeal origin from engorged female Culicoides biting midges. All bloodfed females were opportunistically collected as part of an ongoing surveillance programme using Onderstepoort light traps in two provinces in South Africa. DNA of individuals was extracted and subjected to PCR targeting the cytochrome B (CytB) gene region of mammals and avians as well as cytochrome oxidase I (COI) for species identification. In total, 21 new reference barcodes were generated for C. bedfordi, C imicola, C. leucosticus, C. magnus, and C. pycnostictus. Seventy-four blood meals were identified, originating from 12 mammal and three avian species. COI sequence data performed well for species delimitation and 54 Culicoides specimens were identified with C. imicola the predominant species identified (41.8%). Generally, Culicoides species feed on a variety of hosts and host availability might be an important factor when selecting a host. Culicoides species thus appear to be opportunistic feeders rather than specialists. This implicates Culicoides as transfer vectors and demonstrates possible transmission routes of arboviruses and other pathogens from wildlife onwards to domestic animals and humans.


Assuntos
Sangue/parasitologia , Ceratopogonidae/classificação , Citocromos b/genética , Código de Barras de DNA Taxonômico , Complexo IV da Cadeia de Transporte de Elétrons/genética , Animais , Arbovírus/fisiologia , Ceratopogonidae/genética , Feminino , Especificidade de Hospedeiro , Humanos , Insetos Vetores/genética , África do Sul
11.
Viruses ; 13(3)2021 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-33801457

RESUMO

Equine encephalosis virus (EEV) is a neglected virus endemic to South Africa and is considered to generally result in mild disease in equines. Specimens were analyzed from live horses that presented with undefined neurological, febrile, or respiratory signs, or sudden and unexpected death. Between 2010 and 2017, 111 of 1523 (7.3%) horse samples tested positive for EEV using a nested real-time reverse transcriptase polymerase chain reaction (rRT-PCR). Clinical signs were reported in 106 (7.2%) EEV positive and 1360 negative horses and included pyrexia (77/106, 72.6%), icterus (20/106, 18.9%) and dyspnea (12/106, 11.3%). Neurological signs were inversely associated with EEV infection (OR < 1, p < 0.05) relative to EEV negative cases despite a high percentage of animals presenting with neurological abnormalities (51/106, 48.1%). Seventeen of the EEV positive horses also had coinfections with either West Nile (5/106, 4.7%), Middelburg (4/106, 3.8%) or African Horse sickness virus (8/106, 7.6%). To investigate a possible genetic link between EEV strains causing the observed clinical signs in horses, the full genomes of six isolates were compared to the reference strains. Based on the outer capsid protein (VP2), serotype 1 and 4 were identified as the predominant serotypes with widespread reassortment between the seven different serotypes.


Assuntos
Genoma Viral , Doenças dos Cavalos , Orbivirus/genética , Infecções por Reoviridae , Animais , Doenças dos Cavalos/epidemiologia , Doenças dos Cavalos/virologia , Cavalos , Prevalência , Infecções por Reoviridae/epidemiologia , Infecções por Reoviridae/veterinária , Sorogrupo , África do Sul/epidemiologia
12.
Emerg Infect Dis ; 27(2): 565-569, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33496223

RESUMO

We describe Shuni virus (SHUV) detection in human neurologic disease cases in South Africa. SHUV RNA was identified in 5% of cerebrospinal fluid specimens collected during the arbovirus season from public sector hospitals. This finding suggests that SHUV may be a previously unrecognized cause of human neurologic infections in Africa.


Assuntos
Infecções por Bunyaviridae , Orthobunyavirus , Infecções por Bunyaviridae/epidemiologia , Humanos , Orthobunyavirus/genética , RNA Viral/genética , África do Sul/epidemiologia
13.
Sci Rep ; 10(1): 13543, 2020 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-32782318

RESUMO

Humans alter the environment at unprecedented rates through habitat destruction, nutrient pollution and the application of agrochemicals. This has recently been proposed to act as a potentially significant driver of pathogen-carrying mosquito species (disease vectors) that pose a health risk to humans and livestock. Here, we use a unique set of locations along a large geographical gradient to show that landscapes disturbed by a variety of anthropogenic stressors are consistently associated with vector-dominated mosquito communities for a wide range of human and livestock infections. This strongly suggests that human alterations to the environment promote the presence and abundance of disease vectors across large spatial extents. As such, it warrants further studies aimed at unravelling mechanisms underlying vector prevalence in mosquito communities, and opens up new opportunities for preventative action and predictive modelling of vector borne disease risks in relation to degradation of natural ecosystems.


