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2.
Malays J Pathol ; 42(1): 23-35, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32342928

RESUMO

INTRODUCTION: To review the present literature on upper respiratory tract sampling in COVID-19 and provide recommendations to improve healthcare practices and directions in future studies. METHODS: Twelve relevant manuscripts were sourced from a total of 7288 search results obtained using PubMed, Medline and Google Scholar. The search keywords used were COVID-19, nasopharyngeal, oropharyngeal, swabs, SARS and CoV2. Original manuscripts were obtained and analysed by all authors. The review included manuscripts which have not undergone rigorous peer-review process in view of the magnitude of the topic discussed. RESULTS: The viral load of SARS-CoV-2 RNA in the upper respiratory tract was significantly higher during the first week and peaked at 4-6 days after onset of symptoms, during which it can be potentially sampled. Nasopharyngeal swab has demonstrated higher viral load than oropharyngeal swab, where the difference in paired samples is best seen at 0-9 days after the onset of illness. Sensitivity of nasopharyngeal swab was higher than oropharyngeal swabs in COVID-19 patients. Patient self-collected throat washing has been shown to contain higher viral load than nasopharyngeal or oropharyngeal swab, with significantly higher sensitivity when compared with paired nasopharyngeal swab. RECOMMENDATIONS: Routine nasopharyngeal swab of suspected COVID-19 infection should take anatomy of the nasal cavity into consideration to increase patient comfort and diagnostic yield. Routine oropharyngeal swab should be replaced by throat washing which has demonstrated better diagnostic accuracy, and it is safe towards others.


Assuntos
Infecções por Coronavirus/diagnóstico , Nasofaringe/virologia , Orofaringe/virologia , Pneumonia Viral/diagnóstico , Manejo de Espécimes , Betacoronavirus , Técnicas de Laboratório Clínico , Humanos , Pandemias , Sensibilidade e Especificidade , Carga Viral
3.
JMIR Public Health Surveill ; 6(2): e19054, 2020 04 24.
Artigo em Inglês | MEDLINE | ID: mdl-32310815

RESUMO

BACKGROUND: The response in the United States to the coronavirus disease (COVID-19) pandemic has been hampered by a lack of aggressive testing for the infection. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cornerstone of an effective public health response. However, efforts to test have been hampered by limited reagents, limitations in the availability of swabs used for the collection of nasopharyngeal swab (NPS) specimens, limitations in personal protective equipment (PPE) for health care providers collecting the NPS specimens, and limitations in viral transport media for transporting the specimens. Therefore, more flexible options for screening for SARS-CoV-2 RNA and serologic responses are critical to inform clinical and public health responses. OBJECTIVE: We aim to document the ability of patients to self-collect sufficient specimens for SARS-CoV-2 viral detection and serology. METHODS: Patient self-collection of samples will be done with observation by a health care provider during a telemedicine session. Participants will be mailed a specimen collection kit, engage in a telehealth session with a provider through a HIPPA (Health Insurance Portability and Accountability Act of 1996)-compliant video meeting, and collect specimens while being observed by the provider. Providers will record whether they are confident in the suitability of the specimen for laboratory testing that would inform clinical decision making. We will objectively assess the sufficiency of biological material in the mailed-in specimens. RESULTS: The protocol was approved by the Emory University Institutional Review Board (IRB) on March 30, 2020 (Protocol number 371). To date, we have enrolled 159 participants. CONCLUSIONS: Defining a conceptual framework for assessing the sufficiency of patient-collected samples for the detection of SARS-CoV-2 RNA and serologic responses to infection is critical for facilitating public health responses and providing PPE-sparing options to increase testing. Validation of alternative methods of specimen collection should include objective measures of the sufficiency of specimens for testing. A strong evidence base for diversifying testing modalities will improve tools to guide public health responses to the COVID-19 pandemic.


