Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon.

Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 deletions in Nueva Jerusalén (NJ), a remote, indigenous community in the Peruvian Amazon with high population mobility. We collected samples from November 2019 to May 2020 by active (ACD) and passive case detection (PCD) in NJ. Parasites were identified with microscopy and PCR. Then, we analyzed a representative set of positive-PCR samples (Pv = 68, Pf = 58) using highly-multiplexed deep sequencing assays (AmpliSeq) and compared NJ parasites with ones from other remote Peruvian areas using population genetics indexes. The ACD intervention did not reduce malaria cases in the short term, and persistent malaria transmission was observed (at least one Pv infection was detected in 96% of the study days). In Nueva Jerusalen, the Pv population had modest genetic diversity (He = 0.27). Pf population had lower diversity (He = 0.08) and presented temporal clustering, one of these clusters linked to an outbreak in February 2020. Moreover, Pv and Pf parasites from NJ exhibited variable levels of differentiation (Pv Fst = -0.52 & Pf Fst = 0.11-0.58) with parasites from other remote areas. No artemisin resistance mutations but chloroquine (57%) and sulfadoxine-pyrimethamine (35-67%) were detected in NJ's Pf parasites. Moreover, pfhrp2/3 gene deletions were common (32-50% of parasites with one or both genes deleted). The persistent Pv transmission and the detection of a Pf outbreak with parasites genetically distinct from the local ones highlight the need for tailored interventions focusing on mobility patterns and imported infections in remote areas to eliminate malaria in the Peruvian Amazon.

Malaria seroepidemiology in very low transmission settings in the Peruvian Amazon.

Despite progress towards malaria reduction in Peru, measuring exposure in low transmission areas is crucial for achieving elimination. This study focuses on two very low transmission areas in Loreto (Peruvian Amazon) and aims to determine the relationship between malaria exposure and proximity to health facilities. Individual data was collected from 38 villages in Indiana and Belen, including geo-referenced households and blood samples for microscopy, PCR and serological analysis. A segmented linear regression model identified significant changes in seropositivity trends among different age groups. Local Getis-Ord Gi* statistic revealed clusters of households with high (hotspots) or low (coldspots) seropositivity rates. Findings from 4000 individuals showed a seropositivity level of 2.5% (95%CI: 2.0%-3.0%) for P. falciparum and 7.8% (95%CI: 7.0%-8.7%) for P. vivax, indicating recent or historical exposure. The segmented regression showed exposure reductions in the 40-50 age group (ß1 = 0.043, p = 0.003) for P. vivax and the 50-60 age group (ß1 = 0.005, p = 0.010) for P. falciparum. Long and extreme distance villages from Regional Hospital of Loreto exhibited higher malaria exposure compared to proximate and medium distance villages (p < 0.001). This study showed the seropositivity of malaria in two very low transmission areas and confirmed the spatial pattern of hotspots as villages become more distant.

Dengue and COVID-19 Co-Circulation in the Peruvian Amazon: A Population-Based Study.

The COVID-19 pandemic affected the main Amazon cities dramatically, with Iquitos City reporting the highest seroprevalence of anti-SARS-CoV-2 antibodies during the first COVID-19 wave worldwide. This phenomenon raised many questions about the possibility of a co-circulation of dengue and COVID-19 and its consequences. We carried out a population-based cohort study in Iquitos, Peru. We obtained a venous blood sample from a subset of 326 adults from the Iquitos COVID-19 cohort (August 13-18, 2020) to estimate the seroprevalence of anti-dengue virus (DENV) and anti-SARS-CoV-2 antibodies. We tested each serum sample for anti-DENV IgG (serotypes 1, 2, 3, and 4) and SARS-CoV-2 antibodies anti-spike IgG and IgM by ELISA. We estimated an anti-SARS-CoV-2 seroprevalence of 78.0% (95% CI, 73.0-82.0) and an anti-DENV seroprevalence of 88.0% (95% CI, 84.0-91.6), signifying a high seroprevalence of both diseases during the first wave of COVID-19 transmission in the city. The San Juan District had a lower anti-DENV antibody seroprevalence than the Belen District (prevalence ratio, 0.90; 95% CI, 0.82-0.98). However, we did not observe these differences in anti-SARS-CoV-2 antibody seroprevalence. Iquitos City presented one of the highest seroprevalence rates of anti-DENV and anti-SARS-CoV-2 antibodies worldwide, but with no correlation between their antibody levels.