Assuntos
Culicidae/classificação , Culicidae/crescimento & desenvolvimento , Ecossistema , Atividades Humanas/estatística & dados numéricos , Malária/transmissão , Mosquitos Vetores/patogenicidade , Densidade Demográfica , Animais , Biodiversidade , Humanos , Malária/epidemiologia , Malária/parasitologia , África do Sul
14.
Influenza Other Respir Viruses ; 14(6): 671-677, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32730685

RESUMO

BACKGROUND: External quality assessments (EQAs) for the molecular detection of respiratory syncytial virus (RSV) are necessary to ensure the provision of reliable and accurate results. One of the objectives of the pilot of the World Health Organization (WHO) Global RSV Surveillance, 2016-2017, was to evaluate and standardize RSV molecular tests used by participating countries. This paper describes the first WHO RSV EQA for the molecular detection of RSV. METHODS: The WHO implemented the pilot of Global RSV Surveillance based on the WHO Global Influenza Surveillance and Response System (GISRS) from 2016 to 2018 in 14 countries. To ensure standardization of tests, 13 participating laboratories were required to complete a 12 panel RSV EQA prepared and distributed by the Centers for Disease Control and Prevention (CDC), USA. The 14th laboratory joined the pilot late and participated in a separate EQA. Laboratories evaluated a RSV rRT-PCR assay developed by CDC and compared where applicable, other Laboratory Developed Tests (LDTs) or commercial assays already in use at their laboratories. RESULTS: Laboratories performed well using the CDC RSV rRT-PCR in comparison with LDTs and commercial assays. Using the CDC assay, 11 of 13 laboratories reported correct results. Two laboratories each reported one false-positive finding. Of the laboratories using LDTs or commercial assays, results as assessed by Ct values were 100% correct for 1/5 (20%). With corrective actions, all laboratories achieved satisfactory outputs. CONCLUSIONS: These findings indicate that reliable results can be expected from this pilot. Continued participation in EQAs for the molecular detection of RSV is recommended.


Assuntos
Garantia da Qualidade dos Cuidados de Saúde/estatística & dados numéricos , Infecções por Vírus Respiratório Sincicial/diagnóstico , Vírus Sincicial Respiratório Humano/isolamento & purificação , Humanos , Laboratórios/normas , Técnicas de Diagnóstico Molecular/normas , Projetos Piloto , RNA Viral/genética , Vírus Sincicial Respiratório Humano/genética , Organização Mundial da Saúde
15.
J Vector Ecol ; 45(1): 104-117, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32492270

RESUMO

Most data on species associations and vector potential of mosquitoes in relation to arboviral infections in South Africa date back from the 1940s to late 1990s. Contextual information crucial for disease risk management and control, such as the sampling effort, diversity, abundance, and distribution of mosquitoes in large parts of South Africa still remains limited. Adult mosquitoes were collected routinely from two horse farms in Gauteng Province; two wildlife reserves in Limpopo Province, at Orpen Gate in Kruger National Park (KNP) and Mnisi Area in Mpumalanga Province between 2014-2017, using carbon dioxide-baited light and tent traps. Mosquito diversity and richness are greater in untransformed natural and mixed rural settings. In untransformed wilderness areas, the most dominant species were Culex poicilipes, Anopheles coustani, and Aedes mcintoshi, while in mixed rural settings such as the Mnisi area, the two most abundant species were Cx. poicilipes and Mansonia uniformis. However, in peri-urban areas, Cx. theileri, Cx. univittatus, and Cx. pipiens sensu lato were the most dominant. Aedes aegypti, Ae. mcintoshi, Ae. metallicus, Ae. vittatus, Cx. pipiens s.l., Cx. theileri, and Cx. univittatus had the widest geographical distribution in northern South Africa. Also collected were Anopheles arabiensis and An. vaneedeni, both known malaria vectors in South Africa. Arbovirus surveillance and vector control programs should be augmented in mixed rural and peri-urban areas where the risk for mosquito-borne disease transmission to humans and domestic stock is greater.


