Rapid Epidemic Expansion of Chikungunya Virus East/Central/South African Lineage, Paraguay.

The spread of Chikungunya virus is a major public health concern in the Americas. There were >120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiologic techniques, we characterized the ongoing large chikungunya epidemic in Paraguay.

Perinatal Outcome of Selective Intrauterine Growth Restriction in Monochorionic Twins: Evaluation of a Retrospective Cohort in a Developing Country.

Selective intrauterine growth restriction (sIUGR) in monochorionic twin pregnancies is associated with greater morbidity and mortality for both fetuses when compared to singleton and dichorionic pregnancies. This retrospective cohort study aimed to assess the perinatal outcomes of monochorionic twin pregnancies affected by this disorder and conducted expectantly, by analyzing the results according to the end-diastolic flow in the umbilical artery Doppler of the smaller twin (type I: persistently forward/type II: persistently absent or reversed/type III: intermittently absent or reversed). Seventy-five monochorionic diamniotic twin pregnancies with sIUGR were included in this study. sIUGR was defined by estimated fetal weight below the 3rd centile for gestational age, or below the 10th centile, when associated with at least one of the following three criteria: abdominal circumference below the 10th percentile, umbilical artery pulsatility index of the smaller twin above the 95th percentile, or estimated fetal weight discordance of 25% or more. Perinatal outcomes were analyzed from the prenatal period to hospital discharge and included perinatal death, neurological injury, retinopathy of prematurity (ROP), bronchopulmonary dysplasia (BPD), necrotizing enterocolitis (NEC), and sepsis. The mortality rate was 1.33% in this cohort. The overall morbidity rate was lower in type I twin pregnancies. In conclusion, this study shows that sIUGR type I has lower morbidity than types II and III in expectant management.

Proteomic features predict seroreactivity against leptospiral antigens in leptospirosis patients.

With increasing efficiency, accuracy, and speed we can access complete genome sequences from thousands of infectious microorganisms; however, the ability to predict antigenic targets of the immune system based on amino acid sequence alone is still needed. Here we use a Leptospira interrogans microarray expressing 91% (3359) of all leptospiral predicted ORFs (3667) and make an empirical accounting of all antibody reactive antigens recognized in sera from naturally infected humans; 191 antigens elicited an IgM or IgG response, representing 5% of the whole proteome. We classified the reactive antigens into 26 annotated COGs (clusters of orthologous groups), 26 JCVI Mainrole annotations, and 11 computationally predicted proteomic features. Altogether, 14 significantly enriched categories were identified, which are associated with immune recognition including mass spectrometry evidence of in vitro expression and in vivo mRNA up-regulation. Together, this group of 14 enriched categories accounts for just 25% of the leptospiral proteome but contains 50% of the immunoreactive antigens. These findings are consistent with our previous studies of other Gram-negative bacteria. This genome-wide approach provides an empirical basis to predict and classify antibody reactive antigens based on structural, physical-chemical, and functional proteomic features and a framework for understanding the breadth and specificity of the immune response to L. interrogans.

Identification of immunodominant antigens in canine leptospirosis by Multi-Antigen Print ImmunoAssay (MAPIA).

BACKGROUND: The microscopic agglutination test (MAT), the standard method for serological diagnosis of leptospirosis, may present limitations regarding its sensitivity. Current studies suggest that Leptospira immunoglobulin-like (Lig) proteins and LipL32 are of particular interest as serodiagnostic markers since they are present only in pathogenic species of the Leptospira genus. The purpose of this study was to identify leptospiral immunodominant proteins that are recognized by canine sera from diseased dogs. RESULTS: A total of 109 dogs were studied, including seroreactive dogs (MAT ≥800) and dogs with no seroreactivity detectable by MAT. Eight recombinant fragments (31-70 kDa) of pathogenic Leptospira were tested for their use as diagnostic markers for canine leptospirosis using the Multi-antigen Print Immunoassay (MAPIA) platform: LigB [582-947aa] from L. interrogans serovar Pomona, L. interrogans serovar Copenhageni and L. kirschneri serovar Gryppotyphosa, LigB [131-649aa] from L. interrogans serovar Copenhageni, L. interrogans serovar Canicola and L. kirschneri serovar Gryppotyphosa, LigA [625-1224aa] L. interrogans serovar Copenhageni and LipL32 from L. interrogans serovar Copenhageni. The data were analyzed and ROC curves were generated. Altogether, LigB [131-649aa] L. interrogans Canicola, LigB [131-649aa] L. kirschneri Gryppotyphosa and LipL32 L. interrogans Copenhageni showed best accuracy (AUC = 0.826 to 0.869), with 70% specificity and sensitivity ranging from 89% to 95%. CONCLUSIONS: These results reinforce their potential as diagnostic candidates for the development of new methods for the serological diagnosis of canine leptospirosis.

