Emerging Microbes & Infections

The emergence of multidrug-resistant (MDR) and extremely drug-resistant (XDR) Klebsiella pneumoniae presents a significant challenge to public health, particularly in hospital settings where it is a leading cause of nosocomial infections. Addressing the urgent need for alternative treatments to combat antibiotic-resistant bacteria, this study describes the isolation, characterization, and genomic analysis of a novel bacteriophage, designated as MFS, targeting MDR/XDR K. pneumoniae strains isolated from hospital sewage in Dhaka, Bangladesh. The phage was isolated utilizing a double-agar overlay and characterized using Oxford Nanopore Technologies sequencing. Phage MFS was identified as a member of the Siphoviridae family, under the unclassified Webervirus subfamily, with potent lytic activity against clinical MDR/XDR K. pneumoniae strains. Genomic analysis revealed a 48,780 bp genome with 94 protein-coding sequences, including essential genes for phage replication, structure, and host lysis, but notably lacking genes associated with antimicrobial resistance, virulence, and lysogeny. The presence of specific genes for endolysin and holin underscores the phages lytic capability. Additionally, the study elucidates the phages structural proteins and mechanisms underlying bacterial cell wall degradation, contributing valuable insights into phage-host interactions and applications of phage therapy. Our findings underscore the therapeutic potential of sewage-derived bacteriophages against MDR/XDR clinical K. pneumoniae and emphasize the need for further exploration of bacterio-phage therapy as a viable alternative to traditional antibiotics in combating antibiotic-resistant bacterial infections.

During the first nine months of the SARS-CoV-2 pandemic, Uruguay successfully kept it under control, even when our previous studies support a recurrent viral flux across the Uruguayan-Brazilian border that sourced several local outbreaks in Uruguay. However, towards the end of 2020, a remarkable exponential growth was observed and the TETRIS strategy was lost. Here, we aimed to understand the factors that fueled SARS-CoV-2 viral dynamics during the first epidemic wave in the country. We recovered 84 whole viral genomes from patients diagnosed between November, 2020 and February, 2021 in Rocha, a sentinel eastern Uruguayan department bordering Brazil. The lineage B.1.1.28 was the most prevalent in Rocha during November-December 2020, P.2 became the dominant one during January-February 2021, while the first P.1 sequences corresponds to February, 2021. The lineage replacement process agrees with that observed in several Brazilian states, including Rio Grande do Sul (RS). We observed a one to three month delay between the appearance of P.2 and P.1 in RS and their subsequent detection in Rocha. The phylogenetic analysis detected two B.1.1.28 and one P.2 main Uruguayan SARS-CoV-2 clades, introduced from the southern and southeastern Brazilian regions into Rocha between early November and mid December, 2020. One synonymous mutation distinguishes the sequences of the main B.1.1.28 clade in Rocha from those widely distributed in RS. The minor B.1.1.28 cluster, distinguished by several mutations, harbours non-synonymous changes in the Spike protein: Q675H and Q677H, so far not concurrently reported. The convergent appearance of S:Q677H in different viral lineages and its proximity to the S1/S2 cleavage site raise concerns about its functional relevance. The observed S:E484K-VOI P.2 partial replacement of previously circulating lineages in Rocha might have increased transmissibility as suggested by the significant decrease in Ct values. Our study emphasizes the impact of Brazilian SARS-CoV-2 epidemics in Uruguay and the need of reinforcing real-time genomic surveillance on specific Uruguayan border locations, as one of the key elements for achieving long-term COVID-19 epidemic control.

