Likely future pandemic agents database

Type: Bacteria

Family/Genus: Escherichia

Species: Escherichia coli

Example organism(s)/strain(s): Carbapenemase-producing Escherichia coli

Disease: Variable

Genome length: 4.5-5.5 Mb

Envelope: NA

Segmentation: NA

Genome type: DNA

Primary transmission route: Faecal-oral

Other transmission routes in order of importance: Fomite, Nosocomial

Animal reservoirs (Orders): Mammals, Birds

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Pigs, Poultry

Arthropod vectors: Occaisonal spillover

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): <<1

Asymptomatic transmission: Yes common

Latent period (infection to infectiousness): Carriage possible

Incubation period (infection to symptoms): 3-8 day

Infectious period: ~7days

Case fatality risk: Depends of presentation including urinary tract infections, wound infections, gastroenteritis, meningitis,septicemia and pneumonia

Case hospitalisation rate: Depends of presentation including urinary tract infections, wound infections, gastroenteritis, meningitis,septicemia and pneumonia

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Seasonality: No indication of seasonality

Geographical distribution (WHO Region): Global

Duration of infection: chronic

Availability in NZ: Probably

Global: Carbapenem/antibiotic use

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Virus

Family/Genus: Picornaviridae/Enterovirus

Species: Enterovirus

Example organism(s)/strain(s): Enterovirus C, poliovirus

Disease: Poliomyelitis

Genome length: ~7.5kb

Envelope: non-enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Direct contact

Other transmission routes in order of importance: Foodborne, Waterborne, Fomite

Animal reservoirs (Orders): None

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): NA

Arthropod vectors: NA

Arthropod vectors present in Aotearoa: NA

Incubation period (infection to symptoms): 7-21 days (polio)

Infectious period: 7-14 days

Case fatality risk: 5-10% of those paralysed

Case hospitalisation rate: High, may require respiratory support

Symptoms (general): Neurological

Primary symptoms: muscle weakness

Long term sequelae: Ongoing paralysis and post-polio syndrom

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): Very high

Seasonality: Summer months in temperate regions

Geographical distribution (WHO Region): Global

Duration of infection: chronic

Type: Bacteria

Family/Genus: Francisella

Species: Francisella tularensis

Example organism(s)/strain(s): Francisella tularensis

Disease: Tularensis

Genome length: 1.8 Mb

Envelope: NA

Segmentation: NA

Genome type: DNA

Primary transmission route: Airborne

Other transmission routes in order of importance: Arthropod vector

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Rodents

Arthropod vectors: Occaisonal spillover

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): <<1

Asymptomatic transmission: No

Latent period (infection to infectiousness): NA

Incubation period (infection to symptoms): 3-5 days

Infectious period: NA

Case fatality risk: Untreated 30%Treated 2%

Case hospitalisation rate: 50%

Symptoms (general): Systemic (flu like)

Primary symptoms: Fever, chills, cough

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Geographical distribution (WHO Region): Global

Duration of infection: acute

Availability in NZ: Yes

Global: Bioterrorism, increased animal numbers

Evolution recombination frequency: low

Test availability: Available overseas and agreement not in place

Case definition available: No

Type: Bacteria

Family/Genus: Bacillus

Species: Bacillus anthracis

Example organism(s)/strain(s): Bacillus anthracis

Disease: Inhalational anthrax

Genome length: 5.2 Mb

Envelope: NA

Segmentation: NA

Genome type: DNA

Primary transmission route: Airborne

Other transmission routes in order of importance: Injection

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Cattle, Sheep, Goats, Horses

Arthropod vectors: NA

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 0

Asymptomatic transmission: No

Latent period (infection to infectiousness): NA

Incubation period (infection to symptoms): 1-7 days

Infectious period: NA

Case fatality risk: 45%

Case hospitalisation rate: 100%

Symptoms (general): Systemic (flu like)

Primary symptoms: fever, fatigue, muscle pain, cough. chest pain, abdominal pain, difficulty breathing and cyanosis.