Gastric outlet obstruction in an 11-year-old girl: A case report.

Pyloric stenosis commonly affects infants and rarely causes gastric outlet obstruction in adolescents and older children. We present the case of an 11-year-old girl with a 2-month history of recurrent postprandial vomiting and weight loss. On physical examination, the patient presented with abdominal distension. Upper gastrointestinal endoscopy revealed a very small pyloric orifice through which the endoscope could not be advanced. Abdominal ultrasonography and a computed tomography confirmed pylorus thickening. She underwent Heineke-Mikulicz pyloroplasty with symptom resolution.

Exploring the Genomic Dynamics of the Monkeypox Epidemic in Paraguay.

In recent months, Paraguay has been grappled with a notable monkeypox outbreak, straining its healthcare infrastructure. The sudden spike in cases underlines the imperative need for a comprehensive understanding of the virus's dynamics, enabling the formulation of robust containment measures. To address this challenge, our team joined forces with the Central Public Health Laboratory of Asunción and the Pan-American Health Organization. Through this collaboration, we employed portable whole-genome sequencing combined with phylodynamic analysis to examine the MPXV strains circulating in Paraguay. Our genomic monitoring approach has produced the first 30 whole-genome sequences from Paraguay, all of which were identified under lineage IIb. Interestingly, our data suggest that the origin of the monkeypox virus in Paraguay at the beginning of 2022 can be traced back to Brazil. This introduction subsequently catalyzed further community spread that was further exacerbated by several independent introduction events as time progressed. These findings not only shed light on the transmission patterns of the virus but also highlight the pivotal role such insights play in sculpting effective response strategies and driving impactful public health measures. Furthermore, our findings strongly advocate intensified surveillance at international borders, ensuring swift detection and proactive countermeasures against potential outbreaks in the future.

Phylogeny-based classification of human rhinoviruses detected in hospitalized children with acute lower respiratory infection in Paraguay, 2010-2011.

Human rhinovirus (HRV), a single-stranded, positive-sense RNA virus, is associated with mild upper respiratory tract infections in children. The aim of this study was to carry out a molecular characterization and phylogeny-based classification of the circulating genotypes of HRV in hospitalized children with clinical manifestations of acute lower respiratory infection in Paraguay. Nasopharyngeal aspirates were collected from 101 children under 5 years of age, hospitalized with symptoms of acute lower respiratory infection, between May 2010 and December 2011, at the largest public pediatric hospital in the Central Department of Paraguay. Detection was performed by a real-time polymerase chain reaction, followed by conventional amplification of the VP4/VP2 genomic region, sequencing, and phylogenetic analysis. Rhinovirus was detected in 33.7% of the samples. Amplification of 18 samples showed the presence of all three species (HRV-A, -B, and -C). Different genotypes were found for each species: 11 for HRV-A (-9, -12, -22, -30, -36, -43, -59, -61, -68, -88, and -89), one for HRV-B (-4), and four for HRV-C (-C2, -C3, -C6, and -C9). In South America, information about HRV diversity is scarce. This is the first report on HRV genotype diversity in South America.

Retrospective Spatio-Temporal Dynamics of Dengue Virus 1, 2 and 4 in Paraguay.