SummaryThe Oropouche virus, initially detected in Trinidad and Tobago in 1955, has been historically confined to the Amazon Basin. However, since late 2022, it has been reported elsewhere, from northern Brazil to urban centers in Bolivia, Colombia, Cuba, and Peru. In this report we describe the doubling of publicly available full genomes by generating 133 new entries. We show how the virus evolved via recombination and how it rapidly spread across multiple states in Brazil, causing the largest outbreak ever recorded outside the Amazon basin including the first ever detected deaths. This work highlights the need for heightened epidemiological and genomic surveillance and the implementation of adequate responses in order to avoid Oropouche becoming another widespread arboviral public health threat. BackgroundThe Oropouche virus was first identified in 1955 in Trinidad and Tobago and later found in Brazil in 1960. Historically, it has been reported to have caused around 30 outbreaks, most of which within the Amazon Basin where it circulates among forest animals, but also in urban areas where it is known to be transmitted by the midge Culicoides paraensis. Recently, Brazil has seen a surge in cases, with 6000 reported by mid-2024 alone. MethodsIn a collaboration with Central Public Health Laboratories across Brazilian regions, we integrated epidemiological metadata with genomic analyses of recently sampled cases. This initiative resulted in the generation of 133 whole genome sequences from the three genomic segments (L, M, and S) of the virus, including the first genomes obtained from regions outside the Amazon and from the first ever recorded fatal cases. FindingsAll of the 2024 genomes form a monophyletic clade in the phylogenetic tree with sequences from the Amazon Basin sampled since 2022. Our analyses reveal a fast and clear pattern of north-to-south viral movement from the Amazon Basin into historically non-endemic regions. We identified 21 recombinant events, but it remains unclear if such genomic changes mirror potential adaptations and the emergence of new viral phenotypes of public health importance. InterpretationBoth the recent rapid spatial expansion and the first reported fatalities associated with Oropouche underscore the importance of enhancing surveillance at both national and continental levels. Without any obvious changes in the human population over the past 2 years, it remains likely that either alone or in combination, viral adaptation, deforestation and climate change trends in the recent past may have propelled the Oropouche virus beyond the Amazon Basin. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSBefore this study, the Oropouche virus was known to cause periodic outbreaks primarily within the Amazon Basin. Initially identified in Trinidad and Tobago in 1955, the virus had been responsible for approximately 30 outbreaks in Latin America, mostly confined to the Amazon region. The virus typically circulates among forest animals and is transmitted to humans by the bite of the midge Culicoides paraensis. There has been an historical dearth of available genomic data, and so far the spread beyond the Amazon Basin has not been well-documented. Added value of this studyThis study provides a timely and comprehensive analysis of epidemiological and genomic data of the Oropouche virus from regions outside the Amazon Basin. By generating 133 whole genome sequences from various regions across Brazil, the study doubles the number of publicly available genomes. Our findings reveal the virus movement over the past few years across Brazil, highlighting a north-south spatial trend from regions of historic endemicity to regions with clear epidemic potential. We identify 21 recombinant events, of which the potential for adaptation and the emergence of novel viral phenotypes remains possible but unclear. This study also reports the first fatal cases of Oropouche virus infection in patients without underlying relevant comorbidities, underscoring the public health risk of future outbreaks and the need for increased awareness and surveillance. Implications of all the available evidenceThe rapid spread of the Oropouche virus beyond the Amazon Basin into regions of Brazil further away than 3500 Km, coupled with the identification of genome recombinant events, raises the possibility that the virus is adapting to the new environments of its increasing spatial landscape. This evolution could lead to the emergence of new viral phenotypes, with potential changes at various levels, from vector efficiency, to disease outcome, raising the challenge of managing future outbreaks. The evidence underscores the critical need for enhanced surveillance systems at national and continental levels, in particular in urban centers which appear to have been particularly hit during the spatial expansion, to detect and respond to Oropouche virus outbreaks promptly.

In order to curb the rapid transmission of SARS-CoV-2, nation-wide lockdowns were implemented as a preliminary measure. Since most countries enforced travel-bans during end of March 2020, the country-specific patterns should be discernible in the subsequent months. We identified frequently mutated non-synonymous mutations in 2,15,000 SARS-CoV-2 sequences during pre and post-travel-ban periods in 35 countries. We further investigated the mutational profile on a bi-monthly basis and traced the progress over the time. Several new mutations have emerged post-travel-ban and on the rise in specific countries, chief among them being A222V and S477N in Spike, and A220V in Nucleocapsid protein. Consequently, we examined the Spike protein epitopes to inspect whether any of these country-specific mutations overlapped with these epitopes. Several mutations were found to be contained within one or more epitopes, including the highly mutated residues of Spike protein, advocating the requirement of active monitoring of vaccine efficacies in respective countries.

