The increase in SARS-CoV-2 lineages during 2020-2022 in a state in the Brazilian Northeast is associated with a number of cases.

SARS-CoV-2 has caused a high number of deaths in several countries. In Brazil, there were 37 million confirmed cases of COVID-19 and 700,000 deaths caused by the disease. The population size and heterogeneity of the Brazilian population should be considered in epidemiological surveillance due to the varied tropism of the virus. As such, municipalities and states must be factored in for their unique specificities, such as socioeconomic conditions and population distribution. Here, we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and their dynamics in each microregion from Sergipe state, northeastern Brazil, in the first 3 years of the pandemic. We analyzed 586 genomes sequenced between March 2020 and November 2022 extracted from the GISAID database. Phylogenetic analyses were carried out for each data set to reconstruct evolutionary history. Finally, the existence of a correlation between the number of lineages and infection cases by SARS-CoV-2 was evaluated. Aracaju, the largest city in northeastern Brazil, had the highest number of samples sequenced. This represented 54.6% (320) of the genomes, and consequently, the largest number of lineages identified. Studies also analyzed the relationship between mean lineage distributions and mean monthly infections, daily cases, daily deaths, and hospitalizations of vaccinated and unvaccinated patients. For this, a correlation matrix was created. Results revealed that the increase in the average number of SARS-CoV-2 variants was related to the average number of SARS-CoV-2 cases in both unvaccinated and vaccinated individuals. Thus, our data indicate that it is necessary to maintain epidemiological surveillance, especially in capital cities, since they have a high rate of circulation of resident and non-resident inhabitants, which contributes to the dynamics of the virus.

The spread of visceral leishmaniasis in Brazil: the first canine cases described in Ji-Paraná, Rondônia, Brazil.

Leishmaniases are zoonotic diseases caused by protozoa of the genus Leishmania. The disease has two clinical manifestations described in humans: visceral (VL) and cutaneous (CL) leishmaniasis. In Brazil, there has been an expansion of human VL. The participation of the dog as a reservoir of Leishmania infantum, the agent of VL, is important for the epidemiology of the disease since canine cases generally precede human cases. The present study aimed to evaluate the occurrence of Leishmania spp. infection in dogs in the municipality of Ji-Paraná by PCR assays using blood samples. Leishmania DNA was detected in two of the 105 studied dogs. The PCR products were sequenced and confirmed that the two samples (1.90%) correspond to L. infantum. The dogs had allochthonous history. Therefore, the positive results found here should serve as a warning to public health agencies. This is because Ji-Paraná is the third municipality to register cases of canine leishmaniasis (CanL) in Rondônia state. Thus, reinforcing the importance of expanding studies on the epidemiology and surveillance of VL in the region.

DNA-based blood meal analysis of Culicoides (Diptera: Ceratopogonidae) species from Jamari National Forest, Southwestern Amazon, Brazil.

Culicoides biting midges are insects involved in the transmission of filarial nematodes, protozoans, and viruses. Greater knowledge of Culicoides blood meal sources could improve our understanding of parasite transmission cycles. Our study used molecular tools to evaluate the blood meal sources of Culicoides biting midges from sylvatic environments. This study was conducted in Jamari National Forest, Rondônia, Brazil. Culicoides were captured using HP light traps positioned at ground level (1.5 m above ground) and in canopy (15 m above ground). To identify blood meal sources, females were subjected to DNA extraction and PCR targeting the cytb gene fragment, and the obtained sequences were analyzed and compared with sequences from GenBank. DNA extraction and PCR were performed on 455 Culicoides females, and blood meal sources were identified in 186 females. Thirty Culicoides specimens were collected from the Potosi trail and 156 were collected from the Santa Maria trail. A total of 22 species were captured; all 22 species were collected in canopy (100%) but only three species were collected at ground level (13.6%). The cytb fragment was amplified in 162 of 186 samples. Sample sequencing identified cytb DNA from nine blood-meal sources: Pauxi sp., Psophia viridis, Ramphastos tucanus tucanus, Choloepus didactylus, Choloepus hoffmanni, Tamandua tetradactyla, Ateles chamek, Homo sapiens and Pithecia irrorata. We observed that several different blood meal sources were utilized by a high diversity of Culicoides species. The abundance of Culicoides in the canopy may be related to the fact that the majority of blood meal hosts feed in treetops. We observed that C. (Hoffmania) sp. and C. coutinhoi tend to be more generalist, feeding on a range of mammals and piciform, gruiform and galliform birds. This data improves our knowledge of the feeding profile of biting midges from forest environments and should serve as a future basis for defining zoonotic transmission cycles.

Detection of Leishmania species (Kinetoplastida, Trypanosomatidae) in phlebotomine sand flies (Diptera, Psychodidae) from Porto Velho, Northern Brazil.