Long term sequelae: Significant long-term health problems 

Geographical distribution (WHO Region): Global

Duration of infection: acute

Availability in NZ: Yes

Global: Bioterrorism

Evolution recombination frequency: low

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Bacteria

Family/Genus: Mycobacterium

Species: Mycobacterium tuberculosis

Example organism(s)/strain(s): Mycobacterium tuberculosis XDR

Disease: XDR TB

Genome length: 4.4 Mb

Envelope: NA

Segmentation: NA

Genome type: DNA

Primary transmission route: Droplet

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Cattle

Arthropod vectors: NA

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 0.24-4.3

Incubation period (infection to symptoms): 2-10 weeks

Infectious period: Years

Case fatality risk: 39%

Case hospitalisation rate: Low

Symptoms (general): Respiratory

Primary symptoms: cough

Long term sequelae: Spectrum of disorders affecting airways

Geographical distribution (WHO Region): Global

Duration of infection: chronic

Availability in NZ: Yes

Global: Migration, decrease in dedicated Tb healthcase services

Evolution recombination frequency: low

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Bacteria

Family/Genus: Yersinia

Species: Yersinia pestis

Example organism(s)/strain(s): Yersinia pestis

Disease: Pneumonic plague

Genome length: 4.65 Mb

Envelope: NA

Segmentation: NA

Genome type: DNA

Primary transmission route: Arthropod vector

Other transmission routes in order of importance: Droplet, Faecal-oral, Direct contact

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Rodents

Arthropod vectors: Fleas, Fleas, Xenopsylla cheopis and Nosopsyllus fasciatus

Arthropod vectors present in Aotearoa: Yes (Xenopsylla)

Basic reproduction number (human-human): 1.3 (variance 3.1)

Asymptomatic transmission: No

Incubation period (infection to symptoms): 1-3 days

Infectious period: 2-3 days

Effective non-pharmaceutical interventions: Animal cull

Case fatality risk: Untreated nearly 100%, treated 25-60%

Case hospitalisation rate: 91%

Symptoms (general): Respiratory

Primary symptoms: fever, headache, weakness, pneumonia, chest pain, and cough.

Long term sequelae: No

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): Limited data

Seasonality: Yes - related to flea reservoir with an increase of cases in autumn and decreases in winter

Geographical distribution (WHO Region): Africa, Americas, Asia

Duration of infection: acute

Availability in NZ: Yes

Global: Climate change, insecticide resistance, human behaviour. Bioterrorism.

Evolution recombination frequency: high

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Bacteria

Family/Genus: Yersinia

Species: Yersinia pestis

Example organism(s)/strain(s): Yersinia pestis

Disease: Bubonic plague

Genome length: 4.65 Mb

Envelope: NA

Segmentation: NA

Genome type: DNA

Primary transmission route: Arthropod vector

Other transmission routes in order of importance: Faecal-oral, Droplet, Direct contact

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Rodents

Arthropod vectors: Fleas, Fleas, Xenopsylla cheopis and Nosopsyllus fasciatus

Arthropod vectors present in Aotearoa: Yes (Xenopsylla)

Basic reproduction number (human-human): 1.4-2.1

Asymptomatic transmission: No

Latent period (infection to infectiousness): Days

Incubation period (infection to symptoms): 1-7 days

Effective non-pharmaceutical interventions: Animal cull

Case fatality risk: Untreated 60%, treated 5%

Case hospitalisation rate: 91%

Symptoms (general): Bubonic - systemic flulike, Pneumonic, respiratory, septicaemic - gastro

Primary symptoms: Bubonic: fever, headache, chills, weakness and swollen lymph nodes

Long term sequelae: No

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): Limited data

Seasonality: Yes - related to flea bite frequency with increase in cases in autumn and decreases in winter

Geographical distribution (WHO Region): Africa, Americas, Asia

Duration of infection: acute

Availability in NZ: Yes

Global: Climate change, insecticide resistance, human behaviour

Evolution recombination frequency: high

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Virus

Family/Genus: Poxviridae

Species: Variola major virus

Example organism(s)/strain(s): Variola

Disease: Smallpox

Genome length: 186103

Envelope: enveloped

Segmentation: non-segmented

Genome type: DNA

Primary transmission route: Direct contact

Other transmission routes in order of importance: Fomite, Droplet, Airborne

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Rodents

Arthropod vectors: NA

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 6.9 (95% CI 4.5 - 10.1)