Ebola virus is a highly pathogenic RNA virus that causes haemorrhagic fever in human. With very high mortality rate, Ebola virus is considered as one of the dangerous viruses in the world. Although, the Ebola outbreaks claimed many lives in the past, no satisfactory treatment or vaccine have been discovered yet to fight against Ebola. For this reason, in this study, various tools of bioinformatics and immunoinformatics were used to design possible vaccines against Zaire Ebola virus strain Mayinga-76. To construct the vaccine, three potential antigenic proteins of the virus, matrix protein VP40, envelope glycoprotein and nucleoprotein were selected against which the vaccines would be designed. The MHC class-I, MHC class-II and B-cell epitopes were determined and after robust analysis through various tools and molecular docking analysis, three vaccine candidates, designated as EV-1, EV-2 and EV-3, were constructed. Since the highly conserved epitopes were used for vaccine construction, these vaccine constructs are also expected to be effective on other strains of Ebola virus like strain Gabon-94 and Kikwit-95. Next, the molecular docking study on these vaccine constructs were analyzed by molecular docking study and EV-1 emerged as the best vaccine construct. Later, molecular dynamics simulation study revealed the good performances as well as good stability of the vaccine protein. Finally, codon adaptation and in silico cloning were conducted to design a possible plasmid (pET-19b plasmid vector was used) for large scale, industrial production of the EV-1 vaccine.

The emergence of SARS-CoV-2 in the human population has caused a huge pandemic that is still unfolding in many countries around the world. Multiple epicenters of the pandemic have emerged since the first pneumonia cases in Wuhan, first in Italy followed by the USA and Brazil. Up to now, Brazil is the second most affected country, however, genomic sequences of SARS-CoV-2 strains circulating in the country are restricted to some highly impacted states. Although the Pernambuco state, located in the Northeast Region, is the sixth most affected brazilian state and the second considering lethality rate, there is a lack of high quality genomic sequences from the strains circulating in this region. Here, we sequenced 38 strains of SARS-CoV-2 from patients presenting Covid-19 symptoms. Phylogenetic reconstructions revealed that three lineages were circulating in the state and 36 samples belong to B1.1 lineage. We detected two introductions from European countries and five clades, corroborating the community spread of the virus between different municipalities of the state. Finally, we detected that all except one strain showed the D614G spike protein amino acid change that may impact virus infectivity in human cells. Our study brought new light to the spread of SARS-CoV-2 strains in one of the most heavily impacted states of Brazil.

The recent emergence of a previously unknown coronavirus (SARS-CoV-2), first confirmed in the city of Wuhan in China in December 2019, has caused serious public health and economic issues due to its rapid dissemination worldwide. Although 61,888 confirmed cases had been reported in Brazil by 28 April 2020, little was known about the SARS-CoV-2 epidemic in the country. To better understand the recent epidemic in the second most populous state in southeast Brazil (Minas Gerais, MG), we looked at existing epidemiological data from 3 states and sequenced 40 complete genomes from MG cases using Nanopore. We found evidence of multiple independent introductions from outside MG, both from genome analyses and the overly dispersed distribution of reported cases and deaths. Epidemiological estimates of the reproductive number using different data sources and theoretical assumptions all suggest a reduction in transmission potential since the first reported case, but potential for sustained transmission in the near future. The estimated date of introduction in Brazil was consistent with epidemiological data from the first case of a returning-traveler from Lombardy, Italy. These findings highlight the unique reality of MGs epidemic and reinforce the need for real-time and continued genomic surveillance strategies as a way of understanding and therefore preparing against the epidemic spread of emerging viral pathogens.