Assuntos
Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Coronavirus/genética , Orofaringe/virologia , Pneumonia Viral/diagnóstico , RNA Viral/isolamento & purificação , Saliva/virologia , Autocuidado , Síndrome Respiratória Aguda Grave/genética , Manejo de Espécimes/métodos , Betacoronavirus , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Surtos de Doenças , Humanos , Cavidade Nasal/virologia , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Síndrome Respiratória Aguda Grave/diagnóstico , Telemedicina
4.
Euro Surveill ; 25(14)2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32290902

RESUMO

The World Health Organization has declared COVID-19 caused by the newly discovered SARS-CoV-2 a pandemic. Due to growing demand for reagents and/or kits to extract SARS-CoV-2 RNA for subsequent RT-qPCR diagnostics, there is a worldwide risk of shortages. With a detection sensitivity of 97.4% (95% CI: 86.2-99.9%), we describe a simple, fast, alternative workflow for molecular detection of SARS-CoV-2, where samples are simply heat-processed for 5 min at 98 °C before a commonly-used RT-qPCR procedure.


Assuntos
Infecções por Coronavirus/diagnóstico , Coronavirus/genética , Coronavirus/isolamento & purificação , Orofaringe/virologia , Pneumonia Viral/diagnóstico , RNA Viral/análise , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Betacoronavirus , Dinamarca , Humanos , Pandemias , RNA Viral/genética , RNA Viral/isolamento & purificação , Sensibilidade e Especificidade , Síndrome Respiratória Aguda Grave/diagnóstico , Fluxo de Trabalho
5.
S Afr Fam Pract (2004) ; 62(1): e1-e4, 2020 03 31.
Artigo em Inglês | MEDLINE | ID: mdl-32242438

RESUMO

South Africa is in the grip of a novel coronavirus pandemic (COVID-19). Primary care providers are in the frontline. COVID-19 is spread primarily by respiratory droplets contaminating surfaces and hands that then transmit the virus to another person's respiratory system. The incubation period is 2-9 days and the majority of cases are mild. The most common symptoms are fever, cough and shortness of breath. Older people and those with cardiopulmonary co-morbidities or immunological deficiency will be more at risk of severe disease. If people meet the case definition, the primary care provider should immediately adopt infection prevention and control measures. Diagnosis is made by a RT-PCR test using respiratory secretions, usually nasopharyngeal and oropharyngeal swabs. Mild cases can be managed at home with self-isolation, symptomatic treatment and follow-up if the disease worsens. Contact tracing is very important. Observed case fatality is between 0.5% and 4%, but may be overestimated as mild cases are not always counted. Primary care providers must give clear, accurate and consistent messages on infection prevention and control in communities and homes.


Assuntos
Infecções por Coronavirus , Coronavirus/isolamento & purificação , Surtos de Doenças/prevenção & controle , Nasofaringe/virologia , Orofaringe/virologia , Pandemias , Pneumonia Viral , Guias de Prática Clínica como Assunto , Atenção Primária à Saúde , Betacoronavirus , Busca de Comunicante , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/terapia , Infecções por Coronavirus/transmissão , Tosse/etiologia , Dispneia/etiologia , Febre/etiologia , Humanos , Pneumonia Viral/diagnóstico , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , África do Sul
6.
Emerg Infect Dis ; 26(6): 1266-1273, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32160149

RESUMO

The etiologic agent of an outbreak of pneumonia in Wuhan, China, was identified as severe acute respiratory syndrome coronavirus 2 in January 2020. A patient in the United States was given a diagnosis of infection with this virus by the state of Washington and the US Centers for Disease Control and Prevention on January 20, 2020. We isolated virus from nasopharyngeal and oropharyngeal specimens from this patient and characterized the viral sequence, replication properties, and cell culture tropism. We found that the virus replicates to high titer in Vero-CCL81 cells and Vero E6 cells in the absence of trypsin. We also deposited the virus into 2 virus repositories, making it broadly available to the public health and research communities. We hope that open access to this reagent will expedite development of medical countermeasures.