Asymptomatic transmission: Negligible

Incubation period (infection to symptoms): 7-19 days

Infectious period: 16 days

Effective non-pharmaceutical interventions: Cover coughs/sneezes, Distancing, Handwashing, Isolation when ill, Mask wearing

Symptoms (general): Skin, Systemic (flu like)

Primary symptoms: fever, headache, vomiting , pustules, rash

Long term sequelae: 65-80% deep pitted scars

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): 95% effective after a single dose. If a person received a second dose within the first few years, the efficacy was believed to approach 98-99%, 95% effective after a single dose. Not evaluated in RCTs by epi evidence suggests high level of protection up t

Availability in NZ: Not listed on Medsafe

Global: Bioterrorism

Evolution recombination frequency: high

Test availability: Available overseas and agreement not in place

Case definition available: Yes

Type: Virus

Family/Genus: Paramyxoviridae/Morbillivirus

Species: Measles morbillivirus

Example organism(s)/strain(s): Measles virus

Disease: Measles

Genome length: 15,894

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Airborne

Other transmission routes in order of importance: Direct contact, Airborne, Fomite, Droplet

Animal reservoirs (Orders): None

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): NA

Arthropod vectors: NA

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 12 to 18

Asymptomatic transmission: No

Incubation period (infection to symptoms): 10-14 days

Case fatality risk: 0-40% (median 1%)

Case hospitalisation rate: 36% hospitalisation risk recorded in NZ's 2019 measles outbreak

Symptoms (general): Systemic (flu like)

Primary symptoms: rash

Long term sequelae: immune supporession; neurological complications in the post-acute phase; subacute sclerosing panencephalitis (SSPE) 7-10 years later

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): Two doses of MMR vaccine are about 97% effective at preventing measles; one dose is about 93% effective

Seasonality: Dry season in tropical regions; late winter/early spring in temperate regions

Geographical distribution (WHO Region): Global

Duration of infection: acute

Global: Vaccine hesitancy and disinformation

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Virus

Family/Genus: Poxviridae

Species: Mpox

Example organism(s)/strain(s): Mpox (Monkeypox virus)

Disease: Mpox

Genome length: 194,711

Envelope: enveloped

Segmentation: non-segmented

Genome type: DNA

Primary transmission route: Direct contact

Other transmission routes in order of importance: Bodily fluids, Sexual contact

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Squirrels, Rodents

Arthropod vectors: NA

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 1.x to 4

Asymptomatic transmission: Yes rare

Incubation period (infection to symptoms): 5.6 (4.3-7.8 CI) days

Serial interval/generation time: 8.5 days (4.3-7.8 CI)

Case fatality risk: 0.13%; HIV coinfection is a major predictor of fatality risk

Case hospitalisation rate: 35% (95% CI 14–59%)

Symptoms (general): Skin

Primary symptoms: rash

Long term sequelae: Mpox-related ophthalmic disease (MPXROD) is a recognised complication

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): Two doses point estimates range from 66% (95%CI47-78%) to 89% (95%CI 44-98%). Single doses pointe estimates range from 36-75%

Seasonality: No

Geographical distribution (WHO Region): Global

Duration of infection: acute

Global: Change in population demographic; human movement; bush meat trade

Evolution recombination frequency: high

Test availability: Available and validated in Aotearoa but not routinely used

Case definition available: Yes

Type: Virus

Family/Genus: Arenaviridae

Species: (40 species including Lassa mammarenavirus)

Example organism(s)/strain(s): Machupo mammareavirus, Chapare virus

Disease: Bolivian haemorrhagic fever

Genome length: ~11kb

Envelope: enveloped

Segmentation: segmented

Genome type: RNA

Primary transmission route: Zoonotic

Other transmission routes in order of importance: Fomite, Bodily fluids

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Rodents

Arthropod vectors: NA

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): <<1

Asymptomatic transmission: Unknown

Incubation period (infection to symptoms): 3-16 days

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Geographical distribution (WHO Region): Region of the Americas (AMR)