The Coronavirus 2019 (COVID-19) pandemic has caused worldwide concern and has become a major medical problem. Vaccines and therapeutics are important interventions for the management of this outbreak. This study aims to used bibliometric methods to identify research trends in the domain of therapeutics and vaccines to cure patients with COVID-19 since the beginning of the pandemic. The Web of Science Core Collection database was retrieved for articles on therapeutic approaches to coronavirus disease management published between January 1, 2020 and May 20, 2020. Identified and analyzed the data included title, corresponding author, language, publication time, publication type, research focus. A total of 1569 articles on coronavirus therapeutic means from 84 countries were published in 620 journals. We note the remarkable progressive increase in the number of publications related to research on therapies and vaccines for COVID-19. The United States provided the largest number of articles (405), followed by China (364). Journal of Medical Virology published most of them (n = 40). 1005 (64.05%) were articles, 286 (18.23%) were letters, 230 (14.66%) were reviews. The terms "COVID- 19" or "SARS-CoV-2" or "Coronavirus" or "hydroxychloroquine" or "chloroquine" or "2019-nCOV" or "ACE2" or "treatment" or "remdesivir" or "pneumonia" were most frequently used, as shown in the density visualization map. A network analysis based on keyword co-occurrence revealed five distinct types of studies: clinical, biological, epidemiological, pandemic management, and therapeutics (vaccines and treatments). COVID-19 is a major disease that has had an impact on international public health at the global level. Several avenues for treatment and vaccines have been explored. Most of them focus on older drugs used to treat other diseases that have been effective for other types of coronaviruses. There is a discrepancy in the results obtained from the studies of the drugs included in this study. Randomized clinical trials are needed to evaluate older drugs and develop new treatment options.

The spread of the corona virus around the world has spurred travel restrictions and community lockdowns to manage the transmission of infection. In the Philippines, with a large population of overseas Filipino contract workers (OFWs), as well as foreign workers in the local online gaming industry and visitors from nearby countries, the first reported cases were from a Chinese couple visiting the country in mid-January 2020. Three months on, by mid-March, the COVID-19 cases in the Philippines had reached its first 100, before it exploded to the present 178,022 cases (as of August 20, 2020). Here, we report a genomic survey of six (6) whole genomes of the SARS-CoV-2 virus collected from COVID-19 patients seen at the Philippine General Hospital, the major referral hospital for COVID-19 cases in Metro Manila at about the time the Philippines had over a hundred cases. Analysis of commonly observed variants did not reveal a clear pattern of the virus evolving towards a more infectious and severe strain. When combined with other available viral sequences from the Philippines and from GISAID, phylogenomic analysis reveal that the sequenced Philippine isolates can be classified into three primary groups based on collection dates and possible infection sources: (1) January samples collected in the early phases of the pandemic that are closely associated with isolates from Wuhan, China; (2) March samples that are mainly linked to the M/V Diamond Princess Cruise Ship outbreak; and (3) June samples that clustered with European isolates, one of which already harbor the globally prevalent D614G mutation which initially circulated in Europe. The presence of community-acquired viral transmission amidst compulsory and strict quarantine protocols, particularly for repatriated Filipino workers, highlights the need for a refinement of the quarantine, testing, and tracing strategies currently being implemented to adapt to the current pandemic situation.

BackgroundOropouche virus (OROV; species Orthobunyavirus oropoucheense) is an arthropod-borne virus that has caused outbreaks of Oropouche fever in Central and South America since the 1950s. This study investigates virological factors contributing to the reemergence of Oropouche fever in Brazil between 2023 and 2024. MethodsIn this study, we combined OROV genomic, molecular, and serological data from Brazil from 1 January 2015 to 29 June 2024, along with in vitro and in vivo characterization. Molecular screening data included 93 patients with febrile illness between January 2023 and February 2024 from the Amazonas State. Genomic data comprised two genomic OROV sequences from patients. Serological data were obtained from neutralizing antibody tests comparing the prototype OROV strain BeAn 19991 and the 2024 epidemic strain. Epidemiological data included aggregated cases reported to the Brazilian Ministry of Health from 1 January 2014 to 29 June 2024. FindingsIn 2024, autochthonous OROV infections were detected in previously non-endemic areas across all five Brazilian regions. Cases were reported in 19 of 27 federal units, with 83.2% (6,895 of 8,284) of infections in Northern Brazil and a nearly 200-fold increase in incidence compared to reported cases over the last decade. We detected OROV RNA in 10.8% (10 of 93) of patients with febrile illness between December 2023 and May 2024 in Amazonas. We demonstrate that the 2023-2024 epidemic was caused by a novel OROV reassortant that replicated approximately 100-fold higher titers in mammalian cells compared to the prototype strain. The 2023-2024 OROV reassortant displayed plaques earlier than the prototype, produced 1.7 times more plaques, and plaque sizes were 2.5 larger compared to the prototype. Furthermore, serum collected in 2016 from previously OROV-infected individuals showed at least a 32-fold reduction in neutralizing capacity against the reassortment strain compared to the prototype. InterpretationThese findings provide a comprehensive assessment of Oropouche fever in Brazil and contribute to a better understanding of the 2023-2024 OROV reemergence. The recent increased incidence may be related to a higher replication efficiency of a new reassortant virus that also evades previous immunity.