Evidence-Based Malaria Control and Elimination in the Amazon: Input from the International Center of Excellence in Malaria Research Network in Peru and Brazil.

Malaria remains endemic in 17 countries in the Americas, where 723,000 cases were reported in 2019. The majority (> 90%) of the regional malaria burden is found within the Amazon Basin, which includes nine countries and territories in South America. Locally generated evidence is critical to provide information to public health decision makers upon which the design of efficient and regionally directed malaria control and elimination programs can be built. Plasmodium vivax is the predominant malaria parasite in the Amazon Basin. This parasite species appears to be more resilient to malaria control strategies worldwide. Asymptomatic Plasmodium infections constitute a potentially infectious reservoir that is typically missed by routine microscopy-based surveillance and often remains untreated. The primary Amazonian malaria vector, Nyssorhynchus (formerly Anopheles) darlingi, has changed its behavior to feed and rest predominantly outdoors, reducing the efficiency of core vector control measures such as indoor residual spraying and distribution of long-lasting insecticide-treated bed nets. We review public health implications of recent field-based research carried out by the Amazonia International Center of Excellence in Malaria Research in Peru and Brazil. We discuss the relative role of traditional and novel tools and strategies for better malaria control and elimination across the Amazon, including improved diagnostic methods, new anti-relapse medicines, and biological larvicides, and emphasize the need to integrate research and public health policymaking.

Seroprevalence of anti-SARS-CoV-2 antibodies in Iquitos, Peru in July and August, 2020: a population-based study.

BACKGROUND: Detection of anti-SARS-CoV-2 antibodies among people at risk of infection is crucial for understanding both the past transmission of COVID-19 and vulnerability of the population to continuing transmission and, when done serially, the intensity of ongoing transmission over an interval in a community. We aimed to estimate the seroprevalence of COVID-19 in a representative population-based cohort in Iquitos, one of the regions with the highest mortality rates from COVID-19 in Peru, where a devastating number of cases occurred in March, 2020. METHODS: We did a population-based study of SARS-CoV-2 transmission in Iquitos at two timepoints: July 13-18, 2020 (baseline), and Aug 13-18, 2020 (1-month follow-up). We obtained a geographically stratified representative sample of the city population using the 2017 census data, which was updated on Jan 20, 2020. We included people who were inhabitants of Iquitos since COVID-19 was identified in Peru (March 6, 2020) or earlier. We excluded people living in institutions, people receiving any pharmacological treatment for COVID-19, people with any contraindication for phlebotomy, and health workers or individuals living with an active health worker. We tested each participant for IgG and IgM anti-SARS-CoV-2 antibodies using the COVID-19 IgG/IgM Rapid Test (Zhejiang Orient Gene Biotech, China). We used survey analysis methods to estimate seroprevalence accounting for the sampling design effect and test performance characteristics. FINDINGS: We identified 726 eligible individuals and enrolled a total of 716 participants (99%), distributed across 40 strata (four districts, two sexes, and five age groups). We excluded ten individuals who: did not have consent from a parent or legal representative (n=3), had moved to Iquitos after March 6, 2020 (n=3), were in transit (n=2), or had respiratory symptoms (n=1). After adjusting for the study sampling effects and sensitivity and specificity of the test, we estimated a seroprevalence of 70% (95% CI 67-73) at baseline and 66% (95% CI 62-70) at 1 month of follow-up, with a test-retest positivity of 65% (95% CI 61-68), and an incidence of new exposures of 2% (95% CI 1-3). We observed significant differences in the seroprevalence between age groups, with participants aged 18-29 years having lower seroprevalence than those aged younger than 12 years (prevalence ratio 0·85 [95% CI 0·73-0·98]; p=0·029). INTERPRETATION: After the first epidemic peak, Iquitos had one of the highest rates of seroprevalence of anti-SARS-CoV-2 antibodies worldwide. Nevertheless, the city experienced a second wave starting in January, 2021, probably due to the emergence of the SARS-CoV-2 P1 variant, which has shown higher transmissibility and reinfection rates. FUNDING: Dirección Regional de Salud de Loreto (DIRESA), Loreto, Peru. TRANSLATION: For the Spanish translation of the abstract see Supplementary Materials section.

