RESUMO
Tick-borne diseases (TBDs), including emerging and re-emerging infectious diseases, are important threats to human and animal health worldwide. Indeed, the number of reported human and animal infectious cases of novel TBD agents has increased in recent decades. However, TBDs tend to be neglected, especially in resource-limited countries that often have limited diagnostic capacity. The aim of this molecular survey was to detect and characterise tick-borne pathogens (Babesia, Theileria, and Hepatozoon parasites and Anaplasmataceae bacteria) in domestic dogs in Zambia. In total, 247 canine peripheral blood samples were collected in Lusaka, Mazabuka, Monze, and Shangombo. Conventional PCR to detect the selected pathogens was performed using DNA extracted from canine blood. One hundred eleven samples were positive for protozoa and 5 were positive for Anaplasmataceae. Sequencing of thirty-five randomly selected protozoa-positive samples revealed the presence of Babesia rossi, Babesia vogeli, and Hepatozoon canis 18S rDNA. Based on these sequences, a multiplex PCR system was developed to yield PCR products with different amplicons, the size of which depended on the parasite species; thus, each species could be identified without the need for sequence analysis. Approximately 40% of dogs were positive for H. canis. In particular, the positive rate (75.2%) of H. canis infection was significantly higher in Shangombo than in other sampling sites. Multiplex PCR assay detected B. rossi and B. vogeli infections in five and seven dogs, respectively, indicating that this approach is useful for detecting parasites with low prevalence. Sequencing analysis of gltA and groEL genes of Anaplasmataceae revealed that two and one dogs in Lusaka were infected with Anaplasma platys and Ehrlichia canis, respectively. The data indicated that Zambian dogs were infected with multiple tick-borne pathogens such as H. canis, B. rossi, B. vogeli, A. platys, E. canis and uncharacterized Ehrlichia sp. Since some of these parasites are zoonotic, concerted efforts are needed to raise awareness of, and control, these tick-borne pathogens.
Assuntos
Infecções por Anaplasmataceae/veterinária , Anaplasmataceae/isolamento & purificação , Doenças do Cão/epidemiologia , Parasitos/isolamento & purificação , Doenças Transmitidas por Carrapatos/veterinária , Carrapatos/microbiologia , Carrapatos/parasitologia , Anaplasma/genética , Anaplasma/isolamento & purificação , Anaplasmataceae/genética , Infecções por Anaplasmataceae/epidemiologia , Animais , Animais Domésticos/microbiologia , Animais Domésticos/parasitologia , Babesia/genética , Babesia/isolamento & purificação , Babesiose/epidemiologia , Coccídios/genética , Coccídios/isolamento & purificação , Coccidiose/epidemiologia , Coccidiose/veterinária , Doenças do Cão/microbiologia , Doenças do Cão/parasitologia , Cães/microbiologia , Cães/parasitologia , Ehrlichia/genética , Ehrlichia/isolamento & purificação , Ehrlichia canis/genética , Ehrlichia canis/isolamento & purificação , Ehrlichiose/epidemiologia , Ehrlichiose/veterinária , Humanos , Parasitos/genética , Reação em Cadeia da Polimerase , Prevalência , Doenças Transmitidas por Carrapatos/epidemiologia , Doenças Transmitidas por Carrapatos/microbiologia , Doenças Transmitidas por Carrapatos/parasitologia , Zâmbia/epidemiologiaRESUMO
During a COVID-19 outbreak in a prison in Zambia from 14th to 19th December 2021, a case control study was done to measure vaccine effectiveness (VE) against infection and symptomatic infection, when the Omicron variant was the dominant circulating variant. Among 382 participants, 74.1% were fully vaccinated and the median time since full vaccination was 54 days. There were no hospitalizations or deaths. COVID-19 VE against any SARS-CoV-2 infection was 64.8% and VE against symptomatic SARS-CoV-2 infection was 72.9%. COVID-19 vaccination helped protect incarcerated persons against SARS-CoV-2 infection during an outbreak while Omicron was the dominant variant in Zambia.
RESUMO
BackgroundSparse data documenting the impact of COVID-19 in Africa has fostered the belief that COVID-19 skipped Africa. We previously published results from a systematic postmortem surveillance at a busy inner-city morgue in Lusaka, Zambia. Between June-October 2020, we detected COVID-19 in 15-19% of all deaths and concentrated in community settings where testing for COVID-19 was absent. Yet these conclusions rested on a small cohort of 70 COVID-19+ decedents. Subsequently, we conducted a longer and far larger follow-on survey using and expanding on the same methodology. MethodsWe obtained a nasopharyngeal swab from each enrolled decedent and tested these using reverse transcriptase quantitative PCR (RT-qPCR). A subset of samples with a PCR cycle threshold <30 underwent genotyping to identify viral lineages. We weighted our results to adjust for enrolment ratios and stratified them by setting (facility vs. community), time of year, age, and location. ResultsFrom 1,118 enrolled decedents, COVID-19 was detected among 32.0% (358/1,116). We observed three waves of transmission that peaked in July 2020, January 2021, and [~]June 2021 (end of surveillance). These were dominated by the AE.1 lineage and the Beta and Delta variants, respectively. During peak transmission, COVID-19 was detected in [~]90% of all deaths. Roughly four COVID-19 deaths occurred in the community for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths and overall, only [~]10% of COVID-19+ deaths were identified in life. ConclusionsCOVID-19 had a devastating impact in Lusaka. COVID-19+ deaths occurred in all age groups and was the leading cause of death during peak transmission periods. Testing was rarely done for the vast majority of COVID-19 deaths that occurred in the community, yielding a substantial undercount. What is already known on this topicO_LIPreviously, we reported that COVID-19 was present among 15-19% of all decedents passing through a busy city morgue in Lusaka. C_LIO_LIData documenting the mortal impact of COVID-19 in Africa remain sparse. C_LIO_LISeveral modeling groups have also argued that COVID-19s impact in Africa has been underreported and hence underestimated. C_LI What this study addsO_LIAntemortem testing for COVID-19 captured only [~]10% of COVID-19 positive individuals indicating a substantial gap in surveillance. C_LIO_LIDuring peak transmission periods, [~]90% of all deceased individuals tested positive for COVID-19. C_LIO_LIMost COVID-19 positive deceased adults presented with symptoms typical of COVID-19, arguing that COVID-19 caused their deaths and was not a co-incidental finding. C_LIO_LIDeaths occurred across the age spectrum, including among young children, indicating a different pattern of impact from what has been seen in high income country settings. C_LIO_LIWe document three waves of transmission, attributable to the AE.1 lineage, and the Beta and Delta variants, respectively. C_LI
RESUMO
The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations, predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1. Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.
RESUMO
Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks. One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.