In early 2024, explosive outbreaks of Oropouche virus (OROV) linked to a novel viral lineage were documented in the Brazilian Amazon. Here, we report the introduction of this emerging orthobunyavirus into Colombia and its co-circulation with another OROV lineage. This investigation highlights the complex arbovirus dynamics in South America.

We assessed the pharmacokinetics of favipiravir (FPV) in adults with symptomatic SARS-CoV-2 infection without pneumonia in Thailand. FPV dosing was 1800 mg twice-daily on day 1, then 800 mg twice-daily for 14 days. Eight subjects (7 female), median (range) age 39 (19-53) years and BMI 27.9 (18.0-33.6) were included. Inter-subject variability was high but all achieved minimum plasma concentrations (Cmin) above EC50 (9.7 mg/L). FPV was well tolerated; 1 subject stopped prematurely due to rash.

There is an urgent need to ameliorate the transport of the reconstituted vaccines to the vaccination sites to improve the COVID-19 vaccination campaigns. The maintenance of the integrity of the mRNA of the different COVID-19 reconstituted vaccines after continuous movement at room temperature during at least three hours ensures the safety of a ground transportation.

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 LineGenomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay

The Amazonas was one of the most heavily affected Brazilian states by the COVID-19 epidemic. Despite a large number of infected people, particularly during the second wave associated with the spread of the Variant of Concern (VOC) Gamma (lineage P.1), SARS-CoV-2 continues to circulate in the Amazonas. To understand how SARS-CoV-2 persisted in a human population with a high immunity barrier, we generated 1,188 SARS-CoV-2 whole-genome sequences from individuals diagnosed in the Amazonas state from 1st January to 6th July 2021, of which 38 were vaccine breakthrough infections. Our study reveals a sharp increase in the relative prevalence of Gamma plus (P.1+) variants, designated as Pango Lineages P.1.3 to P.1.6, harboring two types of additional Spike changes: deletions in the N-terminal (NTD) domain (particularly{Delta} 144 or{Delta} 141-144) associated with resistance to anti-NTD neutralizing antibodies or mutations at the S1/S2 junction (N679K or P681H) that probably enhance the binding affinity to the furin cleavage site, as suggested by our molecular dynamics simulations. As lineages P.1.4 (S:N679K) and P.1.6 (S:P681H) expanded (Re > 1) from March to July 2021, the lineage P.1 declined (Re < 1) and the median Ct value of SARS-CoV-2 positive cases in Amazonas significantly decreases. Still, we found no overrepresentation of P.1+ variants among breakthrough cases of fully vaccinated patients (71%) in comparison to unvaccinated individuals (93%). This evidence supports that the ongoing endemic transmission of SARS-CoV-2 in the Amazonas is driven by the spread of new local Gamma/P.1 sub-lineages that are more transmissible, although not more efficient to evade vaccine-elicited immunity than the parental VOC. Finally, as SARS-CoV-2 continues to spread in human populations with a declining density of susceptible hosts, the risk of selecting new variants with higher infectivity are expected to increase.