Duration of infection: acute

Type: Virus

Family/Genus: Arenaviridae

Species: (40 species including Lassa mammarenavirus)

Example organism(s)/strain(s): Lassa virus

Disease: Lassa Fever

Genome length: ~11kb

Envelope: enveloped

Segmentation: segmented

Genome type: RNA

Primary transmission route: Zoonotic

Other transmission routes in order of importance: Fomite, Bodily fluids, Nosocomial

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Rodents

Arthropod vectors: NA

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 1.1 to 1.8

Asymptomatic transmission: Yes common

Incubation period (infection to symptoms): 6-21 days

Infectious period: 4-11days (possibly)

Serial interval/generation time: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288732/

Effective non-pharmaceutical interventions: Zoonotic is rodent control/hygiene, after that PPE like other VHF viruses

Symptoms (general): Systemic (flu like)

Primary symptoms: sore throat

Long term sequelae: Late sequelae include alopecia, iridocyclitis, and transient blindness

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Geographical distribution (WHO Region): African Region (AFR)

Duration of infection: acute

Global: Bioterrorism

Test availability: Available overseas and agreement not in place

Case definition available: Yes

Type: Virus

Family/Genus: Togaviridae/Alphavirus

Species: Chikungunya virus

Example organism(s)/strain(s): Chikungunya virus

Disease: Chikungunya;

Genome length: ~12kb

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Vector

Other transmission routes in order of importance: Vertical

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Primates

Arthropod vectors: Aedes (albopictus)

Arthropod vectors present in Aotearoa: No

Basic reproduction number (human-human): 2.8-4.1

Asymptomatic transmission: Yes common

Incubation period (infection to symptoms): 3-7days (range 1-12)

Infectious period: 2 days before signs; 5 days after

Case fatality risk: 0.024 - 0.8%

Case hospitalisation rate: 0.6 - 13%

Symptoms (general): Systemic (flu like)

Primary symptoms: joint pain

Long term sequelae: Joint pain may persist for months to years after primary infection

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Seasonality: Follows vector distribution

Geographical distribution (WHO Region): Global

Duration of infection: acute

Availability in NZ: No

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Virus

Family/Genus: Picornaviridae/Enterovirus

Species: 15 Enterovirus species

Example organism(s)/strain(s): Includes coxsackieviruses, echoviruses, numbered enteroviruses and rhinoviruses

Disease: Hand Foot and Mouth Disease; several clinical neurological syndromes; lower respiratory tract infections

Genome length: 7.5kb

Envelope: non-enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Direct contact

Animal reservoirs (Orders): Birds, Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Cattle, Pigs, Primates

Arthropod vectors: NA

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 1.1-7.7

Asymptomatic transmission: Yes common

Incubation period (infection to symptoms): 3-5 days (HFMD)

Infectious period: 7-10 days

Case fatality risk: 0.03% (HFMD)

Case hospitalisation rate: HFMD case-severity rate 1·1% (0·2–1·6%)

Symptoms (general): Neurological

Primary symptoms: fever

Long term sequelae: Several including neurological, eye, nail

Seasonality: Major peak in spring/early summer, smaller peak in autumn (HFMD)

Geographical distribution (WHO Region): Global

Duration of infection: acute

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Virus

Family/Genus: Coronaviridae

Species: Severe acute respiratory syndrome coronavirus 2

Example organism(s)/strain(s): SARS-CoV-2

Disease: COVID-19

Genome length: 30000

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Airborne

Other transmission routes in order of importance: Droplet, Direct contact

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Mink, Deer, Bats, Racoon dog, Ferret

Arthropod vectors: No evidence

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 5

Asymptomatic transmission: Yes common

Latent period (infection to infectiousness): 5 days

Incubation period (infection to symptoms): 5 days

Infectious period: 2-10 days

Effective non-pharmaceutical interventions: Mask wearing, Contact tracing, Distancing, Isolation when ill

Case fatality risk: Low in Aotearoa <0.1% overall

Case hospitalisation rate: variable during pandemic, dependent on many factors including age, ethnicity, vaccination status, treatment availability and variant. Overall estimate 1.25% as of 3/7/2023

Symptoms (general): Respiratory

Primary symptoms: cough, fever, headache, sore throat, diarrhoea, difficulty breathing

Long term sequelae: Long COVID

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): 45% asymptomatic infection, 77% symptomatic infection (wanes 14% per month).