Assuntos
Culicidae/classificação , Aedes/classificação , Animais , Anopheles/classificação , Culex/classificação , Vetores de Doenças , Humanos , Controle de Mosquitos , África do Sul
16.
Emerg Infect Dis ; 26(7): 1521-1525, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32568048

RESUMO

We screened nonequine animals with unexplained neurologic signs or death in South Africa during 2010-2018 for Shuni virus (SHUV). SHUV was detected in 3.3% of wildlife, 1.1% of domestic, and 2.0% of avian species. Seropositivity was also demonstrated in wildlife. These results suggest a range of possible SHUV hosts in Africa.


Assuntos
Animais Selvagens , Infecções por Bunyaviridae , Animais , Animais Domésticos , Orthobunyavirus , África do Sul/epidemiologia
17.
J Clin Pathol ; 73(7): 370-377, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32404473

RESUMO

Countries globally are affected by the COVID-19 pandemic, with nearly two million cases and 120 000 deaths occurring within 4 months of the discovery of the severe acute respiratory syndrome coronavirus-2 in December 2019 in China. Accurate diagnoses of cases is key in managing the pandemic by identification, isolation and treatment of patients and defining the epidemiology of the virus. By mid-January 2020, a scientist from China published the full genome of the virus, which facilitated the development of accurate molecular diagnostic assays. By the end of January 2020, the WHO, in collaboration with laboratories in Asia, Europe and the USA, published several real-time reverse transcriptase PCR (rtRT-PCR) protocols that allowed identification of cases and development of commercial assays. Clinical investigations facilitated development of accurate case definition and guidance for laboratories on the optimum specimens and procedures for diagnoses. Currently, laboratory-based rtRT-PCR is the recommended test for diagnoses of acute cases to ensure patients can be identified and isolated and to facilitate the public health response. However, due to delays in diagnoses, severe shortage of tests and laboratory capacity, point-of-care molecular or antigen tests are becoming more attractive. Although serological tests are not suitable for diagnoses of acute cases, they are important to define epidemiological questions, including attack rate in the population, and to identify immune individuals. This review aimed to summarise the current available information for diagnoses of cases and to aid laboratories and healthcare workers to select the best assays and procedures.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , COVID-19 , Teste para COVID-19 , Vacinas contra COVID-19 , Infecções por Coronavirus/virologia , Humanos , Técnicas de Diagnóstico Molecular/métodos , Pandemias , Pneumonia Viral/virologia , Sistemas Automatizados de Assistência Junto ao Leito , Reação em Cadeia da Polimerase em Tempo Real , Reação em Cadeia da Polimerase Via Transcriptase Reversa , SARS-CoV-2 , Testes Sorológicos/métodos
18.
Emerg Infect Dis ; 26(6): 1182-1191, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32441633

RESUMO

Alphaviruses from Africa, such as Middelburg virus (MIDV), and Sindbis virus (SINV), were detected in horses with neurologic disease in South Africa, but their host ranges remain unknown. We investigated the contribution of alphaviruses to neurologic infections and death in wildlife and domestic animals in this country. During 2010-2018, a total of 608 clinical samples from wildlife and nonequine domestic animals that had febrile, neurologic signs or unexplained deaths were tested for alphaviruses. We identified 32 (5.5%) of 608 alphavirus infections (9 SINV and 23 MIDV), mostly in neurotissue of wildlife, domestic animals, and birds. Phylogenetic analysis of the RNA-dependent RNA polymerase gene confirmed either SINV or MIDV. This study implicates MIDV and SINV as potential causes of neurologic disease in wildlife and nonequine domestic species in Africa and suggests a wide host range and pathogenic potential.


