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      Re-analyzing the SARS-CoV-2 series using an extended integer-valued time series models: A situational assessment of the COVID-19 in Mauritius

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          Abstract

          This paper proposes some high-ordered integer-valued auto-regressive time series process of order p (INAR( p)) with Zero-Inflated and Poisson-mixtures innovation distributions, wherein the predictor functions in these mentioned distributions allow for covariate specification, in particular, time-dependent covariates. The proposed time series structures are tested suitable to model the SARs-CoV-2 series in Mauritius which demonstrates excess zeros and hence significant over-dispersion with non-stationary trend. In addition, the INAR models allow the assessment of possible causes of COVID-19 in Mauritius. The results illustrate that the event of Vaccination and COVID-19 Stringency index are the most influential factors that can reduce the locally acquired COVID-19 cases and ultimately, the associated death cases. Moreover, the INAR(7) with Zero-inflated Negative Binomial innovations provides the best fitting and reliable Root Mean Square Errors, based on some short term forecasts. Undeniably, these information will hugely be useful to Mauritian authorities for implementation of comprehensive policies.

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          Impact and effectiveness of mRNA BNT162b2 vaccine against SARS-CoV-2 infections and COVID-19 cases, hospitalisations, and deaths following a nationwide vaccination campaign in Israel: an observational study using national surveillance data

          Eric J Haas, Frederick Angulo, John M. McLaughlin … (2021)
          Background Following the emergency use authorisation of the Pfizer–BioNTech mRNA COVID-19 vaccine BNT162b2 (international non-proprietary name tozinameran) in Israel, the Ministry of Health (MoH) launched a campaign to immunise the 6·5 million residents of Israel aged 16 years and older. We estimated the real-world effectiveness of two doses of BNT162b2 against a range of SARS-CoV-2 outcomes and to evaluate the nationwide public-health impact following the widespread introduction of the vaccine. Methods We used national surveillance data from the first 4 months of the nationwide vaccination campaign to ascertain incident cases of laboratory-confirmed SARS-CoV-2 infections and outcomes, as well as vaccine uptake in residents of Israel aged 16 years and older. Vaccine effectiveness against SARS-CoV-2 outcomes (asymptomatic infection, symptomatic infection, and COVID-19-related hospitalisation, severe or critical hospitalisation, and death) was calculated on the basis of incidence rates in fully vaccinated individuals (defined as those for whom 7 days had passed since receiving the second dose of vaccine) compared with rates in unvaccinated individuals (who had not received any doses of the vaccine), with use of a negative binomial regression model adjusted for age group (16–24, 25–34, 35–44, 45–54, 55–64, 65–74, 75–84, and ≥85 years), sex, and calendar week. The proportion of spike gene target failures on PCR test among a nationwide convenience-sample of SARS-CoV-2-positive specimens was used to estimate the prevelance of the B.1.1.7 variant. Findings During the analysis period (Jan 24 to April 3, 2021), there were 232 268 SARS-CoV-2 infections, 7694 COVID-19 hospitalisations, 4481 severe or critical COVID-19 hospitalisations, and 1113 COVID-19 deaths in people aged 16 years or older. By April 3, 2021, 4 714 932 (72·1%) of 6 538 911 people aged 16 years and older were fully vaccinated with two doses of BNT162b2. Adjusted estimates of vaccine effectiveness at 7 days or longer after the second dose were 95·3% (95% CI 94·9–95·7; incidence rate 91·5 per 100 000 person-days in unvaccinated vs 3·1 per 100 000 person-days in fully vaccinated individuals) against SARS-CoV-2 infection, 91·5% (90·7–92·2; 40·9 vs 1·8 per 100 000 person-days) against asymptomatic SARS-CoV-2 infection, 97·0% (96·7–97·2; 32·5 vs 0·8 per 100 000 person-days) against symptomatic COVID-19, 97·2% (96·8–97·5; 4·6 vs 0·3 per 100 000 person-days) against COVID-19-related hospitalisation, 97·5% (97·1–97·8; 2·7 vs 0·2 per 100 000 person-days) against severe or critical COVID-19-related hospitalisation, and 96·7% (96·0–97·3; 0·6 vs 0·1 per 100 000 person-days) against COVID-19-related death. In all age groups, as vaccine coverage increased, the incidence of SARS-CoV-2 outcomes declined. 8006 of 8472 samples tested showed a spike gene target failure, giving an estimated prevalence of the B.1.1.7 variant of 94·5% among SARS-CoV-2 infections. Interpretation Two doses of BNT162b2 are highly effective across all age groups (≥16 years, including older adults aged ≥85 years) in preventing symptomatic and asymptomatic SARS-CoV-2 infections and COVID-19-related hospitalisations, severe disease, and death, including those caused by the B.1.1.7 SARS-CoV-2 variant. There were marked and sustained declines in SARS-CoV-2 incidence corresponding to increasing vaccine coverage. These findings suggest that COVID-19 vaccination can help to control the pandemic. Funding None.
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            Zero-Inflated Poisson Regression, with an Application to Defects in Manufacturing