Brazils COVID-19 response has faced challenges due to the continuous emergence of variants of concern (VOCs), emphasizing the need for ongoing genomic surveillance and retrospective analyses of past epidemic waves. Rio Grande do Sul (RS), Brazils southernmost state, has crucial international borders and trades with Argentina and Uruguay, along with significant domestic connections. The source and sink of transmission with both national and international hubs raises questions about the RS role in the transmission of the virus, which has not been fully explored. Nasopharyngeal samples from various municipalities in RS were collected between June 2020 and July 2022. SARS-CoV-2 whole genome amplification and sequencing were performed using high-throughput Illumina sequencing. Bioinformatics analysis encompassed the development of scripts and tools to take into account epidemiological information to reduce sequencing disparities bias among the regions/countries, genome assembly, and large-scale phylogenetic reconstruction. Here, we sequenced 1,480 SARS-CoV-2 genomes from RS, covering all major regions. Sequences predominantly represented Gamma (April-June 2021) and Omicron (January-July 2022) variants. Phylogenetic analysis revealed a regional pattern for transmission dynamics, particularly with Southeast Brazil for Gamma, and a range of inter-regional connections for Delta and Omicron within the country. On the other hand, international and cross-border transmission with Argentina and Uruguay was rather limited. We evaluated the three VOCs circulation over two years in RS using a new subsampling strategy based on the number of cases in each state during the circulation of each VOC. In summary, the retrospective analysis of genomic surveillance data demonstrated that virus transmission was less intense between country borders than within the country. These findings suggest that while non-pharmacological interventions were effective to mitigate transmission across international land borders in RS, they were unsuficient to contain transmission at the domestic level.

Oropouche virus is an arbovirus endemic to the Americas. Periodic outbreaks have occurred since its description in 1955. In late 2023, an outbreak occurred in Peru, centered in and around Iquitos in the Eastern Peruvian Amazon. An existing acute febrile illness (AFI) surveillance program was able to document its emergence and characterize arthralgia and dysuria and the absence of diarrhea as distinctive clinical features of Oropouche virus-associated febrile illness relative to other causes of AFI. Sequencing of isolates from the outbreak demonstrated that strains from this region were distinct from those causing disease in Brazil, despite the large-scale movement of people along the Amazon corridor, but highly similar to strains from Colombia and Ecuador. Our findings suggest that the current outbreak in South America is fundamentally multifocal in origin and not the result of geographic spread from Brazil, which experienced an outbreak between 2022 and 2024.

The novel coronavirus disease (COVID-19) pandemic caused by SARS-CoV-2 is a major threat to humans. Recently, we encountered two seemingly separate COVID-19 clusters in a tertiary care medical center. Whole viral genome sequencing detected the haplotype of the SARS-CoV-2 genome and the two clusters were successfully distinguished by the viral genome haplotype. Concurrently, there were nine COVID-19 patients clinically unlinked to clusters #1 or #2 that necessitated the determination of the source of infection. Such patients had similar haplotypes to those in cluster #2 but were devoid of two rare mutations characteristic to cluster #2. This suggested that these nine cases of "probable community infection" indeed had community infection and were not derived from cluster #2. Whole viral genome sequencing of SARS-CoV-2 is a powerful measure not only for monitoring the global trend of SARS-CoV-2 but also for identifying the source of infection of COVID-19 at a level of institution.