Cutaneous Leishmaniasis (CL) is a vector-borne disease caused by Leishmania species and transmitted by infected female sand flies. CL is widely distributed in Brazil, but knowledge about vectors and transmission cycles could be complex according to localities. The sand fly fauna in Rondônia State is extensive, diverse, and largely unexplored. Although the state records a mean of 1,000 CL cases per year, the vectors of CL are unknown. The aim of this study was to assess phlebotomine sand fly fauna composition using diversity indexes (Shannon [H'] and Simpson [1/D]) and to detect the prevalence of Leishmania infection to verify potential vectors in three ecotopes: (i) forest fragment (FF), (ii) forest edge (FE), and (iii) peridomicile (PE). Captures were performed in four rural districts in the municipality of Porto Velho. A total of 7,026 specimens were captured comprising 72 species, and individuals classified in subgenus level. Overall, the most abundant species were Lutzomyia davisi (n: 1,105), Lutzomyia melloi (n: 760), Lutzomyia auraensis (n: 738) and Lutzomyia antunesi (n: 479). Fauna was most diverse in the FF ecotope (H' = 20.2, 1/D = 11.2), followed by the FE (H' = 18.0, 1/D = 10.1) and PE (H' = 16.6, 1/D = 10.1) ecotopes. Leishmania DNA was detected in 24 of 232 pools. In every ecotope, Leishmania naiffi DNA was identified in the following sand fly species: Lu. antunesi, Lu. davisi, Lu. hirsuta hirsuta, Lu. shawi, Lu. sordellii and Lu. (Trichophoromyia) spp. This observation may indicate that a Le. naiffi transmission focus is present in the study localities. In addition, Leishmania lainsoni was detected in Lutzomyia (Trichophoromyia) spp. Our findings show that sand fly fauna in the study localities is diverse, that Leishmania parasites are circulating in all three ecotopes, and that some sand fly species may be implicated in the transmission of Leishmania to humans in localities evaluated.

The spread of visceral leishmaniasis in Brazil: the first canine cases described in Ji-Paraná, Rondônia, Brazil / A disseminação da leishmaniose visceral no Brasil: os primeiros casos caninos descritos em Ji-Paraná, Rondônia, Brasil

Abstract Leishmaniases are zoonotic diseases caused by protozoa of the genus Leishmania. The disease has two clinical manifestations described in humans: visceral (VL) and cutaneous (CL) leishmaniasis. In Brazil, there has been an expansion of human VL. The participation of the dog as a reservoir of Leishmania infantum, the agent of VL, is important for the epidemiology of the disease since canine cases generally precede human cases. The present study aimed to evaluate the occurrence of Leishmania spp. infection in dogs in the municipality of Ji-Paraná by PCR assays using blood samples. Leishmania DNA was detected in two of the 105 studied dogs. The PCR products were sequenced and confirmed that the two samples (1.90%) correspond to L. infantum. The dogs had allochthonous history. Therefore, the positive results found here should serve as a warning to public health agencies. This is because Ji-Paraná is the third municipality to register cases of canine leishmaniasis (CanL) in Rondônia state. Thus, reinforcing the importance of expanding studies on the epidemiology and surveillance of VL in the region.

Resumo As leishmanioses são doenças causadas por protozoários do gênero Leishmania. A doença apresenta duas manifestações clínicas: leishmaniose visceral (LV) e cutânea (LC). No Brasil, a LV está em expansão. A participação do cão como reservatório é importante para a epidemiologia da doença, pois os casos caninos geralmente precedem os humanos. O presente estudo avaliou a ocorrência de LV em cães (LVC) do município de Ji-Paraná por meio de ensaios de PCR, utilizando-se amostras de sangue. O DNA de Leishmania foi detectado em dois dos 105 cães estudados. Os produtos da PCR foram sequenciados e confirmaram que duas amostras (1,90%) eram Leishmania infantum. Os cães tinham histórico alóctone. Os resultados positivos encontrados servem de alerta aos órgãos públicos de saúde. Isso porque Ji-Paraná é o terceiro município a registrar casos de LVC no estado de Rondônia. Dessa forma, reforça-se a importância da ampliação dos estudos sobre a epidemiologia e vigilância da LV na região.

Vertical stratification of sand fly diversity in relation to natural infections of Leishmania sp. and blood-meal sources in Jamari National Forest, Rondônia State, Brazil.