Dengue virus (DENV) has been a major public health concern in Paraguay, with frequent outbreaks occurring since early 1988. Although control measures have been implemented, dengue remains a significant health threat in the country, and continued efforts are required for prevention and control. In response to that, in collaboration with the Central Public Health Laboratory in Asunción, we conducted a portable whole-genome sequencing and phylodynamic analysis to investigate DENV viral strains circulating in Paraguay over the past epidemics. Our genomic surveillance activities revealed the co-circulation of multiple DENV serotypes: DENV-1 genotype V, the emerging DENV-2 genotype III, BR4-L2 clade, and DENV-4 genotype II. Results additionally highlight the possible role of Brazil as a source for the international dispersion of different viral strains to other countries in the Americas emphasizing the need for increased surveillance across the borders, for the early detection and response to outbreaks. This, in turn, emphasizes the critical role of genomic surveillance in monitoring and understanding arbovirus transmission and persistence locally and over long distances.

Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay.

The spread of vector-borne viruses, such as CHIKV, is a significant public health concern in the Americas, with over 120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiological techniques, we characterized the ongoing large CHIKV epidemic in Paraguay. Article Summary Line: Genomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay.

Routine spirometry in cystic fibrosis patients: impact on pulmonary exacerbation diagnosis and FEV1 decline.

OBJECTIVE: Pulmonary disease in cystic fibrosis (CF) is characterised by recurrent episodes of pulmonary exacerbations (PExs), with acute and long-term declines in lung function (FEV1). The study sought to determine whether routine spirometry increases the frequency of PEx diagnosis, resulting in benefits to long-term pulmonary function. METHODS: CF patients in the 5- to 18-year age bracket were followed for 1 year, during which they underwent spirometry before every medical visit. The main variables were the frequency of PEx diagnosis and use of antibiotics; the use of spirometry as a criterion for PEx diagnosis (a decline ≥ 10% in baseline FEV1); and median percent predicted FEV1 over time. The data were compared with those for the previous 24-month period, when spirometry was performed electively every 6 months. RESULTS: The study included 80 CF patients. PExs were diagnosed in 27.5% of the visits, with a mean frequency of 1.44 PExs per patient/year in 2014 vs. 0.88 PExs per patient/year in 2012 (p = 0.0001) and 1.15 PExs per patient/year in 2013 (p = 0.05). FEV1 was used as a diagnostic feature in 83.5% of PExs. In 21.9% of PExs, the decision to initiate antibiotics was solely based on an acute decline in FEV1. The median percent predicted FEV1 during the follow-up year was 85.7%, being 78.5% in 2013 and 76.8% in 2012 (p > 0.05). The median percent predicted FEV1 remained above 80% during the two years after the study. CONCLUSIONS: Routine spirometry is associated with higher rates of diagnosis and treatment of PExs, possibly impacting long-term pulmonary function.

Minimally invasive treatment of pilonidal sinus disease in a paediatric population: comparison of two techniques.

BACKGROUND: Pilonidal disease (PD) is a common and debilitating inflammatory condition with significant impact on quality of life. Minimally invasive techniques (MIT) have shown promising results comparing to traditional excision. Herein we present a comparison of two MIT techniques -sinusectomy (SE) and pit-picking plus laser ablation (PPL). METHODS: All cases of paediatric PD treated by PPL and SE at our center between August 2018 and August 2020 were retrospectively reviewed. RESULTS: One-hundred and six patients were included, with a median age of 16 years (IQR 15-16). PPL was the procedure of choice in 36 patients (34%) and the remaining underwent SE (66%). Median healing time was significantly lower in SE group (20 days), comparing to PPL (30 days) (p = 0.002). Early healing failure occurred more frequently in the PPL group (p = 0.003). Recurrence rate was similar between groups - PPL 17% versus SE 16% (p = 0.89). Overall complication rate was 9% and was significantly higher in PPL (p = 0.03). CONCLUSIONS: MIT techniques are promising solutions in PD treatment. Although similarly easy and fast to perform, SE technique showed better healing profile and lower complication rate but no significant difference on recurrence rates was observed.

Thoracic Outlet Syndrome after Minimally Invasive Repair of Pectus Excavatum in a 15-Year-Old Boy: A Case Report.