Population Genetics of Plasmodium vivax in the Peruvian Amazon.

BACKGROUND: Characterizing the parasite dynamics and population structure provides useful information to understand the dynamic of transmission and to better target control interventions. Despite considerable efforts for its control, vivax malaria remains a major health problem in Peru. In this study, we have explored the population genetics of Plasmodium vivax isolates from Iquitos, the main city in the Peruvian Amazon, and 25 neighbouring peri-urban as well as rural villages along the Iquitos-Nauta Road. METHODOLOGY/ RESULTS: From April to December 2008, 292 P. vivax isolates were collected and successfully genotyped using 14 neutral microsatellites. Analysis of the molecular data revealed a similar proportion of monoclonal and polyclonal infections in urban areas, while in rural areas monoclonal infections were predominant (p = 0.002). Multiplicity of infection was higher in urban (MOI = 1.5-2) compared to rural areas (MOI = 1) (p = 0.003). The level of genetic diversity was similar in all areas (He = 0.66-0.76, p = 0.32) though genetic differentiation between areas was substantial (PHIPT = 0.17, p<0.0001). Principal coordinate analysis showed a marked differentiation between parasites from urban and rural areas. Linkage disequilibrium was detected in all the areas ([Formula: see text] = 0.08-0.49, for all p<0.0001). Gene flow among the areas was stablished through Bayesian analysis of migration models. Recent bottleneck events were detected in 4 areas and a recent parasite expansion in one of the isolated areas. In total, 87 unique haplotypes grouped in 2 or 3 genetic clusters described a sub-structured parasite population. CONCLUSION/SIGNIFICANCE: Our study shows a sub-structured parasite population with clonal propagation, with most of its components recently affected by bottleneck events. Iquitos city is the main source of parasite spreading for all the peripheral study areas. The routes of transmission and gene flow and the reduction of the parasite population described are important from the public health perspective as well for the formulation of future control policies.

[Lessons learned in the control of Aedes aegypti to address dengue and the emergency of chikungunya in Iquitos, Peru]. / Lecciones aprendidas en el control de Aedes aegypti para afrontar el dengue y la emergencia de chikungunya en Iquitos, Perú.

Dengue has affected Iquitos since 1990 causing outbreaks of major impact on public health and for this reason great efforts have been made for its temporal control. Currently, with the expansion of the chikungunya virus in the Americas and the threat of the emergence of the virus in Iquitos, we reflect on lessons learned by way of the activities undertaken in the area of vector control; epidemiological surveillance, diagnosis and clinical management during periods of outbreaks of dengue, in a way that will allow us to better face the threat of an outbreak of chikungunya virus in the largest city in the Peruvian Amazon.

Lecciones aprendidas en el control de Aedes aegypti para afrontar el dengue y la emergencia de chikungunya en Iquitos, Perú / Lessons learned in the control of Aedes aegypti to address dengue and the emergency of chikungunya in Iquitos, Peru

El dengue ha afectado a Iquitos desde 1990 causando varios brotes de gran impacto en la salud pública y por el que se desplegaron grandes esfuerzos para su control temporal. Actualmente, ante la expansión del virus chikungunya en las Américas y la amenaza de la emergencia del virus en Iquitos, reflexionamos a modo de lecciones aprendidas las actividades emprendidas en el área del control vectorial; la vigilancia epidemiológica; el diagnóstico y el manejo clínico durante los periodos de brotes de dengue, de modo que nos permita enfrentar mejor la amenaza de un brote del virus chikunguña en la ciudad más grande de la Amazonía peruana.