Assuntos
Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Animais , Betacoronavirus/genética , Betacoronavirus/fisiologia , Linhagem Celular , Chlorocebus aethiops , Genoma Viral , Humanos , Nasofaringe/virologia , Orofaringe/virologia , Pandemias , Células Vero , Tropismo Viral , Replicação Viral , Washington
8.
BMC Infect Dis ; 20(1): 168, 2020 Feb 22.
Artigo em Inglês | MEDLINE | ID: mdl-32087697

RESUMO

BACKGROUND: Respiratory tract infection (RTI) in young children is a leading cause of morbidity and hospitalization worldwide. There are few studies assessing the performance for bronchoalveolar lavage fluid (BALF) versus oropharyngeal swab (OPS) specimens in microbiological findings for children with RTI. The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. METHODS: We collected paired OPS and BALF specimens from 76 hospitalized children with respiratory illness. The samples were tested simultaneously for 8 respiratory viruses and 5 bacteria by suspension microarray. RESULTS: Of 76 paired specimens, 62 patients (81.6%) had at least one pathogen. BALF and OPS identified respiratory pathogen infections in 57 (75%) and 49 (64.5%) patients, respectively (P > 0.05). The etiology analysis revealed that viruses were responsible for 53.7% of the patients, whereas bacteria accounted for 32.9% and Mycoplasma pneumoniae for 13.4%. The leading 5 pathogens identified were respiratory syncytial virus, Streptococcus pneumoniaee, Haemophilus influenzae, Mycoplasma pneumoniae and adenovirus, and they accounted for 74.2% of etiological fraction. For detection of any pathogen, the overall detection rate of BALF (81%) was marginally higher than that (69%) of OPS (p = 0.046). The differences in the frequency distribution and sensitivity for most pathogens detected by two sampling methods were not statistically significant. CONCLUSIONS: In this study, BALF and OPS had similar microbiological yields. Our results indicated the clinical value of OPS testing in pediatric patients with respiratory illness.


Assuntos
Líquido da Lavagem Broncoalveolar/microbiologia , Líquido da Lavagem Broncoalveolar/virologia , Criança Hospitalizada , Testes Diagnósticos de Rotina/métodos , Orofaringe/microbiologia , Orofaringe/virologia , Infecções Respiratórias/diagnóstico , Criança , Pré-Escolar , Feminino , Hospitalização , Humanos , Lactente , Recém-Nascido , Masculino , Infecções Pneumocócicas/diagnóstico , Infecções Pneumocócicas/microbiologia , Infecções por Vírus Respiratório Sincicial/diagnóstico , Infecções por Vírus Respiratório Sincicial/virologia , Vírus Sincicial Respiratório Humano/genética , Vírus Sincicial Respiratório Humano/isolamento & purificação , Infecções Respiratórias/microbiologia , Infecções Respiratórias/virologia , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/isolamento & purificação
9.
J Korean Med Sci ; 35(7): e84, 2020 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-32080990

RESUMO

Novel coronavirus (SARS-CoV-2) is found to cause a large outbreak started from Wuhan since December 2019 in China and SARS-CoV-2 infections have been reported with epidemiological linkage to China in 25 countries until now. We isolated SARS-CoV-2 from the oropharyngeal sample obtained from the patient with the first laboratory-confirmed SARS-CoV-2 infection in Korea. Cytopathic effects of SARS-CoV-2 in the Vero cell cultures were confluent 3 days after the first blind passage of the sample. Coronavirus was confirmed with spherical particle having a fringe reminiscent of crown on transmission electron microscopy. Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan.


Assuntos
Betacoronavirus , Infecções por Coronavirus , Orofaringe/virologia , Pneumonia Viral , Sequenciamento Completo do Genoma , Adulto , Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Feminino , Humanos , Microscopia Eletrônica de Transmissão , Filogenia , Pneumonia Viral/diagnóstico , República da Coreia
10.
BMC Res Notes ; 12(1): 628, 2019 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-31551085

RESUMO

OBJECTIVE: We conducted four cross-sectional studies over 1 year among humans and pigs in three slaughterhouses in Central and Western Kenya (> 350 km apart) to determine infection and exposure to influenza A viruses. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from participants who reported acute respiratory illness (ARI) defined as fever, cough or running nose. Nasal swabs and blood samples were collected from pigs. Human NP/OP and pig nasal swabs were tested for influenza A virus by real-time reverse transcriptase polymerase chain reaction (PCR) and pig serum was tested for anti-influenza A antibodies by ELISA. RESULTS: A total of 288 participants were sampled, 91.3% of them being male. Fifteen (5.2%) participants had ARI but the nine swabs collected from them were negative for influenza A virus by PCR. Of the 1128 pigs sampled, five (0.4%) nasal swabs tested positive for influenza A/H1N1/pdm09 by PCR whereas 214 of 1082 (19.8%) serum samples tested for Influenza A virus antibodies. There was higher seroprevalence in colder months and among pigs reared as free-range. These findings indicate circulation of influenza A/H1N1/pdm09 among pigs perhaps associated with good adaptation of the virus to the pig population after initial transmission from humans to pigs.