Nuss procedure has become the treatment of choice in pectus excavatum mainly because of the excellent functional and cosmetic results. Despite the good results, several complications have been reported. The aim of this study is to describe a case of thoracic outlet syndrome (TOS) after Nuss procedure and review the management of such rare complication. A 15-year-old boy otherwise healthy was submitted to Nuss procedure, with no perioperative complications. Two-weeks later, the patient complained of right-hand paresthesia, progressive weakness of the right arm and coldness. After imaging and electromyography, TOS diagnosis was established. Removal of the bar was proposed but refused by the patient. Conservative management with rehabilitation exercising and nerve nourishing was initiated. At 7 months, the patient recovered arm and hand function. Abrupt structural changes of thoracic cavity with marked elevation of the upper chest induce nerve and vascular compression arousing a TOS and should be acknowledged as one potential complication of Nuss procedure. Conservative management can be an alternative treatment to bar removal, showing good results on functional recovery in early stages of compression.

15-Year varicocelectomy outcomes in pediatric age: Beware of genitofemoral nerve injury.

BACKGROUND: Varicocele affects 15% of adolescents. The main postoperative complications are recurrence and hydrocele; nerve injury is rarely reported. OBJECTIVE: The aims of this study are: to assess the complications after laparoscopic varicocelectomy, namely nerve injury; and to assess if nerve injury is more frequent using "hot" or "cold" ligation. STUDY DESIGN: Retrospective study of varicocele cases submitted to laparoscopic correction in our department from April 2006 to March 2020. Parameters analyzed were: age, clinical findings, surgical indication, operative technique, and outcomes. Comparison was done between the "cold" versus "hot" vessel section technique. RESULTS: 110 patients, with median age 14-years-old, were included. Most cases were on the left side and grade 3. Fifty patients (45%) presented complications: 21% recurrence; 18% hydrocele; and 3% genitofemoral nerve injury. Nerve injury was independent of the technique used. DISCUSSION: Genitofemoral nerve injury is a complication with unknown cause and all cases are related to laparoscopic technique. It was suggested that "hot" methods of ligation of the vessels can lead to higher incidence of the lesion, but that was not corroborated in our analysis. Possible explanations for its occurrence are: a wide peritoneal window opening created with electrocautery near the internal inguinal ring; and additional dissection required to isolate the testicular veins from the artery. Prospective studies are needed to clarify the real incidence of genitofemoral nerve injury and its causes. CONCLUSIONS: Laparoscopic varicocelectomy seems to be safe and effective, although complications remain frequent regardless of the technique used. Genitofemoral nerve injury is a complication rarely described that may require rehabilitation, and so awareness for this problem is of paramount importance.

Testing the genomic stability of the Brazilian yellow fever vaccine strain using next-generation sequencing data.

The live attenuated yellow fever (YF) vaccine was developed in the 1930s. Currently, the 17D and 17DD attenuated substrains are used for vaccine production. The 17D strain is used for vaccine production by several countries, while the 17DD strain is used exclusively in Brazil. The cell passages carried out through the seed-lot system of vaccine production influence the presence of quasispecies causing changes in the stability and immunogenicity of attenuated genotypes by increasing attenuation or virulence. Using next-generation sequencing, we carried out genomic characterization and genetic diversity analysis between vaccine lots of the Brazilian YF vaccine, produced by BioManguinhos-Fiocruz, and used during 11 years of vaccination in Brazil. We present 20 assembled and annotated genomes from the Brazilian 17DD vaccine strain, eight single nucleotide polymorphisms and the quasispecies spectrum reconstruction for the 17DD vaccine, through a pipeline here introduced. The V2IDA pipeline provided a relationship between low genetic diversity, maintained through the seed lot system, and the confirmation of genetic stability of lots of the Brazilian vaccine against YF. Our study sets precedents for use of V2IDA in genetic diversity analysis and in silico stability investigation of attenuated viral vaccines, facilitating genetic surveillance during the vaccine production process.

Sanger-based sequencing technology for yellow fever vaccine genetic quality control.