Seasonality: No indication of seasonality yet - driven by susceptible hosts however might become seasonal

Geographical distribution (WHO Region): Global

Duration of infection: acute

Availability in NZ: Yes

Global: Wildlife trade

Evolution recombination frequency: high

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Virus

Family/Genus: Phenuiviridae/Phlebovirus

Species: Rift Valley Fever phlebovirus

Example organism(s)/strain(s): Rift Valley Fever virus

Disease: Rift Valley fever 

Genome length: 11980

Envelope: enveloped

Segmentation: segmented

Genome type: RNA

Primary transmission route: Arthropod vector

Other transmission routes in order of importance: Multiple

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Cattle, Sheep, Goats, Camelids

Arthropod vectors: Aedes (primary), Culex, Mansonia and Anopheles (secondary)

Arthropod vectors present in Aotearoa: Yes

Basic reproduction number (human-human): <<1

Asymptomatic transmission: Yes common

Incubation period (infection to symptoms): 2-6 days

Case fatality risk: <1%

Symptoms (general): Systemic (flu like), Neurological, Systemic (haemorrhagic fever)

Primary symptoms: muscle pain, fever, joint pain, headache

Long term sequelae: Occular disease (0.5-2% cases), meningoencephalitis (<1%), heamorrhagic fever (<1%)

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Availability in NZ: No

Test availability: Available overseas and agreement not in place

Case definition available: Yes

Type: Virus

Family/Genus: Peribunyaviridae/Orthobunyavirus

Species: La Crosse orthobunyavirus

Example organism(s)/strain(s): LaCrosse Virus

Disease: LaCrosse encephalitis

Genome length: 12491

Envelope: enveloped

Segmentation: segmented

Genome type: RNA

Primary transmission route: Arthropod vector

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Chipmunks, Squirrels

Arthropod vectors: Aedes (main); possibly Culex and others

Arthropod vectors present in Aotearoa: Yes

Basic reproduction number (human-human): <<1

Incubation period (infection to symptoms): 5-15 days

Effective non-pharmaceutical interventions: Prevent mosquito bites

Case fatality risk: <1%

Case hospitalisation rate: can be high, particulallry in children under 16 years of age

Symptoms (general): Systemic (flu like), Neurological

Primary symptoms: fever, vomiting , nausea, fatigue, lethargy, encephalitis, neck stiffness, coma, tremors, seizures, muscle weakness, vision loss, numbness, paralysis

Long term sequelae: recurrent seizures and cognitive or behavioral impairments

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Geographical distribution (WHO Region): South-East Asian Region (SEAR)

Availability in NZ: No

Global: Introduction of invasive mosquitoes, changes in climate, changes in wildlife densities

Evolution recombination frequency: high

Test availability: Available overseas and agreement not in place

Case definition available: Yes

Type: Virus

Family/Genus: Paramyxoviridae/Henipavirus

Species: Nipah henipavirus; Hendra henipavirus

Example organism(s)/strain(s): Nipah virus; Hendra virus

Disease: Nipah virus disease

Genome length: 18246

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Zoonotic

Other transmission routes in order of importance: Foodborne, Direct contact

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Bats, Pigs, Horses

Arthropod vectors: No evidence

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 0.48

Asymptomatic transmission: No

Incubation period (infection to symptoms): 5-15 days

Effective non-pharmaceutical interventions: Animal cull, Handwashing, Food safety measures

Case fatality risk: 40-75%

Case hospitalisation rate: ~100%

Symptoms (general): Respiratory, Neurological

Primary symptoms: fever, headache, cough, sore throat, difficulty breathing, vomiting , seizures, coma, encephalitis, drowsiness/confusion

Geographical distribution (WHO Region): South-East Asian Region (SEAR)