Assuntos
Animais Selvagens , Vírus Sindbis , Animais , Animais Domésticos , Cavalos , Filogenia , África do Sul/epidemiologia
19.
Viruses ; 12(4)2020 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-32316542

RESUMO

The genus Orthobunyavirus (family Peribunyaviridae, order Bunyavirales) comprises over 170 named mosquito- and midge-borne viruses, several of which cause severe disease in animals or humans. Their three-segmented genomes enable reassortment with related viruses, which may result in novel viruses with altered host or tissue tropism and virulence. One such reassortant, Schmallenberg virus (SBV), emerged in north-western Europe in 2011. Shuni virus (SHUV) is an orthobunyavirus related to SBV that is associated with neurological disease in horses in southern Africa and recently caused an outbreak manifesting with neurological disease and birth defects among ruminants in Israel. The zoonotic potential of SHUV was recently underscored by its association with neurological disease in humans. We here report a reverse genetics system for SHUV and provide first evidence that the non-structural (NSs) protein of SHUV functions as an antagonist of host innate immune responses. We furthermore report the rescue of a reassortant containing the L and S segments of SBV and the M segment of SHUV. This novel reverse genetics system can now be used to study SHUV virulence and tropism, and to elucidate the molecular mechanisms that drive reassortment events.


Assuntos
Infecções por Bunyaviridae/epidemiologia , Infecções por Bunyaviridae/virologia , Doenças Transmissíveis Emergentes/epidemiologia , Doenças Transmissíveis Emergentes/virologia , Orthobunyavirus/genética , Genética Reversa , Zoonoses Virais/epidemiologia , Zoonoses Virais/virologia , Animais , Infecções por Bunyaviridae/transmissão , Doenças Transmissíveis Emergentes/transmissão , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Camundongos , Fases de Leitura Aberta , Orthobunyavirus/classificação , Filogenia , RNA Viral , Ratos , Reino Unido/epidemiologia , Zoonoses Virais/transmissão
20.
Influenza Other Respir Viruses ; 14(6): 622-629, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-31444997

RESUMO

BACKGROUND: Respiratory syncytial virus (RSV)-associated acute lower respiratory infection is a common cause for hospitalization and hospital deaths in young children globally. There is urgent need to generate evidence to inform immunization policies when RSV vaccines become available. The WHO piloted a RSV surveillance strategy that leverages the existing capacities of the Global Influenza Surveillance and Response System (GISRS) to better understand RSV seasonality, high-risk groups, validate case definitions, and develop laboratory and surveillance standards for RSV. METHODS: The RSV sentinel surveillance strategy was piloted in 14 countries. Patients across all age groups presenting to sentinel hospitals and clinics were screened all year-round using extended severe acute respiratory infection (SARI) and acute respiratory infection (ARI) case definitions for hospital and primary care settings, respectively. Respiratory specimens were tested for RSV at the National Influenza Centre (NIC) using standardized molecular diagnostics that had been validated by an External Quality Assurance program. The WHO FluMart data platform was adapted to receive case-based RSV data and visualize interactive visualization outputs. RESULTS: Laboratory standards for detecting RSV by RT-PCR were developed. A review assessed the feasibility and the low incremental costs for RSV surveillance. Several challenges were addressed related to case definitions, sampling strategies, the need to focus surveillance on young children, and the data required for burden estimation. CONCLUSIONS: There was no evidence of any significant adverse impact on the functioning of GISRS which is primarily intended for virologic and epidemiological surveillance of influenza.


Assuntos
Influenza Humana/epidemiologia , Infecções por Vírus Respiratório Sincicial/epidemiologia , Vigilância de Evento Sentinela , Algoritmos , Saúde Global , Hospitais , Humanos , Influenza Humana/diagnóstico , Laboratórios , Orthomyxoviridae/genética , Orthomyxoviridae/isolamento & purificação , Projetos Piloto , Infecções por Vírus Respiratório Sincicial/diagnóstico , Vírus Sincicial Respiratório Humano/genética , Vírus Sincicial Respiratório Humano/isolamento & purificação , Organização Mundial da Saúde
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