Yellow Fever (YF) is an acute viral hemorrhagic disease prevalent mainly in Africa and Americas, with 20-60% fatality rate in severe forms. Currently, antiviral drugs for the infection are not available, reinforcing the importance of vaccination in resident populations and travelers. Manufactured in 7 different countries, the YF vaccine was first created in 1937 and two substrains are used for production, 17DD and 17D-204. The vaccine produced in Bio-Manguinhos/Brazil uses 17DD substrain and more than 160 million doses have been exported to over 74 countries. The World Health Organization (WHO) recommends that new seed- and working-lots should have the viral genome sequenced in order to check vaccine genetic stability. The aim of this study was to develop and standardize a Sanger-based sequencing protocol for the genetic monitoring of the Brazilian 17DD vaccine. We designed 54 oligos to access the complete YF vaccine genome by RT-PCR and sequencing approach. After protocol standardization, we tested 45 vaccine lots and the corresponding secondary and working seed lots. All 45 lots presented 100% nucleotide identity to each other and to the seed lots. We also detected 2 heterogeneous positions at nucleotides 4523 (C/T) and 6673 (C/T) that may indicate a quasispecies diversity of YF 17DD strain. When compared to the Brazilian GenBank sequence YFU17066, the Brazilian 17DD vaccine presented 6 silent mutations. By applying the sequencing methodology to two YF 17D-204 strains, we showed that our method can also be used to sequence different YF vaccine virus. In summary, we have developed a robust method for the genetic monitoring of YF vaccines, which has been successfully applied in Bio-Manguinhos since 2009 and could also be used by other manufacturers for YF17D-based vaccines. There were no genetic variation in the Brazilian tested lots, highlighting the safety, production consistency and, more importantly, the genetic stability of Bio-Manguinhos' YF vaccine in the last 3 decades.

Routine spirometry in cystic fibrosis patients: impact on pulmonary exacerbation diagnosis and FEV1 decline / Espirometria de rotina em pacientes com fibrose cística: impacto no diagnóstico de exacerbação pulmonar e no declínio do VEF1

ABSTRACT Objective: Pulmonary disease in cystic fibrosis (CF) is characterised by recurrent episodes of pulmonary exacerbations (PExs), with acute and long-term declines in lung function (FEV1). The study sought to determine whether routine spirometry increases the frequency of PEx diagnosis, resulting in benefits to long-term pulmonary function. Methods: CF patients in the 5- to 18-year age bracket were followed for 1 year, during which they underwent spirometry before every medical visit. The main variables were the frequency of PEx diagnosis and use of antibiotics; the use of spirometry as a criterion for PEx diagnosis (a decline ≥ 10% in baseline FEV1); and median percent predicted FEV1 over time. The data were compared with those for the previous 24-month period, when spirometry was performed electively every 6 months. Results: The study included 80 CF patients. PExs were diagnosed in 27.5% of the visits, with a mean frequency of 1.44 PExs per patient/year in 2014 vs. 0.88 PExs per patient/year in 2012 (p = 0.0001) and 1.15 PExs per patient/year in 2013 (p = 0.05). FEV1 was used as a diagnostic feature in 83.5% of PExs. In 21.9% of PExs, the decision to initiate antibiotics was solely based on an acute decline in FEV1. The median percent predicted FEV1 during the follow-up year was 85.7%, being 78.5% in 2013 and 76.8% in 2012 (p > 0.05). The median percent predicted FEV1 remained above 80% during the two years after the study. Conclusions: Routine spirometry is associated with higher rates of diagnosis and treatment of PExs, possibly impacting long-term pulmonary function.

RESUMO Objetivo: A doença pulmonar na fibrose cística (FC) é caracterizada por episódios recorrentes de exacerbações pulmonares (EP), com declínio agudo e em longo prazo da função pulmonar (VEF1). O objetivo deste estudo foi determinar se a espirometria de rotina aumenta a frequência de diagnóstico de EP, beneficiando a função pulmonar em longo prazo. Métodos: Pacientes com FC na faixa etária de 5 a 18 anos foram acompanhados durante 1 ano, ao longo do qual foram submetidos a espirometria antes de cada consulta médica. As principais variáveis foram a frequência de diagnóstico de EP e uso de antibióticos; o uso da espirometria como critério de diagnóstico de EP (declínio do VEF1 basal ≥ 10%); e a mediana do VEF1 em porcentagem do previsto ao longo do tempo. Os dados foram comparados àqueles referentes aos 24 meses anteriores, período durante o qual a espirometria era realizada eletivamente a cada 6 meses. Resultados: O estudo incluiu 80 pacientes com FC. EP foram diagnosticadas em 27,5% das consultas, com média de frequência de 1,44 EP por paciente/ano em 2014 vs. 0,88 EP por paciente/ano em 2012 (p = 0,0001) e 1,15 EP por paciente/ano em 2013 (p = 0,05). O VEF1 foi usado como recurso diagnóstico em 83,5% das EP. Em 21,9% das EP, a decisão de iniciar a antibioticoterapia baseou-se exclusivamente no declínio agudo do VEF1. A mediana do VEF1 em porcentagem do previsto foi de 85,7% durante o ano de acompanhamento, de 78,5% em 2013 e de 76,8% em 2012 (p > 0,05). A mediana do VEF1 em porcentagem do previsto permaneceu acima de 80% durante os dois anos após o estudo. Conclusões: A espirometria de rotina está associada a taxas mais elevadas de diagnóstico e tratamento de EP e possivelmente tem impacto na função pulmonar em longo prazo.