Dengue has affected Iquitos since 1990 causing outbreaks of major impact on public health and for this reason great efforts have been made for its temporal control. Currently, with the expansion of the chikungunya virus in the Americas and the threat of the emergence of the virus in Iquitos, we reflect on lessons learned by way of the activities undertaken in the area of vector control; epidemiological surveillance, diagnosis and clinical management during periods of outbreaks of dengue, in a way that will allow us to better face the threat of an outbreak of chikungunya virus in the largest city in the Peruvian Amazon.

Population structure and spatio-temporal transmission dynamics of Plasmodium vivax after radical cure treatment in a rural village of the Peruvian Amazon.

BACKGROUND: Despite the large burden of Plasmodium vivax, little is known about its transmission dynamics. This study explored the population structure and spatio-temporal dynamics of P. vivax recurrent infections after radical cure in a two-year cohort study carried out in a rural community of the Peruvian Amazon. METHODS: A total of 37 P. vivax participants recruited in San Carlos community (Peru) between April and December 2008 were treated radically with chloroquine and primaquine and followed up monthly for two years with systematic blood sampling. All samples were screened for malaria parasites and subsequently all P. vivax infections genotyped using 15 microsatellites. Parasite population structure and dynamics were determined by computing different genetic indices and using spatio-temporal statistics. RESULTS: After radical cure, 76% of the study participants experienced one or more recurrent P. vivax infections, most of them sub-patent and asymptomatic. The parasite population displayed limited genetic diversity (He = 0.49) and clonal structure, with most infections (84%) being monoclonal. Spatio-temporal clusters of specific haplotypes were found throughout the study and persistence of highly frequent haplotypes were observed over several months within the same participants/households. CONCLUSIONS: In San Carlos community, P. vivax recurrences were commonly observed after radical treatment, and characterized by asymptomatic, sub-patent and clustered infections (within and between individuals from a few neighbouring households). Moreover low genetic diversity as well as parasite inbreeding are likely to define a clonal parasite population which has important implications on the malaria epidemiology of the study area.

Hyperendemic malaria transmission in areas of occupation-related travel in the Peruvian Amazon.

BACKGROUND: Plasmodium vivax and Plasmodium falciparum cause a significant illness burden in Peru. Anopheline indices for populated communities in the peri-Iquitos region of Loreto have been reported to be remarkably low, with entomological inoculation rates (EIR) estimated at one to 30 infective bites per year based on a few studies in close proximity to the urban centre of Iquitos and surrounding deforested areas. Local reports suggest that a large number of the reported cases are contracted outside of populated communities in undeveloped riverine areas frequented by loggers and fishermen. METHODS: To better understand vectorial capacity in suspected high malaria transmission zones in a rural district near Iquitos, Peru, mosquito collections were conducted at different points in the seasonality of malaria transmission in 21 sites frequented by occupational labourers. Prevalence of Plasmodium spp in vectors was determined by circumsporozoite protein ELISA on individual mosquitoes. Slide surveillance was performed for humans encountered in the zone. RESULTS: In total, of 8,365 adult female mosquitoes examined, 98.5% were identified as Anopheles darlingi and 117 (1.4%) tested positive for sporozoites (P. falciparum, P. vivax VK210 or P. vivax VK247). Measured human biting rates at these sites ranged from 0.102 to 41.13 bites per person per hour, with EIR values as high as 5.3 infective bites per person per night. Six percent of the 284 blood films were positive for P. vivax or P. falciparum; however, 88% of the individuals found to be positive were asymptomatic at the time of sampling. CONCLUSIONS: The results of this study provide key missing indices of prominent spatial and temporal heterogeneity of vectorial capacity in the Amazon Basin of Peru. The identification of a target human subpopulation as a principal reservoir and dispersion source of Plasmodium species has important implications for vaccine development and the delivery of effective targeted malaria control strategies.

