Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru

Possible Spreading of SARS-CoV-2 from Humans to Captive Non-Human Primates in the Peruvian Amazon

Human-to-animal transmission events of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) have been reported in both domestic and wild species worldwide. Despite the high rates of contagion and mortality during the COVID-19 (Coronavirus Diseases 2019) pandemic in Peru, no instances of natural virus infection have been documented in wild animals, particularly in the Amazonian regions where human-wildlife interactions are prevalent. In this study, we conducted a surveillance investigation using viral RNA sequencing of fecal samples collected from 76 captive and semi-captive non-human primates (NHPs) in the Loreto, Ucayali, and Madre de Dios regions between August 2022 and February 2023. We detected a segment of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 by metagenomic sequencing in a pooled fecal sample from captive white-fronted capuchins (Cebus unicolor) at a rescue center in Bello Horizonte, Ucayali. Phylogenetic analysis further confirmed that the retrieved partial sequence of the RdRp gene matched the SARS-CoV-2 genome. This study represents the first documented instance of molecular SARS-CoV-2 detection in NHPs in the Peruvian Amazon, underscoring the adverse impact of anthropic activities on the human-NHP interface and emphasizing the importance of ongoing surveillance for early detection and prediction of future emergence of new SARS-CoV-2 variants in animals.

Creating Peru's patient zero: pandemic narratives through traditional and social media

During the covid-19 pandemic, authorities, journalists, and the public used the term patient zero to refer to the first diagnosed patient. However, experts describe the term as imprecise because it equates the first infected patient with the first identified one. Although the term's inaccuracy, patients zero became relevant actors and sources of information during the pandemic. This was the case with the Peruvian patient zero, who had public media participation and opened his Instagram to establish a communication channel with the public. Despite knowing the term's inaccuracy, he felt responsible for the audience and sought to give his testimony. The Peruvian case shows how patients zero respond to the public interest and establish their agency through traditional and social media.

COVID-19 Excess Deaths in Peru's 25 States in 2020: Nationwide Trends, Confounding Factors, and Correlations With the Extent of Ivermectin Treatment by State

Introduction In 2020, nations hastened to contain an emerging COVID-19 pandemic by deploying diverse public health approaches, but conclusive appraisals of the efficacy of these approaches are elusive in most cases. One of the medicines deployed, ivermectin (IVM), a macrocyclic lactone having biochemical activity against SARS-CoV-2 through competitive binding to its spike protein, has yielded mixed results in randomized clinical trials (RCTs) for COVID-19 treatments. In Peru, an opportunity to track the efficacy of IVM with a close consideration of confounding factors was provided through data for excess deaths as correlated with IVM use in 2020, under semi-autonomous policies in its 25 states. Methods To evaluate possible IVM treatment effects, excess deaths as determined from Peruvian national health data were analyzed by state for ages ≥60 in Peru's 25 states. These data were compared with monthly summary data for excess deaths in Peru for the period 2020-2021 as published by the WHO in 2022. To identify potential confounding factors, Google mobility data, population densities, SARS-CoV-2 genetic variations, and seropositivity rates were also examined. Results Reductions in excess deaths over a period of 30 days after peak deaths averaged 74% in the 10 states with the most intensive IVM use. As determined across all 25 states, these reductions in excess deaths correlated closely with the extent of IVM use (p<0.002). During four months of IVM use in 2020, before a new president of Peru restricted its use, there was a 14-fold reduction in nationwide excess deaths and then a 13-fold increase in the two months following the restriction of IVM use. Notably, these trends in nationwide excess deaths align with WHO summary data for the same period in Peru. Conclusions The natural experiment that was put into motion with the authorization of IVM use for COVID-19 in Peru in May 2020, as analyzed using data on excess deaths by locality and by state from Peruvian national health sources, resulted in strong evidence for the drug's effectiveness. Several potential confounding factors, including effects of a social isolation mandate imposed in May 2020, variations in the genetic makeup of the SARS-CoV-2 virus, and differences in seropositivity rates and population densities across the 25 states, were considered but did not appear to have significantly influenced these outcomes.

Ethnobotanical Survey of Medicinal Plants Used in the Treatment of COVID-19 and Related Respiratory Infections in Ogbomosho South and North Local Government Areas, Oyo State, Nigeria