Availability in NZ: Antivirals only

Global: Agricultural expansion and intensification

Evolution recombination frequency: low

Test availability: Available overseas and agreement not in place

Case definition available: Yes

Type: Virus

Family/Genus: Orthomyxoviridae/betainfluenzavirus

Species: Influenzavirus B virus

Example organism(s)/strain(s): Influenza B

Disease: Influenza

Genome length: 14548

Envelope: enveloped

Segmentation: segmented

Genome type: RNA

Primary transmission route: Airborne

Other transmission routes in order of importance: Droplet

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Pigs, Seals

Arthropod vectors: No evidence

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 1.0-21

Asymptomatic transmission: Yes common

Incubation period (infection to symptoms): 0.6 days (95%CI 0.5-0.6)

Infectious period: 0.6 days (95%CI 0.5-0.6)

Serial interval/generation time: 2-4 days

Effective non-pharmaceutical interventions: Mask wearing, contact tracing, social distancing, isolation when ill, border restrictions

Symptoms (general): Systemic (flu like)

Primary symptoms: fever, cough, sore throat, sneezing, running nose, chills, difficulty breathing, headache, aching muscles, nausea, vomitting,

Seasonality: Winter in temperate climate and year-round in tropical

Geographical distribution (WHO Region): Global

Duration of infection: acute

Availability in NZ: Yes

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Virus

Family/Genus: Bunyaviridae

Species: Crimean-Congo hemorrhagic fever orthonairovirus

Example organism(s)/strain(s): CCHFV

Disease: Crimean-Congo haemorrhagic fever

Genome length: Variable, approximately 11000-14000

Envelope: enveloped

Segmentation: segmented

Genome type: RNA

Primary transmission route: Zoonotic

Other transmission routes in order of importance: Arthropod vector, Bodily fluids, Fomite, Blood, Direct contact

Animal reservoirs (Orders): Mammals, Birds

Arthropod vectors: Ticks

Arthropod vectors present in Aotearoa: Unknown; over 30 species of ticks reportedly infected

Basic reproduction number (human-human): <<1

Asymptomatic transmission: Yes common

Incubation period (infection to symptoms): 5-6 days, max 13 reported

Case fatality risk: 5-30%

Case hospitalisation rate: Unclear

Symptoms (general): Systemic (haemorrhagic fever)

Primary symptoms: fever

Long term sequelae: sequelae not well researched

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Seasonality: Increased cases in spring and summer

Geographical distribution (WHO Region): Eastern Mediterranean Region (EMR)

Duration of infection: acute

Availability in NZ: Yes

Test availability: Available overseas and agreement not in place

Case definition available: Yes

Type: Virus

Family/Genus: Hantaviridae

Species: (38 species including…) Sin Nombre orthohantavirus; Seoul orthohantavirus; Hantaan orthohantavirus

Example organism(s)/strain(s): Hantaviruses, e.g. Seoul virus / Sin nombre virus. This is a generic name for a whole family.

Disease: hantavirus hemorrhagic fever with renal syndrome (HFRS) or hantavirus pulmonary syndrome (HPS)

Genome length: Approximately 12000, various widely

Envelope: enveloped

Segmentation: segmented

Genome type: RNA

Primary transmission route: Zoonotic

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Rodents, Bats, Insectivores (shrews, hedgehogs)

Arthropod vectors: No evidence

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): <1

Asymptomatic transmission: Yes rare

Incubation period (infection to symptoms): 14-18 days

Case fatality risk: 36-43%

Symptoms (general): Systemic (haemorrhagic fever)

Primary symptoms: fever

Long term sequelae: Renal failure (HHFRS) or cadiocascular

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Seasonality: Seasonality is complex and relates to vector populations, eg dry season in Brazil

Geographical distribution (WHO Region): Global

Duration of infection: acute

Availability in NZ: No

Test availability: Available overseas and agreement not in place

Case definition available: Yes

Type: Virus

Family/Genus: Flaviviridae

Species: Japanese encephalitis virus

Example organism(s)/strain(s): Japanese encephalitis virus

Disease: Japanese encephalitis

Genome length: 10,976

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Arthropod vector

Animal reservoirs (Orders): Birds, Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Pigs

