African helminth infection out of Africa: Paleoparasitological and paleogenetic investigations in Pretos Novos cemetery, Rio de Janeiro, Brazil (1769-1830).

Pretos Novos cemetery (PNC), Rio de Janeiro, Brazil (1769-1830) was created exclusively to bury enslaved Africans who died upon arrival at the city or before being sold in the slave market. The PNC site may be unique in the Americas in allowing the study of African parasite infections acquired in Africa. We aimed to identify parasites infecting PNC individuals through paleoparasitological and paleogenetic analyses. The bodies had been dismembered, placed in mass graves, and burned, and most human remains collected from the site are highly fragmented and show extensive degradation. Sacrum and pelvic sediments were collected from five individuals along with seven samples of sediment from other areas of the body, as controls. Samples were submitted to three parasitological techniques and, in paleogenetic analysis, to four molecular targets. Larvae, mites, pollen grains, and structure suggestive of plants and fungus were observed, but we found no evidence of helminth infection. Ascaris sp. cytb sequence was recovered in one individual. We emphasize that, even with the extensive degradation of PNC human remains and the process of curation of samples, it was possible to recover helminth aDNA. The origin of PNC individuals confirms that these infections were brought to Brazil from western and central Africa during the colonial era.

First Paleogenetic Evidence of Probable Syphilis and Treponematoses Cases in the Brazilian Colonial Period.

Despite interest in the origins of syphilis, paleopathological analysis has not provided answers, and paleogenetic diagnosis remains a challenge. Even venereal syphilis has low infectivity which means there are few circulating bacteria for most of the individual's life. Human remains recovered from the Nossa Senhora do Carmo Church (17th to 19th centuries) and the Praça XV Cemetery (18th to 19th centuries), Rio de Janeiro, Brazil, were subjected to Treponema paleogenetic analysis. Historical data point to endemic treponemal infections in the city, including venereal syphilis. Based on the physiopathology of Treponema pallidum infection, 25 samples, mostly from skull remains of young adults, with no visible paleopathological evidence of treponematoses, were analyzed. PCR with three molecular targets, tpp47, polA, and tpp15, were applied. Ancient DNA tpp15 sequences were recovered from two young adults from each archaeological site and revealed the polymorphism that characterizes T. p. subsp. pallidum in a female up to 18 years old, suggesting a probable case of syphilis infection. The results indicated that the epidemiological context and the physiopathology of the disease should be considered in syphilis paleogenetic detection. The findings of Treponema sp. aDNA are consistent with historical documents that describe venereal syphilis and yaws as endemic diseases in Rio de Janeiro. Data on the epidemiological characteristics of the disease and its pathophysiology offer new perspectives in paleopathology.

Paleoparasitological analysis of human remains from a European cemetery of the 17th-19th century in Rio de Janeiro, Brazil.

Most paleoparasitological studies based on archeological sites in the New World are from pre-Columbian times. However, understanding of the introduction and spread of parasites with the arrival of European settlers and African slaves in America remains a topic for investigation. This study evaluated the presence of intestinal parasites in human remains from an archeological site of the colonial period, and compared the sensitivity of three parasitological techniques for paleoparasitological study. Samples were collected from the archeological site Nossa Senhora do Carmo Church, Rio de Janeiro, Brazil. Paleoparasitological examination revealed intestinal helminths in 2/17 (11.8%) individuals. Trichuris trichiura and Ascaris sp. eggs were found. The spontaneous sedimentation technique showed a greater numerical recovery of parasites, while the flotation techniques were superior in retrieving more parasite types. The study demonstrated that combining the three techniques improves the recovery of parasites in terms of number and diversity. Similar diversity of parasites to that of a previous historical archeological site suggests that the distribution of intestinal parasites was widespread in Rio de Janeiro, regardless of social status.

Paleoparasitological results from XVIII century human remains from Rio de Janeiro, Brazil.

Paleoparasitological studies of the Brazilian colonial period are scarce. A paleoparasitological analysis was performed on human remains from the archeological site Praça XV Cemetery in Rio de Janeiro, dating from the early 18th to 19th Centuries. The samples were obtained from the Institute of the Brazilian Archaeology collection, and showed evidence of washing and brushing. Sediments were extracted from sacral foramina by scraping. Sediments from skulls were used as negative paleoparasitological controls. Spontaneous sedimentation method was performed prior to microscopic analysis. The results revealed that 8 of 10 individuals were infected with intestinal helminths and/or protozoa. Eggs of the nematodes Trichuris sp. and Ascaris sp. as well as a single taeniid egg were found. Protozoa cysts suggestive of Entamoeba sp. were also observed. Trichuris sp. was the most frequent and abundant parasite, found in 70% of individuals (26 eggs). The study showed the importance of analysis of sediment from human remains preserved in museum or scientific collections, even those subjected to a curating procedure. The levels of infection revealed here should be considered underestimations. This is the first paleoparasitological study from Rio de Janeiro city for the Brazilian colonial period and the first report of human Taenia sp. in the New World.

Mycobacterium tuberculosis complex detection in human remains: tuberculosis spread since the 17th century in Rio de Janeiro, Brazil.

Paleogenetic analysis for tuberculosis (TB) was conducted on bone and sediment samples dating from the 17th to 19th centuries from the archeological site of Nossa Senhora do Carmo Church in Rio de Janeiro, Brazil. Forty samples were analyzed, corresponding to 32 individuals from 28 burials, 22 of primary type and 6 of secondary type. The samples were collected following strict paleogenetic investigation guidelines and submitted to ancient DNA (aDNA) extraction. In order to detect TB infection, aDNA hybridizations with the molecular targets of Mycobacterium tuberculosis complex (MTC) IS6110 and IS1081 were applied. Additionally, the ancestry of individuals was assessed by human mitochondrial DNA (mtDNA) analysis of hypervariable segment I (HVS-I) sequence polymorphisms. The results of aDNA hybridizations demonstrated varying levels of MTC intensity in 17/32 individuals (53.1%), using the IS6110 target. The IS1081 MTC target showed lower sensitivity, confirming TB positivity in 10/32 (31.2%) individuals. The mtDNA analysis allowed the recovery of HVS-I sequences in 23/32 individuals (71.8%). The majority of these individuals (21/23, 91.3%) were of European ancestry, especially in primary burials. Haplogroups U, J, V, T, K, N, H and R, were identified with haplogroup U being the most frequent at 6/23 (26.1%). African and Amerindian mtDNA haplogroups were observed in two individuals in secondary burials. In spite of the ecclesiastic and aristocratic bias of the population of the study, human ancestry analysis revealed the prominent contribution of Europeans in the introduction or spread of TB in the New World.