Coronavirus disease 2019 (COVID-19) has extensively spread worldwide with high mortality. Besides vaccination, the United States Food and Drug Administration approved only one oral medication as a treatment. Medicinal plants with antiviral and immunomodulatory properties could be explored as complementary treatments for COVID-19. Ogbomosho is home to such plants traditionally used to treat infectious diseases in Nigeria, making it relevant in complementary medicine. An ethnobotanical survey of medicinal plants used to treat COVID-19 and related ailments, including cough and flu in Ogbomosho South and North Local Government Areas, Nigeria, was conducted using a semi-structured questionnaire. Information was obtained from 56 participants, consisting of different groups of individuals with native knowledge of medicinal plants, and ethnobotanical indices, including the frequency of citation (FC), relative frequency of citation (RFC), and fidelity level (FL) were computed. Twenty-six medicinal plants (17 families) were used to treat COVID-19, 31 (20 families) for cough, and 29 (19 families) for flu. The most cited plant was Zingiber officinale (FC = 10; RFC = 0.18; FL = 18%) for treating COVID-19, Citrus limon (FC = 13; RFC = 0.23; FL = 23%) for cough, and Zingiber officinale (FC = 9; RFC = 0.16; FL = 16%) for flu. Leaves were the most used plant part for treating COVID-19 and flu, while the bark was the most used for cough. Trees and herbs were the most cited plant growth forms. The herbal remedies were mostly prepared by decoction and infusion and were mainly administered orally. Further research should be conducted on the identified species for the scientific validation of their antiviral and immunomodulatory efficacies and safety for use.

Confirmed SARS-CoV-2 reinfections after a second wave with predominance of Lambda in Lima and Callao, Peru

Background

Coronavirus disease 2019 (COVID-19) infection is a major public health problem in the world and reinfections are becoming more frequent. Our main objective was to describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the capital of Lima and Callao, Peru.

Methods

We searched in the Peruvian laboratory information system from April 2020 up to May 2021, looking for cases having 2 positive molecular tests for SARS-CoV-2 with more than 90 days between them. We performed genomic sequencing to the available pairs of samples and described the clinical characteristics, epidemiological impact, and genomic analysis of the confirmed reinfections.

Results

There were 1 694 164 people with a positive diagnostic test for SARS-CoV-2 in Lima/Callao during the study period. Of these, 1695 had 2 positive molecular tests with more than 90 days between them. Two hundred eleven had both samples available for genomic analysis according to our selection criteria, and these were retrieved and submitted to sequencing. Thirty cases were confirmed to be SARS-CoV-2 reinfections with 2 different lineages in the 2 episodes. The variant Lambda (C.37) was the most common during the second infection and accounted for 19 (63.3%) of the 30 cases.

Conclusions

We report 30 cases of confirmed SARS-CoV-2 reinfections. The Lambda variant was the most common cause of the second infections, in concordance with its predominant circulation during Peru’s second wave. This report describes the largest series of confirmed reinfections by SARS-CoV-2 in Latin America.

We describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 in Lima and Callao, durante la segunda ola en Peru. The Lambda variant (C.37) was the most common cause of the second infections.

The impact of sampling bias on viral phylogeographic reconstruction

Genomic epidemiology plays an ever-increasing role in our understanding of and response to the spread of infectious pathogens. Phylogeography, the reconstruction of the historical location and movement of pathogens from the evolutionary relationships among sampled pathogen sequences, can inform policy decisions related to viral movement among jurisdictions. However, phylogeographic reconstruction is impacted by the fact that the sampling and virus sequencing policies differ among jurisdictions, and these differences can cause bias in phylogeographic reconstructions. Here we assess the potential impacts of geographic-based sampling bias on estimated viral locations in the past, and on whether key viral movements can be detected. We quantify the effect of bias using simulated phylogenies with known geographic histories, and determine the impact of the biased sampling and of the underlying migration rate on the accuracy of estimated past viral locations. We find that overall, the accuracy of phylogeographic reconstruction is high, particularly when the migration rate is low. However, results depend on sampling, and sampling bias can have a large impact on the numbers and nature of estimated migration events. We apply these insights to the geographic spread of Ebolavirus in the 2014-2016 West Africa epidemic. This work highlights how sampling policy can both impact geographic inference and be optimized to best ensure the accuracy of specific features of geographic spread.

Introduction of SARS-CoV-2 C.37 (WHO VOI lambda) in the Sao Paulo State, Southeast Brazil

The Lambda variants of interest (VOI) (C37/GR/452Q.V1/21G) was initially reported in Lima, Peru but has gained rapid dissemination through other Latin American countries. Nevertheless, the dissemination and molecular epidemiology of the Lambda VOI in Brazil is unknown apart from a single case report. In this respect, we characterized the circulation of the SARS‐CoV‐2 Lambda VOI (C37/GR/452Q.V1/21G) in Sao Paulo State, Brazil. From March to June 2021, we identified seven Lambda isolates in a set of approximately 8000 newly sequenced genomes of the Network for Pandemic Alert of Emerging SARS‐CoV‐2 variants from Sao Paulo State. Interestingly, in three of the positive patients, the Lambda VOI infection was probably related to a contact transmission. These individuals were fully vaccinated to COVID‐19 and presented mild symptoms. The remaining positive for Lambda VOI individuals showed different levels of COVID‐19 symptoms and one of them needed hospitalization (score 5, WHO). In our study, we present a low level of Lambda VOI circulation in the Sao Paulo State. This reinforces the essential role of molecular surveillance for the effective SARS‐CoV‐2 pandemic response, especially in regard to circulating variants.