Assuntos
Matadouros , Vírus da Influenza A Subtipo H1N1/genética , Influenza Humana/diagnóstico , Infecções por Orthomyxoviridae/diagnóstico , Doenças dos Suínos/diagnóstico , Adulto , Animais , Anticorpos Antivirais/sangue , Estudos Transversais , Feminino , Geografia , Humanos , Vírus da Influenza A Subtipo H1N1/fisiologia , Influenza Humana/transmissão , Influenza Humana/virologia , Quênia/epidemiologia , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Orofaringe/virologia , Infecções por Orthomyxoviridae/epidemiologia , Infecções por Orthomyxoviridae/virologia , Pandemias , Suínos , Doenças dos Suínos/epidemiologia , Doenças dos Suínos/virologia , Adulto Jovem
11.
Vet Microbiol ; 233: 1-4, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31176393

RESUMO

Domestic ducks are considered as the interface between wild aquatic birds and terrestrial poultry and play an important role in the transmission and evolution of avian influenza viruses (AIVs). However, the infectivity of H9N2 AIVs in different domestic duck species has not been systematically evaluated. Here we investigated the infectivity of various genotypes of chicken H9N2 AIVs in Pekin duck (Anas Platyrhynchos), Mallard duck (Anas Platyrhynchos) and Muscovy duck (Cairina Moschata) through intranasal inoculation. We found that Pekin ducks and Mallard ducks were generally resistant to chicken H9N2 virus infection, while Muscovy ducks were relatively susceptible to H9N2 AIVs. All the tested viruses were isolated from oropharynx, trachea and lung tissues of Muscovy ducks. Additionally, genotype 57 (G57) H9N2 AIVs, which was predominant in chickens since 2010, showed increased virus replication in this duck species, indicating an improved interspecies transmission ability of recent H9N2 viruses from chickens to ducks. Our results demonstrated the role of Muscovy ducks in the ecology of H9N2 AIVs. More attentions should be paid to this host during viral surveillances. Additionally, inactivated H9N2 vaccine may be unnecessarily used in Pekin and Mallard ducks.


Assuntos
Patos/virologia , Influenza Aviária/transmissão , Doenças das Aves Domésticas/virologia , Replicação Viral , Animais , Galinhas/virologia , Suscetibilidade a Doenças , Vírus da Influenza A Subtipo H9N2/genética , Vírus da Influenza A Subtipo H9N2/fisiologia , Pulmão/virologia , Orofaringe/virologia , Traqueia/virologia
12.
Virol J ; 16(1): 84, 2019 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-31234918

RESUMO

BACKGROUND: Advances in molecular laboratory techniques are changing the prospects for the diagnosis of viral infectious diseases. Multiplex polymerase chain reaction assay (multiplex-PCR) can detect dozens of pathogens simultaneously, greatly reducing turnaround time (TAT) and improving detection sensitivity. But as a double-edged sword, due to the high sensitivity of PCR, the type of respiratory specimens is critical to diagnosis. In this work, we performed a head-to-head comparison to evaluate the multiplex-PCR yields between two samples, sputum and flocked oropharyngeal swabs (OPS). METHODS: Eleven common respiratory pathogens were tested in hospitalized children< 13 years of age who met the criteria for lower respiratory tract infection by GeXP-based multiplex-PCR of paired OPS and sputum. RESULTS: From January to June 2018, 440 children with paired OPS and sputum were tested. The positive rate was 84% (369/440) for OPS and 88% (386/440) for sputum (p = .007). The frequency of detection of HRV, RSV, Influenza A virus, HMPV, parainfluenza virus, adenovirus, M. pneumoniae, coronavirus, bocavirus and C. pneumoniae in sputa was higher than that of OPSs (all p < .001). Both types of specimens had similarly very good kappa values for most of pathogens, except for Mycoplasma pneumonia (κ = 0.61) and Chlamydia pneumoniae (κ = 0.24). Additionally, 79.3% (349/440) of cases showed consistent results between the two types of samples, and they were significantly younger than patients with inconsistent results (p = .002). CONCLUSIONS: Flocked oropharyngeal swabs and sputum performed similarly for the detection of common respiratory pathogens in hospitalized children by multiplex-PCR, except for Mycoplasma pneumoniae and Chlamydia pneumoniae. Young patients are likely to have consistent results between the two specimens.