            Diane Lambert (1992)
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              FIRST-ORDER INTEGER-VALUED AUTOREGRESSIVE (INAR(1)) PROCESS

              M. Al-Osh, A. A. Alzaid (1987)
              Article 0 comments Cited 96 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Ashwinee Devi Soobhug:
                ORCID: https://orcid.org/0000-0002-3960-8924
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: MethodologyRole: Project administrationRole: SoftwareRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Homeswaree Jowaheer: Role: ConceptualizationRole: Software
                Naushad Mamode Khan: Role: Data curationRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Neeshti Reetoo: Role: Formal analysisRole: InvestigationRole: SupervisionRole: ValidationRole: Writing – review & editing
                Kursheed Meethoo-Badulla: Role: Formal analysisRole: InvestigationRole: SupervisionRole: Validation
                Laurent Musango: Role: Validation
                Célestin C. Kokonendji: Role: Methodology
                Azmi Chutoo: Role: Methodology
                Nawel Aries:
                ORCID: https://orcid.org/0000-0002-6656-4525
                Role: Project administrationRole: Software
                Gang Qin: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS One
                Journal ID (publisher-id): plos
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date Collection: 2022
                Publication date (Electronic): 8 February 2022
                Publication date PMC-release: 8 February 2022
                Volume: 17
                Issue: 2
                Electronic Location Identifier: e0263515
                Affiliations
                [1 ] Statistics Mauritius, Ministry of Finance, Economic Planning and Development, Port Louis, Mauritius
                [2 ] Department of Economics and Statistics, University of Mauritius, Moka, Mauritius
                [3 ] Department of Health And Wellness, Ministry of Education, Tertiary Education, Science and Technology, Vacoas-Phoenix, Mauritius
                [4 ] Communicable Disease Control Unit, Ministry of Health and Wellness, Port Louis, Mauritius
                [5 ] World Health Organization Country Representative in Mauritius, Port Louis, Mauritius
                [6 ] Laboratoire de Mathématiques de Besançon, UMR 6623 CNRS-UBFC, Université Bourgogne Franche-Comté, Besançon, France
                [7 ] Department of Mathematics, University of Bangui, Bangui, Central African Republic
                [8 ] Faculty of Mathematics, University of Science and Technology Houari Boumediene, Algiers, Bab Ezzouar, Algeria
                Nantong University, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0002-3960-8924
                https://orcid.org/0000-0002-6656-4525
                Article
                Publisher ID: PONE-D-21-18647
                DOI: 10.1371/journal.pone.0263515
                PMC ID: 8824322
                PubMed ID: 35134059
                SO-VID: 2a588d30-d2f6-4dfe-a373-6b02d4135b0a
                Copyright © © 2022 Soobhug et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 10 June 2021
                Date accepted : 20 January 2022
                Page count
                Figures: 6, Tables: 4, Pages: 17
                Funding
                The author(s) received no specific funding for this work.
                Categories
                Subject: Research Article
                Subject: Medicine and Health Sciences
                Subject: Medical Conditions
                Subject: Infectious Diseases
                Subject: Viral Diseases
                Subject: Covid 19
                Subject: Biology and Life Sciences
                Subject: Immunology
                Subject: Vaccination and Immunization
                Subject: Medicine and Health Sciences
                Subject: Immunology
                Subject: Vaccination and Immunization
                Subject: Medicine and Health Sciences
                Subject: Public and Occupational Health
                Subject: Preventive Medicine
                Subject: Vaccination and Immunization
                Subject: People and Places
                Subject: Geographical Locations
                Subject: Africa
                Subject: Mauritius
                Subject: Medicine and Health Sciences
                Subject: Medical Conditions
                Subject: Infectious Diseases
                Subject: Infectious Disease Control
                Subject: Vaccines
                Subject: Biology and life sciences
                Subject: Organisms
                Subject: Viruses
                Subject: RNA viruses
                Subject: Coronaviruses
                Subject: SARS coronavirus
                Subject: SARS CoV 2
                Subject: Biology and life sciences
                Subject: Microbiology
                Subject: Medical microbiology
                Subject: Microbial pathogens
                Subject: Viral pathogens
                Subject: Coronaviruses
                Subject: SARS coronavirus
                Subject: SARS CoV 2
                Subject: Medicine and health sciences
                Subject: Pathology and laboratory medicine
                Subject: Pathogens
                Subject: Microbial pathogens
                Subject: Viral pathogens
                Subject: Coronaviruses
                Subject: SARS coronavirus
                Subject: SARS CoV 2
                Subject: Biology and life sciences
                Subject: Organisms
                Subject: Viruses
                Subject: Viral pathogens
                Subject: Coronaviruses
                Subject: SARS coronavirus
                Subject: SARS CoV 2
                Subject: Medicine and Health Sciences
                Subject: Diagnostic Medicine
                Subject: Virus Testing
                Subject: Physical Sciences
                Subject: Mathematics
                Subject: Probability Theory
                Subject: Probability Distribution
                Subject: Medicine and Health Sciences
                Subject: Epidemiology
                Subject: Pandemics
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