Seroepidemiology of leptospirosis among febrile patients in a rapidly growing suburban slum and a flood-vulnerable rural district in Mozambique, 2012-2014: Implications for the management of fever.

OBJECTIVE: Leptospirosis is one of the most widespread zoonoses in the world and is caused by spirochetes of the genus Leptospira. In Mozambique, the disease is largely ignored and its epidemiology is unknown. The objective of this study was to investigate the occurrence of leptospirosis in febrile patients. METHODS: This cross-sectional study was performed between July 2012 and September 2015 among febrile patients. A total of 373 paired serum samples were drawn from febrile patients; 208 were from Caia District Hospital (rural setting) in Sofala Province and 165 were from Polana Caniço General Hospital (suburban setting) in Maputo City. Samples were initially screened using an in-house ELISA for IgM and IgG antibodies. Double positive samples were confirmed using a microagglutination test (MAT). RESULTS: Of the 373 febrile patients, five (1.3%) had acute leptospirosis (MAT ≥400) and 38 (10.2%) had a presumptive infection (IgM-positive/MAT <400). While most of the patients with a presumptive infection lived in the rural setting (84.2%, 32/38), the majority of patients with acute infections (60%, 3/5) and with negative results (60.3%, 199/330) lived in the suburban setting (p=0.000). Contact with rodents was significantly higher in patient with acute leptospirosis (100%, 5/5) than in those with a presumptive infection (39.5%, 15/38) or negative results (41.8%, 138/330) (p=0.031). Four out of the five patients (80%) with acute leptospirosis were treated with antimalarial drugs although malaria results were negative. The prevailing serogroup, according to MAT results, was Australis (40%; 4/10), followed by Icterohaemorrhagiae (30%, 3/10). CONCLUSIONS: This study found that leptospirosis is prevalent among Mozambicans, and most cases are misdiagnosed as malaria.

Distinct antibody responses of patients with mild and severe leptospirosis determined by whole proteome microarray analysis.

BACKGROUND: Leptospirosis is an important zoonotic disease worldwide. Humans usually present a mild non-specific febrile illness, but a proportion of them develop more severe outcomes, such as multi-organ failure, lung hemorrhage and death. Such complications are thought to depend on several factors, including the host immunity. Protective immunity is associated with humoral immune response, but little is known about the immune response mounted during naturally-acquired Leptospira infection. METHODS AND PRINCIPAL FINDINGS: Here, we used protein microarray chip to profile the antibody responses of patients with severe and mild leptospirosis against the complete Leptospira interrogans serovar Copenhageni predicted ORFeome. We discovered a limited number of immunodominant antigens, with 36 antigens specific to patients, of which 11 were potential serodiagnostic antigens, identified at acute phase, and 33 were potential subunit vaccine targets, detected after recovery. Moreover, we found distinct antibody profiles in patients with different clinical outcomes: in the severe group, overall IgM responses do not change and IgG responses increase over time, while both IgM and IgG responses remain stable in the mild patient group. Analyses of individual patients' responses showed that >74% of patients in the severe group had significant IgG increases over time compared to 29% of patients in the mild group. Additionally, 90% of IgM responses did not change over time in the mild group, compared to ~51% in the severe group. CONCLUSIONS: In the present study, we detected antibody profiles associated with disease severity and speculate that patients with mild disease were protected from severe outcomes due to pre-existing antibodies, while patients with severe leptospirosis demonstrated an antibody profile typical of first exposure. Our findings represent a significant advance in the understanding of the humoral immune response to Leptospira infection, and we have identified new targets for the development of subunit vaccines and diagnostic tests.

Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.