Assuntos
Bactérias/isolamento & purificação , Orofaringe/virologia , Infecções Respiratórias/diagnóstico , Escarro/virologia , Vírus/isolamento & purificação , Infecções por Adenoviridae/diagnóstico , Bactérias/patogenicidade , Criança , Pré-Escolar , Feminino , Hospitalização , Humanos , Lactente , Recém-Nascido , Masculino , Reação em Cadeia da Polimerase Multiplex , Mycoplasma pneumoniae/isolamento & purificação , Mycoplasma pneumoniae/patogenicidade , Infecções Respiratórias/microbiologia , Infecções Respiratórias/virologia , Vírus/genética
13.
Int J Infect Dis ; 83: 40-43, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30953828

RESUMO

This is the first report of persistent oropharyngeal mucosal infection with type 2 poliovirus (iVDPV2) in a primary immune deficient patient (PID) after wild type 2 poliovirus eradication. The iVDPV2 also established persistence in the gut. iVDPV2 at both loci evolved independently. Persistent oral infections present a potential risk for oral-oral as well as fecal-oral poliovirus transmission during transition to a poliovirus 2-free world.


Assuntos
Orofaringe/virologia , Doenças Faríngeas/virologia , Poliomielite/virologia , Vacinas contra Poliovirus , Poliovirus/isolamento & purificação , Eliminação de Partículas Virais , Pré-Escolar , Humanos
14.
Virol J ; 16(1): 27, 2019 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-30832688

RESUMO

BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel ß and γ types have been isolated in this anatomical site suggesting a wide tropism range. Currently, there are no guidelines recommending HPV oral cavity screening as a mandatory test, and it remains unknown which HPV types should be included in HPV screening programs. Our goal was to assess HPV prevalence in oropharyngeal, anal, and cervical swabs using different sets of primers,which are able to amplify α, ß, γ HPV types. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. All untyped strains were genetically characterized through PCR amplification and direct sequencing of partial L1 region, and the resulting sequences were classified through phylogenetic analysis. RESULTS: HPV prevalence was 20.9% in 124 oropharyngeal swab samples, including infections with multiple HPV types (5.6%). HPV prevalence in this anatomical site was significantly associated with serostatus: 63.3%in HIV positive and 36.3% in HIV negative patients (p < 0.05). Unclassified types were detected in 6 specimens. In our analysis, we did not observe any difference in HPV (α, ß, γ) prevalence between men and women. Overall, ß species were the most frequently detected 69.7%. When using anal swabs, for HIV positive patients, ß genus prevalence was 1% and γ genus was 3.7% including 6 unclassified types. In cervical samples from 43 HIV positive women (18 HPV negative and 25 positive by MY09/11 PCR), only one sample was positivite for ß1 species (2.4%) using FAP primers. Six of the untyped strains clustered with sequences from species 7, 9, 10, 8,12 of γ genus. Four sequences remained unclassified. Finally, ß and γ HPV prevalence was significantly lower than their respective HPV prevalence as identified by the Luminex system in all anatomical sites that were analyzed in previous studies. CONCLUSION: This study provides new information about viral isolates present in oropharyngeal site and it will contribute to improve the monitoring of HPV infection.