Arthropod vectors: Culex species mosquitoes, particularly Culex tritaeniorhynchus

Arthropod vectors present in Aotearoa: Culex quinquefasciatus present (Cuex sitiens eradicated in 2020)

Basic reproduction number (human-human): ~1

Asymptomatic transmission: Yes common

Incubation period (infection to symptoms): 4-14 days

Infectious period: https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0004074

Case fatality risk: Average 18%

Case hospitalisation rate: Low

Symptoms (general): Neurological

Primary symptoms: encephalitis

Long term sequelae: An estimated 44% of survivors do not make a full neurological recovery

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): Variable, but SA14-14-2 LAV vaccine efficacies of 85%-95% have been reported with a single dose, or two doses separated by a short interval in China

Seasonality: Can occur all year round with peaks in late summer in temperate regions

Geographical distribution (WHO Region): African Region (AFR), Region of the Americas (AMR), South-East Asian Region (SEAR), European Region

Duration of infection: acute

Availability in NZ: No

Global: Climate change; farming practices

Evolution recombination frequency: low

Test availability: Readily available overseas and agreement in place

Case definition available: Yes

Type: Virus

Family/Genus: Flaviviridae

Species: Zika virus

Example organism(s)/strain(s): Zika virus

Disease: Zika virus disease

Genome length: 10,794

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Arthropod vector

Other transmission routes in order of importance: Sexual contact

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Primates

Arthropod vectors: Aedes egypti (primary), other Aedes (incl albopictus, africanus, hensilli and vittatus)

Arthropod vectors present in Aotearoa: No

Basic reproduction number (human-human): 1.4-6.6

Asymptomatic transmission: Yes common

Incubation period (infection to symptoms): 3-14 days

Infectious period: up to 1 week, but longer for sexual transmission (which is rare)

Case fatality risk: <0.003%

Case hospitalisation rate: low (difficult to quantify as acute disease typically does not require hospitalisation, but also because the highest incidence is seen in regions with low access to health services)

Symptoms (general): Skin

Primary symptoms: Typically - fever, rash, arthralgia

Long term sequelae: Congenital CNS malformations including microcephaly; Guillain-Barré syndrome

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Seasonality: Yes, relating to vector distribution

Geographical distribution (WHO Region): African Region (AFR), Region of the Americas (AMR), South-East Asian Region (SEAR), European Region

Duration of infection: acute

Availability in NZ: No

Global: Climate change; Human movement; urbanisation

Evolution recombination frequency: low

Test availability: Routine test available in Aotearoa

Case definition available: Yes

Type: Virus

Family/Genus: Filoviridae

Species: Marburg marburgvirus

Example organism(s)/strain(s): Marburg virus; Ravn virus

Disease: Marburg virus disease

Genome length: 18000-19000

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Direct contact

Other transmission routes in order of importance: Droplet, Blood, Bodily fluids, Zoonotic

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Bats

Arthropod vectors: No evidence

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 0.5-1.5

Asymptomatic transmission: No

Latent period (infection to infectiousness): 6.5

Incubation period (infection to symptoms): 3, 5-10 days

Infectious period: 3 days

Serial interval/generation time: 9 days

Effective non-pharmaceutical interventions: As for Ebola

Case fatality risk: 83-8%

Symptoms (general): Gastrointestinal and haemorrhagic

Primary symptoms: fever

Long term sequelae: Multiple, persistence of MARV in semen and aqueous humor

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Seasonality: Yes

Geographical distribution (WHO Region): African Region (AFR)

Duration of infection: acute

Availability in NZ: No

Global: Linked to mining; Bioterrorism

Evolution recombination frequency: low

Test availability: Readily available overseas and agreement in place

Case definition available: Yes

Type: Virus

Family/Genus: Filoviridae

Species: Zaire ebolavirus; Sudan ebolavirus; Bundibugyo ebolavirus …

Example organism(s)/strain(s): Ebola virus

Disease: Ebola virus disease

Genome length: 18000-19000

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Direct contact

Other transmission routes in order of importance: Blood, Faecal-oral, Zoonotic

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Bats, Primates, Pigs

Arthropod vectors: No evidence

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 1.4 to 2

Asymptomatic transmission: Yes rare

Latent period (infection to infectiousness): 12 days

Incubation period (infection to symptoms): 6, 3-13

Infectious period: 14 days

Serial interval/generation time: 10 to 16

Effective non-pharmaceutical interventions: Contact tracing, distancing, isolation, PPE