BACKGROUND: Almost 1000 cases of American cutaneous leishmaniasis have been registered yearly in Rondônia State, Brazil. Little is known about the Leishmania transmission cycle (vectors and reservoirs) in the state. This study aimed to evaluate sand fly fauna from two vertical stratification layers in order to identify potential vectors and their blood-meal sources. METHODS: The study was conducted in Jamari National Forest. Sand flies were collected in the canopy (15 m) and at ground level (1 m) using HP light traps during four months, February, April, August and October, 2018. Insects were identified to the species level, and females were subjected to DNA extraction and PCR targeting minicircle kDNA and hsp70 (for Leishmania detection and species identification), and cytb (to identify blood-meal sources). Exploratory data analysis was used to determine mean of abundance and species richness between stratifications. The hsp70 and cytb sequences were analyzed and compared with sequences from GenBank. RESULTS: Overall, 68 species were identified from 15,457 individuals. On the Potosi trail, 7531 individuals of 49 species were collected; canopy captures totaled 6463 individuals of 46 species, while ground captures totaled 1068 individuals of 38 species. On the Santa Maria trail, 7926 individuals of 61 species were collected; canopy captures totaled 6136 individuals of 51 species, while ground captures totaled 1790 individuals of 53 species. A total of 23 pools were positive for kDNA (canopy n = 21, ground n = 2). Only two samples were sequenced for hsp70 (both in canopy); one sequence exhibited similarity with Leishmania braziliensis (Lutzomyia davisi pool) and another with L. naiffi (Lu. antunesi pool). The cytb fragment was amplified in 11 of 86 samples. Sample sequencing identified cytb DNA from 5 blood-meal sources: Micrastur gilvicollis, Psophia viridis, Tamandua tetradactyla, Homo sapiens and Choloepus didactylus. CONCLUSIONS: Sand fly fauna is more diverse in the canopy than at ground level. Factors such as blood-meal sources, resting sites, and abiotic components probably contribute to high abundance in the canopy. Our results reinforce the possibility that Lu. antunesi and Lu. davisi participate in Leishmania transmission in forest environments and may play an important role in transmission from sylvatic to human hosts.

Genetic structuring and fixed polymorphisms in the gene period among natural populations of Lutzomyia longipalpis in Brazil.

BACKGROUND: Even one hundred years after being originally identified, aspects of the taxonomy of the sand fly Lutzomyia longipalpis, the principal vector of Leishmania infantum in the Americas, remain unresolved for Brazilian populations of this vector. The diversity of morphological, behavioral, biochemical, and ethological characters, as well as the genetic variability detected by molecular markers are indicative of the presence of a complex of species. METHODS: In this study, a 525 bp fragment of the period gene was used to evaluate sympatric populations of L. longipalpis. A combination of probabilistic methods such as maximum likelihood and genetic assignment approach to investigate sympatric species of L. longipalpis were applied in three populations of Northeast Brazil. RESULTS: Fixed polymorphisms in geographically isolated populations of L. longipalpis from two localities in the state of Ceará and one in the state of Pernambuco, Brazil, was identified in a 525 bp fragment of the gene period (per). Our results suggest a direct relationship between the number of spots found in males' tergites and the genetic variation in cryptic species of L. longipalpis. The fragment used in this study revealed the nature of the ancestral morphotype 1S. CONCLUSION: New polymorphisms were identified in the gene per which can be used as a genetic barcode to sympatric taxonomy of L. longipalpis. The per gene fragment confirmed the presence of two siblings species of L. longipalpis in Sobral and showed that these same species are present in two other localities, representing an expansion within the L. longipalpis species complex with regards to the states of Ceará and Pernambuco.

Importância da distribuição geográfica dos vetores da doença de chagas em Pernambuco, Brasil, em 2012 / The importance of the geographical distribution of Chagas disease vectors in Pernambuco during 2012

Objetivos: Ressaltar a importância da distribuição geográfica e do comportamento dos vetores dadoença de Chagas no estado de Pernambuco. Métodos: O material analisado incluiu 100 por cento dosinsetos infectados por Trypanosoma sp. e 40 por cento dos insetos negativos, examinados no Laboratório deEndemias para confirmação taxonômica, pesquisa do parasito nas fezes dos triatomíneos e Controleda Qualidade na confirmação do diagnóstico. Resultados: Foram examinados 3.323 triatomíneos.A infecção natural por tripanossomatídeos foi detectada em 21,3 por cento dos exemplares. Triatomabrasiliensis foi a espécie mais frequente no intradomicílio (24,3 por cento), Triatoma pseudomaculata(14,9 por cento) e Panstrongylus megistus apresentaram proporcionalmente taxa de infecção naturalsuperior às demais (40,8 por cento) no peridomicílio. Conclusão: O conhecimento atualizado da distribuiçãogeográfica dos vetores da doença de Chagas é importante para fundamentar ações integradas entreos serviços de saúde, o que contribui para a vigilância entomológica no controle dos triatomíneos.

Objectives: To underscore the importance of geographic distribution and behavior of vectors ofChagas disease in the state of Pernambuco. Methods: The material analyzed included 100 percent of theinsects infected with Trypanosoma spp., and 40 percent of negative insects, examined at the EndemicDisease Laboratory for taxonomic confirmation, searching for the parasite in feces of the insects,with Quality Control to confirm the diagnosis. Results: A total of 3,323 triatomines. Naturalinfection by trypanosomes was detected in 21.3 percent of the specimens. Triatoma brasiliensis wasthe most frequent intradomiciliary species (24.3 percent), outside the home Triatoma pseudomaculata(14.9 percent) and Panstrongylus megistus had a natural infection rate proportionally superior to the others(40.8 percent). Conclusion: The current knowledge of the geographical distribution of Chagas diseasevectors is important as a platform to integrate actions between health services, contributing to theentomological surveillance and control of the insects.