Assuntos
Canal Anal/virologia , Colo do Útero/virologia , Primers do DNA/genética , Orofaringe/virologia , Papillomaviridae/isolamento & purificação , Infecções por Papillomavirus/diagnóstico , DNA Viral/genética , Feminino , Genótipo , Infecções por HIV/complicações , Humanos , Masculino , Papillomaviridae/classificação , Infecções por Papillomavirus/virologia , Filogenia , Reação em Cadeia da Polimerase , Prevalência , Estudos Retrospectivos , Análise de Sequência de DNA , Carga Viral
15.
Infect Dis (Lond) ; 51(4): 241-248, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30760088

RESUMO

BACKGROUND: Along with the current development of molecular diagnostic methods of respiratory viruses, the bedside patient sampling techniques need to be evaluated. We here asked the question whether the addition of an oropharynx swab to the traditional nasopharynx swab might improve the diagnostic yield of multiplex PCR analysis. Ct values from the two sampling sites were compared as well as patient tolerability. METHODS: In an emergency department in Malmö, Sweden, 98 adult patients with respiratory disease were sampled both from the nasopharynx and oropharynx for virus diagnostics by PCR. RESULTS: Influenza (AH1, AH3, B), human metapneumovirus (hMPV) or respiratory syncytial virus (RSV) were detected by PCR in 58 subjects. The diagnostic yield was improved by combining nasopharyngeal and oropharyngeal sampling - a virus was detected in another 6 patients compared to traditional nasopharyngeal sampling (p = .031, McNemar's test). In 38/55 subjects viral load was higher in the nasopharynx than in the oropharynx. Self-reported discomfort was significantly lower from oropharyngeal sampling than from nasopharyngeal sampling. CONCLUSIONS: Adding an oropharynx sample to a nasopharynx sample increased the diagnostic yield of respiratory viruses. Oropharyngeal sampling was well tolerated.


Assuntos
Nasofaringe/virologia , Orofaringe/virologia , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/virologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Serviço Hospitalar de Emergência , Feminino , Humanos , Limite de Detecção , Masculino , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase Multiplex , Manejo de Espécimes , Suécia , Carga Viral , Adulto Jovem
16.
BMC Infect Dis ; 19(1): 122, 2019 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-30727957

RESUMO

BACKGROUND: Human papillomavirus (HPV) contributes to the development of cervical and oropharyngeal tumors. The increased incidence of HPV associated oropharyngeal tumors is lately being observed also in Polish population. The worldwide distribution of HPV varies and the studies rarely combine analysis of virus genotypes in both: genital and oropharyngeal locations. Therefore, in our study, we investigated HPV distribution in both anatomical sites of females with previous history of cervical cancer or with pre-cancerous lesion and their partners to establish the dominant types in Polish couples in genital and oropharyngeal areas, as they can be easily sexually transmitted. METHODS: The study group consisted of 197 females and their partners. Each female had current or previous cervical pathology and HPV detected in gynecological swab with the use of Anyplex™ II HPV28 Detection system. This system is based on multiplexed real time PCR and enables detection of 19 high-risk and 9 low-risk HPVs. RESULTS: Beside women, the virus was found in 114/197 of men in their foreskin swabs. Additionally, HPV was detected in oropharyngeal swabs of 39/197 female and 56/197 male participants. HPV 16/31/42/39/54 dominated in female and HPV 66/42/16/31/53 in male genital locations. The incidence of HPV in oropharynx was lower, top five genotypes included: HPV 6/39/42/35/16 in women compared to HPV 39/6/42/40/33 in men. HPV16 was the most frequently detected virus type, found in 70/197 examined cervical swabs. It was significantly more prevalent as single infection in females, previously treated for the cervical cancer (p = 0.035). Moreover, regular presence of low risk type 42 was noticeable in both sexes, in both kind of swabs. There was a trend observed towards its prevalence as single infectious agent in women with previous history of cervical cancer (p = 0.069). CONCLUSIONS: Our results showed the distribution of HPV genotypes in Polish couples, in which each woman is HPV positive, indicating a common infection of HPV 42, regardless of sex and anatomical site. These findings shed new light on HPV 42 significance, however they should be verified on a larger group of Polish participants, followed regularly in 6 months intervals, in oral as well as in genital areas.