BackgroundThe Oropouche virus (OROV) is an arthropod-borne virus that causes an acute febrile illness similar to other arboviral diseases. In 2024, Oropouche cases sharply increased in several countries of the Americas, including Bolivia. Here, we performed a genomic study to investigate the origin and spread of OROV in the Bolivian Amazon region. MethodsFull-length OROV genomes from 34 positive samples collected in the three affected Bolivian departments during 2024 were sequenced using an amplicon-based approach. Maximum Likelihood (ML) phylogenetic analyses of separate viral segments were conducted to identify the responsible viral lineage. Bayesian phylogeographic analysis of concatenated viral segments was used to reconstruct the viral spatiotemporal dispersion pattern within the country. FindingsEpidemiological data shows that the first OROV-positive cases in 2024 in Bolivia were reported in samples collected from the Pando department during mid-January, and the peak of OROV-positive cases occurred in mid-April. The phylogenetic analysis of OROV genomes revealed that all cases detected in Bolivia belong to the novel reassortant OROV clade that drove the recent epidemic in Brazil. Our phylogeographic analysis detected at least two exportation events of OROV from the Brazilian state of Acre to the Bolivian municipalities of Guayaramerin and Riberalta, both located in the Beni department, with subsequent dissemination to municipalities of Pando and La Paz departments. Viral introductions probably occurred between early October and early November 2023, thus indicating a lag of about three months between OROV introduction and detection in Bolivia. InterpretationOur findings confirm that OROV spread at least twice from the western Brazilian Amazon to the neighboring Bolivian department of Beni in late 2023, successfully establishing regional transmission chains. The introduction and spread of OROV in Bolivia coincides with the Amazonian rainy season, from November to April, a period likely marked by an increase in vector abundance. These findings underscore the critical need for active OROV surveillance across the cross-border Amazonian region between Brazil and Bolivia. They also confirm the potential for sustained OROV transmission within the Bolivian Amazon, highlighting the importance of preparedness for future outbreaks. FundingThis publication was in part supported by the Cooperative Agreement Number NU50CK000639 awarded to the Pan American Health Organization and funded by the Centers for Disease Control and Prevention. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention or the Department of Health and Human Services. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSBefore 2024, large outbreaks of Oropouche virus (OROV) were predominantly reported in the Amazon regions of Brazil and Peru. However, in 2024, significant outbreaks first emerged in the Brazilian Amazon region. They were soon followed by a surge of cases in the neighboring South American countries of Bolivia, Colombia, and Peru. We searched PubMed and preprint servers (medRxiv and bioRxiv) available as of October 25, 2024, for studies examining the circulation of OROV in Bolivia, using the terms ["Oropouche" AND "Bolivia"]. We identified only one study that reported a few anecdotal cases of past OROV infections in Bolivia, relying on serological tests and a couple of reviews. Added value of this studyThis is the first study to analyze the genomic characteristics of OROV circulating in Bolivia. In this study, we sequenced 34 full-length OROV genomes, representing 10% of all RT-qPCR-confirmed OROV cases across Pando, Beni, and La Paz departments between January and May 2024. The OROV detected in Bolivia belongs to the novel reassortant lineage recently identified in Brazil. We identified at least two introductions of OROV from the western Brazilian Amazon region into the neighboring Bolivian department of Beni around late 2023, followed by its spread to other regions within Bolivia during the rainy season. Our estimates indicate that the virus circulated in Bolivia for approximately three months before the first case was detected. Implications of all the available evidenceOur study confirms that the novel OROV reassortant lineage recently identified in Brazil rapidly disseminated across the Amazonian border into Bolivia. The successful establishment of OROV in Bolivia indicates that the country possesses suitable ecological conditions to support sustained transmissions of this arbovirus. Our findings also emphasize the crucial need for active and sustained molecular surveillance of OROV in the Bolivian Amazon region to enable the timely detection of new outbreaks in the country.

BackgroundAt present, PCR-based nucleic acid detection cannot meet the demands for coronavirus infectious disease (COVID-19) diagnosis. Methods214 confirmed COVID-19 patients who were hospitalized in the General Hospital of Central Theater Command of the Peoples Liberation Army between January 18 and February 26, 2020, were recruited. Two Enzyme-Linked Immunosorbent Assay (ELISA) kits based on recombinant SARS-CoV-2 nucleocapsid protein (rN) and spike protein (rS) were used for detecting IgM and IgG antibodies, and their diagnostic feasibility was evaluated. ResultsAmong the 214 patients, 146 (68.2%) and 150 (70.1%) were successfully diagnosed with the rN-based IgM and IgG ELISAs, respectively; 165 (77.1%) and 159 (74.3%) were successfully diagnosed with the rS-based IgM and IgG ELISAs, respectively. The positive rates of the rN-based and rS-based ELISAs for antibody (IgM and/or IgG) detection were 80.4% and 82.2%, respectively. The sensitivity of the rS-based ELISA for IgM detection was significantly higher than that of the rN-based ELISA. We observed an increase in the positive rate for IgM and IgG with an increasing number of days post-disease onset (d.p.o.), but the positive rate of IgM dropped after 35 d.p.o. The positive rate of rN-based and rS-based IgM and IgG ELISAs was less than 60% during the early stage of the illness 0-10 d.p.o., and that of IgM and IgG was obviously increased after 10 d.p.o. ConclusionsELISA has a high sensitivity, especially for the detection of serum samples from patients after 10 d.p.o, it can be an important supplementary method for COVID-19 diagnosis.