Case fatality risk: 25-89%

Case hospitalisation rate: high (difficult to quantify as described clusters include high rates of nosocomial transmission)

Symptoms (general): Gastrointestinal and haemorrhagic

Primary symptoms: fever

Long term sequelae: Memory loss, uveitis, persistence of EBOV RNA in semen

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): Likely high

Seasonality: Possible seasonal emergence

Geographical distribution (WHO Region): African Region (AFR)

Duration of infection: acute

Availability in NZ: Not listed on Medsafe

Global: Forest fragmentation, wildlife use and contact, bioterrorism

Evolution recombination frequency: low

Test availability: Readily available overseas and agreement in place

Case definition available: Yes

Type: Virus

Family/Genus: Coronaviridae

Species: Severe acute respiratory syndrome coronavirus 1

Example organism(s)/strain(s): SARS-CoV-1

Disease: Severe Acute Respiratory Syndrome

Genome length: 30000

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Airborne

Other transmission routes in order of importance: Droplet, Direct contact

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Bats

Arthropod vectors: No evidence

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 31-Dec

Asymptomatic transmission: Yes rare

Incubation period (infection to symptoms): 2-7 days

Case fatality risk: 3 - 10%

Case hospitalisation rate: high (difficult to quantify as described clusters include high rates of nosocomial transmission)

Symptoms (general): Respiratory

Primary symptoms: difficulty breathing

Long term sequelae: Lung function abnormalities, psychological distress, reduced exercise capacity

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): NA

Seasonality: Winter

Geographical distribution (WHO Region): South-East Asian Region (SEAR)

Duration of infection: acute

Availability in NZ: No

Global: Wildlife trade

Evolution recombination frequency: high

Test availability: Available in Aotearoa but not routinely used or validated

Case definition available: Yes

Type: Virus

Family/Genus: Coronaviridae

Species: Middle East respiratory syndrome coronavirus

Example organism(s)/strain(s): MERS

Disease: Middle East respiratory syndrome

Genome length: 30000

Envelope: enveloped

Segmentation: non-segmented

Genome type: RNA

Primary transmission route: Airborne

Other transmission routes in order of importance: Droplet, Direct contact

Animal reservoirs (Orders): Mammals

Known or reported animal reservoirs/intermediate hosts of potential importance for transmission to people (Species): Bats, Camelids

Arthropod vectors: No evidence

Arthropod vectors present in Aotearoa: NA

Basic reproduction number (human-human): 0.7

Asymptomatic transmission: Yes rare

Latent period (infection to infectiousness): 13-14 days

Incubation period (infection to symptoms): mean 5-6 days (range 2-16 days

Infectious period: Unclear

Serial interval/generation time: 7.6 days (95% CI, 2.5 to 23.1)

Effective non-pharmaceutical interventions: Mask wearing, Contact tracing, Distancing, Isolation when ill

Case fatality risk: 35%

Case hospitalisation rate: high (difficult to quantify as described clusters include high rates of nosocomial transmission)

Symptoms (general): Respiratory

Primary symptoms: difficulty breathing

Long term sequelae: Lung function abnormalities, psychological distress, reduced exercise capacity

Vaccine efficacy susceptibility infection (asymptomatic and symptomatic): Unknown

Seasonality: No indication of true seasonality but increased risk of spillover may occur during camel calving season

Geographical distribution (WHO Region): Eastern Mediterranean Region (EMR)

Duration of infection: acute

Availability in NZ: No

Global: High density camel farming along with increased exposure to humans, combined with the increase of ca

Evolution recombination frequency: high

Test availability: Available and validated in Aotearoa but not routinely used

Case definition available: Yes