[Long-lasting insecticide - treated bednet ownership, retention and usage one year after their distribution in Loreto, Peru]. / Posesión, retención y uso de mosquiteros tratados con insecticidas de larga duración luego de un año de su distribución en Loreto, Perú

OBJECTIVES: To assess long-lasting insecticide - treated bednet (LLITN) ownership, retention and usage one year after their distribution in Loreto, Peru. MATERIALS AND METHODS: From July to September 2007, 26,185 LLITNs Olyset Net ® were delivered in 194 targeted communities in the Peruvian Amazon region, covering 45,331 people. Two cross-sectional community-based surveys in December 2007 and July 2008 were undertaken in a sample of 60 targeted communities (30.9% out of the total). A semi-structured questionnaire was used to collect necessary data to calculate LLITN ownership, retention and usage indicators. RESULTS: High LLITN household ownership was showed in both surveys (99.9% and 98.7%, respectively). LLITN/ person ratio decreased from 0.58 at the end of the LLITN delivery to 0.51 in the second survey, estimating LLITN retention of 87% after 1 year of intervention. In the first survey, 99.0% of all children <5 years and 96,0% of pregnant women slept under a LLITN the previous night, while in the second survey, 77.7% of children <5 years and 66.3% of pregnant women slept under a LLITN the previous night. Big mesh size of LLITN had low people's acceptability, reaching only 39.0% in the second survey. CONCLUSIONS: Although universal LLITN household ownership remained high, their LLITN usage levels have decreased during one-year follow-up period.

Posesión, retención y uso de mosquiteros tratados con insecticidas de larga duración luego de un año de su distribución en Loreto, Perú / Long-lasting insecticide - treated bednet ownership, retention and usage one year after their distribution in Loreto, Peru

Objetivos. Evaluar la posesión, retención y uso de mosquiteros tratados con insecticida de larga duración (MTILD) luego de un año de su distribución en Loreto, Perú. Materiales y métodos. De julio a septiembre de 2007 se distribuyeron 26 185 MTILD Olyset Net® en 194 comunidades objetivo de Loreto, que protegieron a 45 331 personas. Posteriormente, se realizaron visitas de monitoreo (primera en diciembre de 2007 y segunda en julio de 2008) a los hogares de una muestra de 60 comunidades objetivo (30,9 por ciento del total), colectándose mediante un cuestionario semiestructurado los datos necesarios para el cálculo de indicadores de posesión, retención y uso de los MTILD. Resultados. En ambas visitas, la posesión de MTILD en hogares fue elevada (99,9 por ciento y 98,7 por ciento, respectivamente). La razón MTILD/persona disminuyó de 0,58 al momento de la distribución a 0,51 en la segunda visita, estimándose una retención al año de MTILD de 87 por ciento. En la primera visita, 99,0 por ciento de los niños <5 años y 96,0 por ciento de las embarazadas durmieron bajo un MTILD la noche anterior, mientras que en la segunda visita, 77,7 por ciento de los niños<5 años y 66,3 por ciento de las embarazadas durmieron bajo un MTILD la noche anterior. El tamaño de los agujeros de la trama de los MTILD tuvo una baja aceptabilidad por parte del a población durante la segunda visita (39,0 por ciento). Conclusiones. Si bien la posesión de MTILD en los hogares se ha mantenido elevada, su uso por la población beneficiada ha disminuido durante el año de seguimiento.

Objectives. To assess long-lasting insecticide - treated bednet (LLITN) ownership, retention and usage one year after their distribution in Loreto, Peru. Materials and methods. From July to September 2007, 26,185 LLITNs Olyset Net ® were delivered in 194 targeted communities in the Peruvian Amazon region, covering 45,331 people. Two cross-sectional community-based surveys in December 2007 and July 2008 were undertaken in a sample of 60 targeted communities (30.9 percent out of the total). A semi-structured questionnaire was used to collect necessary data to calculate LLITN ownership, retention and usage indicators. Results. High LLITN household ownership was showed in both surveys (99.9 percent and 98.7 percent, respectively). LLITN/ person ratio decreased from 0.58 at the end of the LLITN delivery to 0.51 in the second survey, estimating LLITN retention of 87 percent after 1 year of intervention. In the first survey, 99.0 percent of all children <5 years and 96,0 percent of pregnant women slept under a LLITN the previous night, while in the second survey, 77.7 percent of children <5 years and 66.3 percent of pregnant women slept under a LLITN the previous night. Big mesh size of LLITN had low people´s acceptability, reaching only 39.0 percent in the second survey. Conclusions. Although universal LLITN household ownership remained high, their LLITN usage levels have decreased during one-year follow-up period.