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

Juscamayta-López, Eduardo; Tarazona, David; Valdivia, Faviola; Rojas, Nancy; Carhuaricra, Dennis; Maturrano, Lenin; Gavilán, Ronnie G.

doi:10.1101/2020.09.14.296814

Cited by 16 publications

(18 citation statements)

References 21 publications

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“…Thus, it has become a major threat to public health. A similar epidemiological situation is taking place in Peru, which has one of the highest mortality rates in the current COVID-19 pandemic, with Lima city being one of the major epicenters of SARS-CoV-2 infections in Peru, as of September 11, 2020 ( Juscamayta-López et al., 2020 ; Ministry of Health, Peru, 2020 ). Accurate and timely diagnosis of SARS-CoV-2 infections is key to interrupting the transmission and spread of the virus.…”

Section: Introductionmentioning

confidence: 81%

“…These RNA samples were obtained from nasal and pharyngeal swabs collected from individuals who tested positive for SARS-CoV-2 RNA according to RT-qPCR with a CT value <25 at NIH-Peru. Trimming of low-quality reads, genome assembly, and consensus sequence construction were performed according to methods recently described by Juscamayta-López et al. (2020) .…”

Section: Methodsmentioning

confidence: 99%

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

Juscamayta-López

Valdivia

Horna

et al. 2021

Front. Cell. Infect. Microbiol.

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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.

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Section: Introductionmentioning

confidence: 81%

Section: Methodsmentioning

confidence: 99%

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

Juscamayta-López

Valdivia

Horna

et al. 2021

Front. Cell. Infect. Microbiol.

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“…(1,401) used medicinal plants to prevent respiratory symptoms, and 71.0% (1,241) used medicinal plants to treat respiratory symptoms (Table 1).…”

Section: Sociodemographic Characteristics Of the Respondentsmentioning

confidence: 99%

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

Villena-Tejada

Vera-Ferchau

Cardona-Rivero

et al. 2021

Preprint

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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.

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“…A confirmed case, according to the Ministry of Health guidelines, was defined as an individual with a positive result for either serology or molecular test for SARS-CoV-2. Transmission apparently began in Lima, Peru's capital city, and from there spread to the rest of the country [4]. Lima has one-third of the country's population and accounted for roughly 50% of the cases and deaths reported [5].…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 prevalence associated to low socioeconomic status and overcrowding in an LMIC megacity: A population-based seroepidemiological survey in Lima, Peru

et al. 2021

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Background: Worldwide, Peru has one of the highest infection fatality rates of COVID-19, and its capital city, Lima, accumulates roughly 50% of diagnosed cases. Despite surveillance efforts to assess the extent of the pandemic, reported cases and deaths only capture a fraction of its impact due to COVID-19 0 s broad clinical spectrum. This study aimed to estimate the seroprevalence of SARS-CoV-2 in Lima, stratified by age, sex, region, socioeconomic status (SES), overcrowding, and symptoms. Methods: We conducted a multi-stage, population-based serosurvey in Lima, between June 28th and July 9th, 2020, after 115 days of the index case and after the first peak cases. We collected whole blood samples by finger-prick and applied a structured questionnaire. A point-of-care rapid serological test assessed IgM and IgG antibodies against SARS-CoV-2. Seroprevalence estimates were adjusted by sampling weights and test performance. Additionally, we performed RT-PCR molecular assays to seronegatives and estimated the infection prevalence. Findings: We enrolled 3212 participants from 797 households and 241 sample clusters from Lima in the analysis. The SARS-CoV-2 seroprevalence was 20¢8% (95%CI 17¢2À23¢5), and the prevalence was 25¢2% (95%CI 22¢5À28¢2). Seroprevalence was equally distributed by sex (aPR=0¢96 [95%CI 0¢85À1¢09, p = 0¢547]) and across all age groups, including 60 versus 11 years old (aPR=0¢96 [95%CI 0¢73À1¢27, p = 0¢783]). A gradual decrease in SES was associated with higher seroprevalence (aPR=3¢41 [95%CI 1¢90À6¢12, p<0¢001] in low SES). Also, a gradual increase in the overcrowding index was associated with higher seroprevalence (aPR=1¢99 [95%CI 1¢41À2¢81, p<0¢001] in the fourth quartile). Seroprevalence was also associated with contact with a suspected or confirmed COVID-19 case, whether a household member (48¢9%, aPR=2¢67 [95%CI 2¢06À3¢47, p<0¢001]), other family members (27¢3%, aPR=1¢66 [95%CI 1¢15À2¢40, p = 0¢008]) or a workmate (34¢1%, aPR=2¢26 [95%CI 1¢53À3¢35, p<0¢001]). More than half of seropositive participants reported never having had symptoms (56¢1%, 95% CI 49¢7À62¢3). Interpretation: This first estimate of SARS-CoV-2 seroprevalence in Lima shows an intense transmission scenario, despite the government's numerous interventions early established. Susceptibles across age groups show that physical distancing interventions must not be relaxed. SES and overcrowding households are associated with seroprevalence. This study highlights the importance of considering the existing social inequalities for implementing the response to control transmission in low-and middle-income countries.

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

Cited by 16 publications

References 21 publications

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

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

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

SARS-CoV-2 prevalence associated to low socioeconomic status and overcrowding in an LMIC megacity: A population-based seroepidemiological survey in Lima, Peru

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