Our study shows the low circulation of the Lambda variants of interest (VOI) in the São Paulo State.

Two distinct Lambda VOI introductions may have occurred in the Sao Paulo State.

Epidemiological data revealed Lambda VOI transmission in three cases of fully vaccinated individuals.

Use of medicinal plants for COVID-19 prevention and respiratory symptom treatment during the pandemic in Cusco, Peru: A cross-sectional survey

BACKGROUND

The burden of the COVID-19 pandemic in Peru has led to people seeking alternative treatments as preventives and treatment options such as medicinal plants. This study aimed to assess factors associated with the use of medicinal plants as preventive or treatment of respiratory symptom related to COVID-19 during the pandemic in Cusco, Peru.

METHOD

A web-based cross-sectional study was conducted on general public (20- to 70-year-old) from August 31 to September 20, 2020. Data were collected using a structured questionnaire via Google Forms, it consisted of an 11-item questionnaire that was developed and validated by expert judgment using Aiken's V (Aiken's V > 0.9). Both descriptive statistics and bivariate followed by multivariable logistic regression analyses were conducted to assess factors associated with the use of medicinal plants for COVID-19 prevention and respiratory symptom treatment during the pandemic. Prevalence ratios (PR) with 95% Confidence Interval (CI), and a P-value of 0.05 was used to determine statistical significance.

RESULTS

A total of 1,747 respondents participated in the study, 80.2% reported that they used medicinal plants as preventives, while 71% reported that they used them to treat respiratory symptoms. At least, 24% of respondents used medicinal plants when presenting with two or more respiratory symptoms, while at least 11% used plants for malaise. For treatment or prevention, the multivariate analysis showed that most respondents used eucalyptus (p < 0.001 for both), ginger (p < 0.022 for both), spiked pepper (p < 0.003 for both), garlic (p = 0.023 for prevention), and chamomile (p = 0.011 for treatment). The respondents with COVID-19 (p < 0.001), at older ages (p = 0.046), and with a family member or friend who had COVID-19 (p < 0.001) used more plants for prevention. However, the respondents with technical or higher education used less plants for treatment (p < 0.001).

CONCLUSION

There was a significant use of medicinal plants for both prevention and treatment, which was associated with several population characteristics and whether respondents had COVID-19.

A Multiplex and Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Sensitive and Rapid Detection of Novel SARS-CoV-2

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major threat to public health. Rapid molecular testing for convenient and timely diagnosis of SARS-CoV-2 infections represents a challenge that could help to control the current pandemic and prevent future outbreaks. We aimed to develop and validate a multiplex and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay using lyophilized LAMP reagents for sensitive and rapid detection of SARS-CoV-2. LAMP primers were designed for a set of gene targets identified by a genome-wide comparison of viruses. Primer sets that showed optimal features were combined into a multiplex RT-LAMP assay. Analytical validation included assessment of the limit of detection (LoD), intra- and inter-assay precision, and cross-reaction with other respiratory pathogens. Clinical performance compared to that of real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) was assessed using 278 clinical RNA samples isolated from swabs collected from individuals tested for COVID-19. The RT-LAMP assay targeting the RNA-dependent RNA polymerase (RdRp), membrane (M), and ORF1ab genes achieved a comparable LoD (0.65 PFU/mL, CT=34.12) to RT-qPCR and was 10-fold more sensitive than RT-qPCR at detecting viral RNA in clinical samples. Cross-reactivity to other respiratory pathogens was not observed. The multiplex RT-LAMP assay demonstrated a strong robustness and acceptable intra- and inter-assay precision (mean coefficient of variation, 4.75% and 8.30%). Diagnostic sensitivity and specificity values were 100.0% (95% CI: 97.4-100.0%) and 98.6% (95% CI: 94.9-99.8%), respectively, showing high consistency (Cohen's kappa, 0.986; 95% CI: 0.966-1.000; p<0.0001) compared to RT-qPCR. The novel one-step multiplex RT-LAMP assay is storable at room temperature and showed similar diagnostic accuracy to conventional RT-qPCR, while being faster (<45 min), simpler, and cheaper. The new assay could allow reliable and early diagnosis of SARS-CoV-2 infections in primary health care. It may aid large-scale testing in resource-limited settings, especially if it is integrated into a point-of-care diagnostic device.

Genomic Sequences and Analysis of Five SARS-CoV-2 Variants Obtained from Patients in Lambayeque, Peru

Here, we report the genomic sequences of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains obtained from nasopharyngeal samples from five tested COVID-19-infected patients from the Lambayeque region in Peru during early April 2020.

Here, we report the genomic sequences of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains obtained from nasopharyngeal samples from five tested coronavirus disease 2019 (COVID-19)-infected patients from the Lambayeque region in Peru during early April 2020.