Assuntos
Boca/virologia , Orofaringe/virologia , Papillomaviridae/genética , Infecções por Papillomavirus/virologia , Adulto , Idoso , Feminino , Prepúcio do Pênis/virologia , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Papillomaviridae/isolamento & purificação , Infecções por Papillomavirus/epidemiologia , Polônia/epidemiologia , Prevalência , Reação em Cadeia da Polimerase em Tempo Real , Fatores de Risco , Parceiros Sexuais , Doenças Sexualmente Transmissíveis/virologia , Neoplasias do Colo do Útero/virologia
17.
Virol J ; 16(1): 6, 2019 01 10.
Artigo em Inglês | MEDLINE | ID: mdl-30630503

RESUMO

BACKGROUND: Waterfowl parvoviruses, including goose parvovirus (GPV) and Muscovy duck parvovirus (MDPV), can cause seriously diseases in geese and ducks. Developing a fast and precise diagnosis assay for these two parvoviruses is particularly important. RESULTS: A duplex SYBR Green I-based quantitative real-time PCR assay was developed for the simultaneous detection and differentiation of GPV and MDPV. The assay yielded melting curves with specific single peak (Tm = 87.3 ± 0.26 °C or Tm = 85.4 ± 0.23 °C) when GPV or MDPV was evaluated, respectively. When both parvoviruses were assessed in one reaction, melting curves with specific double peaks were yielded. CONCLUSION: This duplex quantitative RT-PCR can be used to rapid identify of GPV and MDPV in field cases and artificial trials, which make it a powerful tool for diagnosing, preventing and controlling waterfowl parvovirus infections.


Assuntos
Patos/virologia , Gansos/virologia , Infecções por Parvoviridae/veterinária , Parvovirus/classificação , Doenças das Aves Domésticas/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real/métodos , Animais , Cloaca/virologia , Genoma Viral , Compostos Orgânicos , Orofaringe/virologia , Infecções por Parvoviridae/diagnóstico , Parvovirus/isolamento & purificação , Filogenia , Doenças das Aves Domésticas/virologia , Temperatura de Transição , Carga Viral
18.
Mol Ecol Resour ; 19(1): 128-143, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30240114

RESUMO

Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.


Assuntos
Quirópteros/virologia , Metagenômica/métodos , Análise de Sequência de DNA/métodos , Manejo de Espécimes/métodos , Viroses/veterinária , Vírus/classificação , Vírus/genética , Animais , Biodiversidade , Fezes/virologia , Orofaringe/virologia , Peru , Viroses/virologia
20.
Biomed Res Int ; 2018: 6362716, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30581863

RESUMO

Background: Influenza A virus (IAV) has had the highest morbidity globally over the past decade. A growing number of studies indicate that the upper respiratory tract (URT) microbiota plays a key role for respiratory health and that a dysfunctional respiratory microbiota is associated with disease; but the impact of microbiota during influenza is understudied. Methods: We recruited 180 children, including 121 IAV patients and 59 age-matched healthy children. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected to conduct 16S rDNA sequencing and compare microbiota structures in different individuals. Results: Both NP and OP microbiota in IAV patients differed from those in healthy individuals. The NP dominated genera in IVA patients, such as Moraxella, Staphylococcus, Corynebacterium, and Dolosigranulum, showed lower abundance than in healthy children. The Streptococcus significantly enriched in patients' NP and Phyllobacterium could be generally detected in patients' NP microbiota. The most abundant genera in OP microbiota showed a decline tendency in patients, including Streptococcus, Neisseria, and Haemophilus. The URT's bacterial concurrence network changed dramatically in patients. NP and OP samples were clustered into subgroups by different dominant genera; and NP and OP microbiota provided the precise indicators to distinguish IAV patients from healthy children. Conclusion: This is the first respiratory microbiome analysis on pediatric IAV infection which reveals distinct NP and OP microbiota in influenza patients. It provides a new insight into IAV research from the microecology aspect and promotes the understanding of IAV pathogenesis.


Assuntos
Vírus da Influenza A/patogenicidade , Influenza Humana/microbiologia , Nasofaringe/microbiologia , Nasofaringe/virologia , Orofaringe/microbiologia , Orofaringe/virologia , Adolescente , Bactérias/genética , Criança , Pré-Escolar , DNA Bacteriano/genética , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Microbiota/genética , RNA Ribossômico 16S/genética
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