Dynamic clade transitions and the influence of vaccination on the spatiotemporal circulation of SARS-CoV-2 variants.

Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.

Cryptic circulation of chikungunya virus in São Jose do Rio Preto, Brazil, 2015-2019.

BACKGROUND: Chikungunya virus (CHIKV) has spread across Brazil with varying incidence rates depending on the affected areas. Due to cocirculation of arboviruses and overlapping disease symptoms, CHIKV infection may be underdiagnosed. To understand the lack of CHIKV epidemics in São José do Rio Preto (SJdRP), São Paulo (SP), Brazil, we evaluated viral circulation by investigating anti-CHIKV IgG seroconversion in a prospective study of asymptomatic individuals and detecting anti-CHIKV IgM in individuals suspected of dengue infection, as well as CHIKV presence in Aedes mosquitoes. The opportunity to assess two different groups (symptomatic and asymptomatic) exposed at the same geographic region aimed to broaden the possibility of identifying the viral circulation, which had been previously considered absent. METHODOLOGY/PRINCIPAL FINDINGS: Based on a prospective population study model and demographic characteristics (sex and age), we analyzed the anti-CHIKV IgG seroconversion rate in 341 subjects by ELISA over four years. The seroprevalence increased from 0.35% in the first year to 2.3% after 3 years of follow-up. Additionally, we investigated 497 samples from a blood panel collected from dengue-suspected individuals during the 2019 dengue outbreak in SJdRP. In total, 4.4% were positive for anti-CHIKV IgM, and 8.6% were positive for IgG. To exclude alphavirus cross-reactivity, we evaluated the presence of anti-Mayaro virus (MAYV) IgG by ELISA, and the positivity rate was 0.3% in the population study and 0.8% in the blood panel samples. In CHIKV and MAYV plaque reduction neutralization tests (PRNTs), the positivity rate for CHIKV-neutralizing antibodies in these ELISA-positive samples was 46.7%, while no MAYV-neutralizing antibodies were detected. Genomic sequencing and phylogenetic analysis revealed CHIKV genotype ECSA in São José do Rio Preto, SP. Finally, mosquitoes collected to complement human surveillance revealed CHIKV positivity of 2.76% of A. aegypti and 9.09% of A. albopictus (although it was far less abundant than A. aegypti) by RT-qPCR. CONCLUSIONS/SIGNIFICANCE: Our data suggest cryptic CHIKV circulation in SJdRP detected by continual active surveillance. These low levels, but increasing, of viral circulation highlight the possibility of CHIKV outbreaks, as there is a large naïve population. Improved knowledge of the epidemiological situation might aid in outbreaks prevention.

Dynamic clade transitions and the influence of vaccine rollout on the spatiotemporal circulation of SARS-CoV-2 variants in São Paulo, Brazil.

Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.

Checklist and description of three new chromatic patterns of Pachycoris torridus (Scopoli, 1772) (Hemiptera: Scutelleridae)

In the present paper, 27 chromatic patterns of the specie Pachycoris torridus (Scopoli, 1772) were grouped and three new patterns are described. Because of this high phenotypic polymorphism, P. torridus already been registered eight times as a new specie, highlighting the importance of the application of different tools to assist in taxonomy of this hemipterous of economic importance.

No presente artigo, 27 padro˜ es croma´ ticos da espe´cie Pachycoris torridus (Scopoli, 1772) sa˜o agrupados e treˆs novos padro˜ es sa˜o descritos. Devido a esse grande polimorfismo fenoti´pico, P. torridus ja´ foi registrado oito vezes como espe´cie nova, o que ressalta a importaˆncia da aplicac¸a˜o de diferentes ferramentas para auxiliar na taxonomia desse hemi´ptero de importaˆncia econoˆmica.

Morphological aspects of the testes of 18 species of terrestrial of Heteroptera from Northwestern Sao Paulo (Brazil) / Aspectos testiculares de 18 especies terrestres de Heteroptera do Noroeste de Sao Paulo (Brasil)

The Heteroptera are known for their odour, for being pests or for being disease carriers. However, they are still not extensively studied, perhaps because they form a very large group. Therefore, with the aim of enhancing the knowledge of the morphology of the testes of this insect order, we collected and analysed 18 species of terrestrial Heteroptera from the northwestern part of São Paulo. The analysis of these species revealed some differences between the testicles of these species, including their shape (elongated, oval, round or pecten), the morphology of the testicular lobes (elongated and paired side by side or united in a single region), the colours of the peritoneal sheath that surrounds the lobes (red, orange, yellow or translucent), and the number of testicular lobes (one, two, four, five, six or seven). Because the aspects analysed were highly variable, our study suggests a need for further analysis of Heteropteran testicular morphological differences.

Os Heteroptera são organismos conhecidos pelo seu odor, por serem pragas ou por serem transmissores de doenças, contudo, eles ainda são pouco estudados, talvez por formarem um grupo muito grande. Portanto, com o objetivo de ampliarmos as informações dos aspectos testiculares deste grupo analisamos 18 espécies de Heteroptera terrestres pertencentes a oito famílias que foram coletadas no Noroeste Paulista. Através das análises dessas espécies foi observado diferenças testiculares quanto: a sua forma (alongadas; ovalados; forma de concha, denominada pecten; ou arredondados); a morfologia dos lobos (alongados e pareados lado a lado ou unidos em uma única região, na forma de um “ofiuroide”); às cores da bainha peritoneal (alaranjada, amarelada, avermelhada ou transparente); ao número de lobos testiculares (um, dois, quatro, cinco, seis, sete). Devido aos aspectos analisados serem muito variáveis, nosso estudo sugere um aprofundamento maior na questão que envolve as diferenças morfológicas testiculares.